Chemistry › Spectroscopy

Mass Spectrometry Techniques and Applications

Works Count: 122738

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Description

This cluster of papers covers advancements in mass spectrometry techniques, including ionization methods such as electrospray and MALDI, analysis of proteins and peptides, imaging mass spectrometry, and applications under ambient conditions. It also explores ion mobility and its role in proteomics and structural biology.

Keywords

Mass Spectrometry; Ionization; Electrospray; Proteins; Imaging; Ambient Conditions; Ion Mobility; MALDI; Proteomics; Structural Biology

INTERPRETATION OF MASS SPECTRA

1991-11-15

Fred W. McLafferty

ADVERTISEMENT RETURN TO ISSUEPREVArticleINTERPRETATION OF MASS SPECTRACite this: Anal. Chem. 1991, 63, 22, 1093APublication Date (Print):November 15, 1991Publication History Published online30 May 2012Published inissue 15 November 1991https://doi.org/10.1021/ac00022a726RIGHTS & PERMISSIONSArticle Views24Altmetric-Citations-LEARN … ADVERTISEMENT RETURN TO ISSUEPREVArticleINTERPRETATION OF MASS SPECTRACite this: Anal. Chem. 1991, 63, 22, 1093APublication Date (Print):November 15, 1991Publication History Published online30 May 2012Published inissue 15 November 1991https://doi.org/10.1021/ac00022a726RIGHTS & PERMISSIONSArticle Views24Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (157 KB) Get e-Alerts Get e-Alerts

A simple, specific spray for the detection of phospholipids on thin-layer chromatograms

1964-01-01

John C. Dittmer , Robert L. Lester

A chemical reagent spray specific for phosphate esters, based on molybdenum blue, gives an instantaneous, specific reaction with phospholipids on silica gel or alumina thin layer chromatography (TLC) plates. The … A chemical reagent spray specific for phosphate esters, based on molybdenum blue, gives an instantaneous, specific reaction with phospholipids on silica gel or alumina thin layer chromatography (TLC) plates. The reagent is prepared as two solutions: (I) add 40.11 g of MoO 3 to 1 liter of 25 N H 2 SO 4 and boil gently until dissolved, (II) add 1.78 g of powdered molybdenum to 500 ml of the first solution and boil gently for 15 minutes. The greenish yellow spray consists of equal parts of solutions I and II with two volumes of water. It is stable for months. Plates sprayed lightly show phosphate esters as blue spots on a white or light blue-grey background. The spots intensify on standing but are obscured by a darkening background after several hours. Detection limit is 0.005 mumole of phosphatidyl ethanolamine and phosphatidyl choline. The spray can be used with Rhodamine 6G spray (universal lipids) and ninhydrin (amino groups); a sequential procedure of Rhodamine 6G, ninhydrin, and molybdenum spray is described in detail. The sensitivity of the molybdenum spray is halved when used after other sprays. Some of the compounds giving positive and negative reactions are listed in the article.

A Method for Determining the Sedimentation Behavior of Enzymes: Application to Protein Mixtures

1961-05-01

Robert G. Martin , Bruce N. Ames

Preparation and Properties of a Cholesterol Oxidase from Nocardia sp. and Its Application to the Enzymatic Assay of Total Cholesterol in Serum

1973-12-01

W. Richmond

Abstract I describe the characterization, extraction, and purification of a cholesterol:oxygen oxidoreductase (EC 1.1.3.6) from Nocardia sp. This enzyme catalyzes oxidation of cholesterol to Δ4-choIestenone, with production of hydrogen peroxide. … Abstract I describe the characterization, extraction, and purification of a cholesterol:oxygen oxidoreductase (EC 1.1.3.6) from Nocardia sp. This enzyme catalyzes oxidation of cholesterol to Δ4-choIestenone, with production of hydrogen peroxide. It is very stable, active over a wide pH range, and has a Km of 1.4 x 10-5 mol/ liter. It is highly specific for Δ4- or Δ5-3β-hydroxycholestanes, and may be applied to the assay of serum total cholesterol. In the procedure presented here, hydrogen peroxide is measured by reaction with quadrivalent titanium and xylenol orange. This constitutes a one-enzyme assay with stable reagents, which does not require protein precipitation and is not subject to interference from hemoglobin or bilirubin.

Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry

1996-02-01

Matthias Wilm , Andriy Shevchenko , Tony Houthaeve +4 more

Fourier transform ion cyclotron resonance mass spectrometry: A primer

1998-01-01

Alan G. Marshall , Christopher L. Hendrickson , George S. Jackson

This review offers an introduction to the principles and generic applications of FT-ICR mass spectrometry, directed to readers with no prior experience with the technique. We are able to explain … This review offers an introduction to the principles and generic applications of FT-ICR mass spectrometry, directed to readers with no prior experience with the technique. We are able to explain the fundamental FT-ICR phenomena from a simplified theoretical treatment of ion behavior in idealized magnetic and electric fields. The effects of trapping voltage, trap size and shape, and other nonidealities are manifested mainly as perturbations that preserve the idealized ion behavior modified by appropriate numerical correction factors. Topics include: effect of ion mass, charge, magnetic field, and trapping voltage on ion cyclotron frequency; excitation and detection of ICR signals; mass calibration; mass resolving power and mass accuracy; upper mass limit(s); dynamic range; detection limit, strategies for mass and energy selection for MSn; ion axialization, cooling, and remeasurement; and means for guiding externally formed ions into the ion trap. The relation of FT-ICR MS to other types of Fourier transform spectroscopy and to the Paul (quadrupole) ion trap is described. The article concludes with selected applications, an appendix listing accurate fundamental constants needed for ultrahigh-precision analysis, and an annotated list of selected reviews and primary source publications that describe in further detail various FT-ICR MS techniques and applications. © 1998 John Wiley & Sons, Inc., Mass Spec Rev 17, 1–35, 1998

Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons

1988-10-15

Michael Karas , Franz Hillenkamp

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLaser desorption ionization of proteins with molecular masses exceeding 10,000 daltonsMichael. Karas and Franz. HillenkampCite this: Anal. Chem. 1988, 60, 20, 2299–2301Publication Date (Print):October 15, 1988Publication History … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLaser desorption ionization of proteins with molecular masses exceeding 10,000 daltonsMichael. Karas and Franz. HillenkampCite this: Anal. Chem. 1988, 60, 20, 2299–2301Publication Date (Print):October 15, 1988Publication History Published online1 May 2002Published inissue 15 October 1988https://pubs.acs.org/doi/10.1021/ac00171a028https://doi.org/10.1021/ac00171a028research-articleACS PublicationsRequest reuse permissionsArticle Views9681Altmetric-Citations4592LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts

A MODIFIED SPECTROPHOTOMETRIC DETERMINATION OF CHYMOTRYPSIN, TRYPSIN, AND THROMBIN

1959-12-01

Brian C. W. Hummel

The spectrophotometric procedure proposed by Schwert and Takenaka for the assay of chymotrypsin and trypsin has been modified and extended to include the application to N-benzoyl-L-tyrosine ethyl ester and α-p-toluenesulphonyl-L-arginine … The spectrophotometric procedure proposed by Schwert and Takenaka for the assay of chymotrypsin and trypsin has been modified and extended to include the application to N-benzoyl-L-tyrosine ethyl ester and α-p-toluenesulphonyl-L-arginine methyl ester. The greater degree of sensitivity and specificity thus achieved permits the determination of traces of chymotrypsin in the presence of relatively large amounts of trypsin and vice versa. A similar spectrophotometric procedure for the assay of thrombin is described.

Probability-based protein identification by searching sequence databases using mass spectrometry data

1999-12-01

David N. Perkins , Darryl Pappin , David M. Creasy +1 more

Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights … Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be com pared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.

A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates

1988-01-01

Bruno Domon , Catherine E. Costello

Likelihood-enhanced fast translation functions

2005-03-24

Airlie J. McCoy , Ralf W. Grosse‐Kunstleve , Laurent C. Storoni +1 more

This paper is a companion to a recent paper on fast rotation functions [Storoni et al. (2004), Acta Cryst. D60, 432–438], which showed how a Taylor-series expansion of the maximum-likelihood … This paper is a companion to a recent paper on fast rotation functions [Storoni et al. (2004), Acta Cryst. D60, 432–438], which showed how a Taylor-series expansion of the maximum-likelihood rotation function leads to improved likelihood-enhanced fast rotation functions. In a similar manner, it is shown here how linear and quadratic Taylor-series expansions and least-squares approximations of the maximum-likelihood translation function lead to likelihood-enhanced translation functions, which can be calculated by FFT and which are more sensitive to the correct translation than the traditional correlation-coefficient fast translation function. These likelihood-enhanced translation targets for molecular-replacement searches have been implemented in the program Phaser using the Computational Crystallography Toolbox (cctbx).

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Stop and Go Extraction Tips for Matrix-Assisted Laser Desorption/Ionization, Nanoelectrospray, and LC/MS Sample Pretreatment in Proteomics

2002-12-24

Juri Rappsilber , Yasushi Ishihama , Matthias Mann

Proteomics is critically dependent on optimal sample preparation. Particularly, the interface between protein digestion and mass spectrometric analysis has a large influence on the overall quality and sensitivity of the … Proteomics is critically dependent on optimal sample preparation. Particularly, the interface between protein digestion and mass spectrometric analysis has a large influence on the overall quality and sensitivity of the analysis. We here describe a novel procedure in which a very small disk of beads embedded in a Teflon meshwork is placed as a microcolumn into pipet tips. Termed Stage, for STop And Go Extraction, the procedure has been implemented with commercially available material (C18 Empore Disks (3M, Minneapolis, MN)) as frit and separation material. The disk is introduced in a simple and fast process yielding a convenient and completely reliable procedure for the production of self-packed microcolumns in pipet tips. It is held in place free of obstacles solely by the narrowing tip, ensuring optimized loading and elution of analytes. Five disks are conveniently placed in 1 min, adding <0.1 cent in material costs to the price of each tip. The system allows fast loading with low backpressure (>300 μL/min for the packed column using manual force) while eliminating the possibility of blocking. The loading capacity of C18-StageTips (column bed: 0.4 mm diameter, 0.5 mm length) is 2−4 μg of protein digest, which can be increased by using larger diameter or stacked disks. Five femtomole of tryptic BSA digest could be recovered quantitatively. We have found that the Stage system is well-suited as a universal sample preparation system for proteomics.

A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids

1984-04-01

D. Wessel , U.I. Flügge

Electrospray ion source. Another variation on the free-jet theme

1984-09-01

Masamichi Yamashita , John B. Fenn

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrospray ion source. Another variation on the free-jet themeMasamichi Yamashita and John B. FennCite this: J. Phys. Chem. 1984, 88, 20, 4451–4459Publication Date (Print):September 1, 1984Publication History … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrospray ion source. Another variation on the free-jet themeMasamichi Yamashita and John B. FennCite this: J. Phys. Chem. 1984, 88, 20, 4451–4459Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/j150664a002https://doi.org/10.1021/j150664a002research-articleACS PublicationsRequest reuse permissionsArticle Views6644Altmetric-Citations1629LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts

Measurement of the incorporation of radioactive amino acids into protein by a filter-paper disk method

1961-07-01

Rusty J. Mans , G. David Novelli

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

1994-11-01

Jimmy K. Eng , Ashley L. McCormack , John R. Yates

A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (10-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. … A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (10-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mass tolerance of ±1 u of the precursor ion molecular weight A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted from amino acid sequences obtained from the database and the fragment ions observed in the tandem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions of the first- and second-ranked search results indicates a successful match between sequence and spectrum. Searches of species-specific protein databases with tandem mass spectra acquired from peptides obtained from the enzymatically digested total proteins of E. coli and S. cerevisiae cells allowed matching of the spectra to amino acid sequences within proteins of these organisms. The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.

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Analytical Properties of the Nanoelectrospray Ion Source

1996-01-01

Matthias Wilm , Matthias Mann

The nanoelectrospray ion source (nanoES) has recently been developed and described theoretically. It is different from conventional electrospray sources and from other miniaturized electrospray sources by (i) its 1−2 μm … The nanoelectrospray ion source (nanoES) has recently been developed and described theoretically. It is different from conventional electrospray sources and from other miniaturized electrospray sources by (i) its 1−2 μm spraying orifice achieved by pulling the spraying capillary to a fine tip, (ii) its very low flow rate of ∼20 nL/min and the small size of droplets it generates, and (iii) the absence of solvent pumps and inlet valves. The fabrication and operation of nanoES needles is described in detail. Solutions with up to 0.1 M salt contents could be sprayed without sheath flow or pneumatic assist. Improved desolvation in nanoES led to instrument-limited resolution of the signals of a glycoprotein and the ability to signal average extensively allowed the C-terminal sequencing of a 40 kDa protein. Extensive mass spectrometric and tandem mass spectrometric investigation of the components of an unseparated peptide mixture was demonstrated by verification of 93% of the sequence of carbonic anhydrase. A rapid and robust desalting/concentration step coupled to the nanoES procedure allows the direct analysis of impure samples such as peptide mixtures extracted after in-gel digestion.

Total Cross Sections for Ionization and Attachment in Gases by Electron Impact. I. Positive Ionization

1965-09-01

Donald Rapp , Paula Englander‐Golden

The total ionization cross sections of He, Ne, Ar, Kr, Xe, H2, D2, N2, O2, CO, NO, CO2, N2O, and CH4 have been measured from threshold to 1000 eV in … The total ionization cross sections of He, Ne, Ar, Kr, Xe, H2, D2, N2, O2, CO, NO, CO2, N2O, and CH4 have been measured from threshold to 1000 eV in a total ionization tube. More limited measurements were performed in C2H4 and SF6. Great care was taken to assure complete collection of electron and ion currents, and the absence of spurious instrumental errors. A new method was devised for obtaining absolute cross sections of gases relative to H2, and a McLeod gauge was used to obtain the absolute cross section in H2. The cross sections in NO and O2 could not be obtained by this method, and an approximate correction to direct McLeod-gauge readings was used for these gases. It is believed that the results are as accurate as is possible with the present method. It is difficult to explain the differences found between cross sections measured by various investigators. McLeod-gauge errors appear to account for most of the difference in absolute magnitude.

Molecular Imaging of Biological Samples: Localization of Peptides and Proteins Using MALDI-TOF MS

1997-12-01

Richard M. Caprioli , Terry B. Farmer , Jocelyn Gile

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been used to generate ion images of samples in one or more mass-to-charge (m/z) values, providing the capability of mapping specific molecules … Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been used to generate ion images of samples in one or more mass-to-charge (m/z) values, providing the capability of mapping specific molecules to two-dimensional coordinates of the original sample. The high sensitivity of the technique (low-femtomole to attomole levels for proteins and peptides) allows the study of organized biochemical processes occurring in, for example, mammalian tissue sections. The mass spectrometer is used to determine the molecular weights of the molecular in the surface layers of the tissue. Molecules desorbed from the sample typically are singly protonated, giving an ion at (M + H)+, where M is the molecular mass. The procedure involves coating the tissue section, or a blotted imprint of the section, with a thin layer of energy-absorbing matrix and then analyzing the sample to produce an ordered array of mass spectra, each containing nominal m/z values typically covering a range of over 50,000 Da. Images can be displayed in individual m/z values as a selected ion image, which would localize individual compounds in the tissue, or as summed ion images. MALDI ion images of tissue sections can be obtained directly from tissue slices following preparative steps, and this is demonstrated for the mapping of insulin contained in an islet in a section of rat pancreas, hormone peptides in a small area of a section of rat pituitary, and a small protein bound to the membrane of human mucosa cells. Alternatively, imprints of the tissue can be analyzed by blotting the tissue sections on specially prepared targets containing an adsorbent material, e.g., C-18 coated resin beads. Peptides and small proteins bind to the C-18 and create a positive imprint of the tissue which can then be imaged by the mass spectrometer. This is demonstrated for the MALDI ion image analysis of regions of rat splenic pancreas and for an area of rat pituitary traversing the anterior, intermediate, and posterior regions where localized peptides were mapped. In a single spectrum from the anterior/intermediate lobe of a rat pituitary print, over 50 ions corresponding to the peptides present in this tissue were observed as well as precursors, isoforms, and metabolic fragments.

A Film Detection Method for Tritium‐Labelled Proteins and Nucleic Acids in Polyacrylamide Gels

1974-07-01

William M. Bonner , Ronald A. Laskey

A simple method is described for detecting 3 H in polyacrylamide gels by scintillation autography (fluorography) using X‐ray film. The gel is dehydrated in dimethyl sulphoxide, soaked in a solution … A simple method is described for detecting 3 H in polyacrylamide gels by scintillation autography (fluorography) using X‐ray film. The gel is dehydrated in dimethyl sulphoxide, soaked in a solution of 2,5‐diphenyloxazole (PPO) in dimethylsulphoxide, dried and exposed to RP Royal “X‐Omat” film at ‐70 °C. Optimal conditions for each step are described. β‐particles from 3 H interact with the 2,5‐diphenyloxazole emitting light which causes local blackening of an X‐ray film. The image produced resembles that obtained by conventional autoradiography of isotopes with higher emission energies such as 14 C. 3000 dis. 3 H/min in a band in a gel can be detected in a 24‐h exposure. Similarly 500 dis./min can be detected in one week. When applied to the detection of 35 S and 14 C in polyacrylamide gels, this method is ten times more sensitive than conventional autoradiography. 130 dis. 35 S or 14 C/min in a band in a gel can be detected in 24 h.

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Electrospray ionization–principles and practice

1990-01-01

John B. Fenn , Matthias Mann , Chin Kai Meng +2 more

Mass Spectrometry and Protein Analysis

2006-04-13

Bruno Domon , Ruedi Aebersold

Mass spectrometry is a central analytical technique for protein research and for the study of biomolecules in general. Driven by the need to identify, characterize, and quantify proteins at ever … Mass spectrometry is a central analytical technique for protein research and for the study of biomolecules in general. Driven by the need to identify, characterize, and quantify proteins at ever increasing sensitivity and in ever more complex samples, a wide range of new mass spectrometry-based analytical platforms and experimental strategies have emerged. Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science.

Hydrogen Ion Buffers for Biological Research*

1966-02-01

Norman E. Good , G. Douglas Winget , Wilhelmina Winter +3 more

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogen Ion Buffers for Biological Research*Norman E. Good, G. Douglas Winget, Wilhelmina Winter, Thomas N. Connolly, Seikichi Izawa, and Raizada M. M. SinghCite this: Biochemistry 1966, 5, … ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogen Ion Buffers for Biological Research*Norman E. Good, G. Douglas Winget, Wilhelmina Winter, Thomas N. Connolly, Seikichi Izawa, and Raizada M. M. SinghCite this: Biochemistry 1966, 5, 2, 467–477Publication Date (Print):February 1, 1966Publication History Published online1 May 2002Published inissue 1 February 1966https://pubs.acs.org/doi/10.1021/bi00866a011https://doi.org/10.1021/bi00866a011research-articleACS PublicationsRequest reuse permissionsArticle Views17533Altmetric-Citations2152LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts

Blue silver: A very sensitive colloidal Coomassie G‐250 staining for proteome analysis

2004-05-01

Giovanni Candiano , Maurizio Bruschi , Luca Musante +6 more

Abstract A modified Neuhoff's colloidal Coomassie Blue G‐250 stain is reported, dubbed “blue silver” on account of its considerably higher sensitivity, approaching the one of conventional silver staining. The main … Abstract A modified Neuhoff's colloidal Coomassie Blue G‐250 stain is reported, dubbed “blue silver” on account of its considerably higher sensitivity, approaching the one of conventional silver staining. The main modifications, as compared to Neuhoff's protocol, were: a 20% increment in dye concentration (from 0.1% up to 0.12%) and a much higher level of phosphoric acid in the recipe (from 2% up to 10%). The “blue silver” exhibits a much faster dye uptake (80% during the first hour of coloration, vs. none with a commercial preparation from Sigma). Even at equilibrium (24 h staining), the “blue silver” exhibits a much higher sensitivity than all other recipes, approaching (but lower than) the one of the classical silver stain. Measurements of stain sensitivity after sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) of bovine serum albumin (BSA) gave a detection limit (signal‐to‐noise ratio > 3) of 1 ng in a single zone. The somewhat lower sensitivity of “blue silver” as compared to classical silvering protocols in the presence of aldehydes is amply compensated for by its full compatibility with mass spectrometry of eluted polypeptide chains, after a two‐dimensional map analysis, thus confirming that no dye is covalently bound (or permanently modifies) to any residue in the proteinaceous material. It is believed that the higher level of phosphoric acid in the recipe, thus its lower final pH, helps in protonating the last dissociated residues of Asp and Glu in the polypeptide coils, thus greatly favoring ionic anchoring of dye molecules to the protein moiety. Such a binding, though, must be followed by considerable hydrophobic association with the aromatic and hydrophobic residues along the polypeptide backbone.

Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

2003-03-01

Andrew Thompson , Jürgen Schäfer , Karsten Kuhn +5 more

A novel MS/MS-based analysis strategy using isotopomer labels, referred to as "tandem mass tags" (TMTs), for the accurate quantification of peptides and proteins is described. The new tags are designed … A novel MS/MS-based analysis strategy using isotopomer labels, referred to as "tandem mass tags" (TMTs), for the accurate quantification of peptides and proteins is described. The new tags are designed to ensure that identical peptides labeled with different TMTs exactly comigrate in all separations. The tags require novel methods of quantification analysis using tandem mass spectrometry. The new tags and analysis methods allow peptides from different samples to be identified by their relative abundance with greater ease and accuracy than other methods. The new TMTs permit simultaneous determination of both the identity and relative abundances of peptide pairs using a collision induced dissociation (CID)-based analysis method. Relative abundance measurements made in the MS/MS mode using the new tags are accurate and sensitive. Compared to MS-mode measurements, a very high signal-to-noise ratio is achieved with MS/MS based detection. The new tags should be applicable to a wide variety of peptide isolation methods.

Rapid identification of proteins by peptide-mass fingerprinting

1993-06-01

Darryl Pappin , Peter Højrup , Alan J. Bleasby

Tricine–SDS-PAGE

2006-05-12

Hermann Schägger

Fluorometric assay of proteins in the nanogram range

1973-03-01

Peter Böhlen , Stanley J. Stein , Wallace Dairman +1 more

Detection of specific sequences among DNA fragments separated by gel electrophoresis

1975-11-01

E.M. Southern

Time-of-Flight Mass Spectrometer with Improved Resolution

1955-12-01

W. C. Wiley , I. H. McLaren

A new type of ion gun is described which greatly improves the resolution of a nonmagnetic time-of-flight mass spectrometer. The focusing action of this gun is discussed and analyzed mathematically. … A new type of ion gun is described which greatly improves the resolution of a nonmagnetic time-of-flight mass spectrometer. The focusing action of this gun is discussed and analyzed mathematically. The validity of the analysis and the practicability of the gun are demonstrated by the spectra obtained. The spectrometer is capable of measuring the relative abundance of adjacent masses well beyond 100 amu.

Matrix-assisted ultraviolet laser desorption of non-volatile compounds

1987-09-01

Michael Karas , Doris Bachmann , U. Bahr +1 more

Electrospray Ionization for Mass Spectrometry of Large Biomolecules

1989-10-06

John B. Fenn , Matthias Mann , Chin Kai Meng +2 more

Electrospray ionization has recently emerged as a powerful technique for producing intact ions in vacuo from large and complex species in solution. To an extent greater than has previously been … Electrospray ionization has recently emerged as a powerful technique for producing intact ions in vacuo from large and complex species in solution. To an extent greater than has previously been possible with the more familiar "soft" ionization methods, this technique makes the power and elegance of mass spectrometric analysis applicable to the large and fragile polar molecules that play such vital roles in biological systems. The distinguishing features of electrospray spectra for large molecules are coherent sequences of peaks whose component ions are multiply charged, the ions of each peak differing by one charge from those of adjacent neighbors in the sequence. Spectra have been obtained for biopolymers including oligonucleotides and proteins, the latter having molecular weights up to 130,000, with as yet no evidence of an upper limit.

Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels

1996-03-01

Andrej Shevchenko , Matthias Wilm , Ole Vorm +1 more

Proteins from silver-stained gels can be digested enzymatically and the resulting peptides analyzed and sequenced by mass spectrometry. Standard proteins yield the same peptide maps when extracted from Coomassie- and … Proteins from silver-stained gels can be digested enzymatically and the resulting peptides analyzed and sequenced by mass spectrometry. Standard proteins yield the same peptide maps when extracted from Coomassie- and silver-stained gels, as judged by electrospray and MALDI mass spectrometry. The low nanogram range can be reached by the protocols described here, and the method is robust. A silver-stained one-dimensional gel of a fraction from yeast proteins was analyzed by nanoelectrospray tandem mass spectrometry. In the sequencing, more than 1000 amino acids were covered, resulting in no evidence of chemical modifications due to the silver staining procedure. Silver staining allows a substantial shortening of sample preparation time and may, therefore, be preferable over Coomassie staining. This work removes a major obstacle to the low-level sequence analysis of proteins separated on polyacrylamide gels.

Assay of proteins in the presence of interfering materials

1976-01-01

André Bensadoun , David Weinstein

Protein and polymer analyses up to m/z 100 000 by laser ionization time‐of‐flight mass spectrometry

1988-08-01

Koichi Tanaka , Hiroaki Waki , Yutaka Ido +4 more

The catalytic decomposition of hydrogen peroxide by iron salts

1934-11-15

Fritz Haber , Joseph Weiß

[ Note by Dr. O. H. Wansbrough-Jones —Shortly before Professor Haber died, he gave the manuscript of this paper to Professor Sir William Pope. The final revision for the press … [ Note by Dr. O. H. Wansbrough-Jones —Shortly before Professor Haber died, he gave the manuscript of this paper to Professor Sir William Pope. The final revision for the press had not been made and in its original from the paper was not suitable for publication in an English journal. Considerable alterations in the wording have accordingly been made; but since, Professor Haber had considered carefully how he wished to present the results embodied in it, the form and sequence of the paper remain unmodified. The paper is, further, a sequel to some communications in German periodicals which may not be familiar to its readers. In an attempt to make it more quickly understandable, while keeping it as far as possible as it was left by Professor Haber, the following summary has been added.

Primary structure effects on peptide group hydrogen exchange

1993-09-01

Yawen Bai , John Milne , Leland Mayne +1 more

Abstract The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, … Abstract The rate of exchange of peptide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are apparent. The additivity of nearest‐neighbor blocking and inductive effects was tested in oligo‐and polypeptides and, suprisingly, confirmed. Reference rates for alanine‐containing peptides were determined and effects of temperature considered. These results provide the information necessary to evaluate measured protein NH to ND exchange rates by comparing them with rates to be expected for the same amino acid sequence is unstructured aligo‐ and polypeptides. The application of this approach to protein studies is discussed. © 1993 Wiley‐Liss, Inc.

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Quantitative mass spectrometry in proteomics: a critical review

2007-07-31

Marcus Bantscheff , Markus Schirle , Gavain M.A. Sweetman +2 more

The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to … The quantification of differences between two or more physiological states of a biological system is among the most important but also most challenging technical tasks in proteomics. In addition to the classical methods of differential protein gel or blot staining by dyes and fluorophores, mass-spectrometry-based quantification methods have gained increasing popularity over the past five years. Most of these methods employ differential stable isotope labeling to create a specific mass tag that can be recognized by a mass spectrometer and at the same time provide the basis for quantification. These mass tags can be introduced into proteins or peptides (i) metabolically, (ii) by chemical means, (iii) enzymatically, or (iv) provided by spiked synthetic peptide standards. In contrast, label-free quantification approaches aim to correlate the mass spectrometric signal of intact proteolytic peptides or the number of peptide sequencing events with the relative or absolute protein quantity directly. In this review, we critically examine the more commonly used quantitative mass spectrometry methods for their individual merits and discuss challenges in arriving at meaningful interpretations of quantitative proteomic data.

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Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process

1998-03-24

Roman A. Zubarev , Neil L. Kelleher , Fred W. McLafferty

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTElectron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic ProcessRoman A. Zubarev, Neil L. Kelleher, and Fred W. McLaffertyView Author Information Department of Chemistry, Baker Laboratory … ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTElectron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic ProcessRoman A. Zubarev, Neil L. Kelleher, and Fred W. McLaffertyView Author Information Department of Chemistry, Baker Laboratory Cornell University, Ithaca, New York 14853-1301 Cite this: J. Am. Chem. Soc. 1998, 120, 13, 3265–3266Publication Date (Web):March 24, 1998Publication History Received6 October 1997Published online24 March 1998Published inissue 1 April 1998https://doi.org/10.1021/ja973478kCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views5758Altmetric-Citations1640LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (80 KB) Get e-AlertscloseSUBJECTS:Circular dichroism spectroscopy,Crystal cleavage,Dissociation,Ions,Peptides and proteins Get e-Alerts

GROMACS 3.0: a package for molecular simulation and trajectory analysis

2001-08-01

Erik Lindahl , Berk Hess , David van der Spoel

Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry

2004-06-21

John E. P. Syka , Joshua J. Coon , Melanie Schroeder +2 more

Peptide sequence analysis using a combination of gas-phase ion/ion chemistry and tandem mass spectrometry (MS/MS) is demonstrated. Singly charged anthracene anions transfer an electron to multiply protonated peptides in a … Peptide sequence analysis using a combination of gas-phase ion/ion chemistry and tandem mass spectrometry (MS/MS) is demonstrated. Singly charged anthracene anions transfer an electron to multiply protonated peptides in a radio frequency quadrupole linear ion trap (QLT) and induce fragmentation of the peptide backbone along pathways that are analogous to those observed in electron capture dissociation. Modifications to the QLT that enable this ion/ion chemistry are presented, and automated acquisition of high-quality, single-scan electron transfer dissociation MS/MS spectra of phosphopeptides separated by nanoflow HPLC is described.

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Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

2005-10-26

Jesper V. Olsen , Lyris Martins Franco de Godoy , Guoqing Li +7 more

Mass accuracy is a key parameter of mass spectrometric performance. TOF instruments can reach low parts per million, and FT-ICR instruments are capable of even greater accuracy provided ion numbers … Mass accuracy is a key parameter of mass spectrometric performance. TOF instruments can reach low parts per million, and FT-ICR instruments are capable of even greater accuracy provided ion numbers are well controlled. Here we demonstrate sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap (C-trap) to the orbitrap mass spectrometer (LTQ Orbitrap). Prior to acquisition of a spectrum, a background ion originating from ambient air is first transferred to the C-trap. Ions forming the MS or MS(n) spectrum are then added to this species, and all ions are injected into the orbitrap for analysis. Real time recalibration on the "lock mass" by corrections of mass shift removes mass error associated with calibration of the mass scale. The remaining mass error is mainly due to imperfect peaks caused by weak signals and is addressed by averaging the mass measurement over the LC peak, weighted by signal intensity. For peptide database searches in proteomics, we introduce a variable mass tolerance and achieve average absolute mass deviations of 0.48 ppm (standard deviation 0.38 ppm) and maximal deviations of less than 2 ppm. For tandem mass spectra we demonstrate similarly high mass accuracy and discuss its impact on database searching. High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification.

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Ion Suppression in Mass Spectrometry

2003-07-01

Thomas M Annesley

Mass spectrometry (MS) is being introduced into a large number of clinical laboratories. It provides specificity because of its ability to monitor selected mass ions, sensitivity because of the enhanced … Mass spectrometry (MS) is being introduced into a large number of clinical laboratories. It provides specificity because of its ability to monitor selected mass ions, sensitivity because of the enhanced signal-to-noise ratio, and speed because it can help avoid the need for intensive sample cleanup and long analysis times. However, MS is not without problems related to interference, especially through ion suppression effects. Ion suppression results from the presence of less volatile compounds that can change the efficiency of droplet formation or droplet evaporation, which in turn affects the amount of charged ion in the gas phase that ultimately reaches the detector.This review discusses materials shown to cause ion suppression, including salts, ion-pairing agents, endogenous compounds, drugs, metabolites, and proteins. Experimental protocols for examining ion suppression, which should include, at a minimum, signal recovery studies using specimen extracts with added analyte, are also discussed, and a more comprehensive approach is presented that uses postcolumn infusion of the analyte to evaluate protracted ionization effects. Finally, this review presents options for minimizing or correcting ion suppression, which include enhanced specimen cleanup, chromatographic changes, reagent modifications, and effective internal standardization.Whenever mass spectrometric assays are developed, ion suppression studies should be performed using expected physiologic concentrations of the analyte under investigation.

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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

2015-10-01

Robert T. McGibbon , Kyle A. Beauchamp , Matthew P. Harrigan +7 more

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Versatile New Ion Source for the Analysis of Materials in Open Air under Ambient Conditions

2005-03-12

Robert B. Cody , James A. Laramée , H. D. Durst

A new ion source has been developed for rapid, noncontact analysis of materials at ambient pressure and at ground potential. The new source, termed DART (for "Direct Analysis in Real … A new ion source has been developed for rapid, noncontact analysis of materials at ambient pressure and at ground potential. The new source, termed DART (for "Direct Analysis in Real Time"), is based on the reactions of electronic or vibronic excited-state species with reagent molecules and polar or nonpolar analytes. DART has been installed on a high-resolution time-of-flight mass spectrometer (TOFMS) that provides improved selectivity and accurate elemental composition assignment through exact mass measurements. Although DART has been applied to the analysis of gases, liquids, and solids, a unique application is the direct detection of chemicals on surfaces without requiring sample preparation, such as wiping or solvent extraction. DART has demonstrated success in sampling hundreds of chemicals, including chemical agents and their signatures, pharmaceutics, metabolites, peptides and oligosaccharides, synthetic organics, organometallics, drugs of abuse, explosives, and toxic industrial chemicals. These species were detected on various surfaces, such as concrete, asphalt, human skin, currency, airline boarding passes, business cards, fruits, vegetables, spices, beverages, body fluids, horticultural leaves, cocktail glasses, and clothing. DART employs no radioactive components and is more versatile than devices using radioisotope-based ionization. Because its response is instantaneous, DART provides real-time information, a critical requirement for screening or high throughput.

What vibrations tell about proteins

2002-11-01

Andreas Barth , Christian Zscherp

1. Introduction 370 2. Infrared (IR) spectroscopy – general principles 372 2.1 Vibrations 372 2.2 Information that can be derived from the vibrational spectrum 372 2.3 Absorption of IR light … 1. Introduction 370 2. Infrared (IR) spectroscopy – general principles 372 2.1 Vibrations 372 2.2 Information that can be derived from the vibrational spectrum 372 2.3 Absorption of IR light 375 3. Protein IR absorption 376 3.1 Amino-acid side-chain absorption 376 3.2 Normal modes of the amide group 381 4. Interactions that shape the amide I band 382 4.1 Overview 382 4.2 Through-bond coupling 383 4.3 Hydrogen bonding 383 4.4 Transition dipole coupling (TDC) 383 5. The polarization and IR activity of amide I modes 387 5.1 The coupled oscillator system 387 5.2 Optically allowed transitions 388 5.3 The infinite parallel β-sheet 388 5.4 The infinite antiparallel β-sheet 389 5.5 The infinite α-helix 390 6. Calculation of the amide I band 391 6.1 Overview 391 6.2 Perturbation treatment by Miyazawa 393 6.3 The parallel β-sheet 394 6.4 The antiparallel β-sheet 395 6.5 The α-helix 396 6.6 Other secondary structures 398 7. Experimental analysis of protein secondary structure 398 7.1 Band fitting 398 7.2 Methods using calibration sets 401 7.3 Prediction quality 403 8. Protein stability 404 8.1 Thermal stability 404 8.2 1 H/ 2 H exchange 406 9. Molecular reaction mechanisms of proteins 408 9.1 Reaction-induced IR difference spectroscopy 408 9.2 The origin of difference bands 409 9.3 The difference spectrum seen as a fingerprint of conformational change 410 9.4 Molecular interpretation: strategies of band assignment 416 10. Outlook 419 11. Acknowledgements 420 12. References 420 This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1 H/ 2 H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

Velocity map imaging of ions and electrons using electrostatic lenses: Application in photoelectron and photofragment ion imaging of molecular oxygen

1997-09-01

André T. J. B. Eppink , David H. Parker

The application of electrostatic lenses is demonstrated to give a substantial improvement of the two-dimensional (2D) ion/electron imaging technique. This combination of ion lens optics and 2D detection makes “velocity … The application of electrostatic lenses is demonstrated to give a substantial improvement of the two-dimensional (2D) ion/electron imaging technique. This combination of ion lens optics and 2D detection makes “velocity map imaging” possible, i.e., all particles with the same initial velocity vector are mapped onto the same point on the detector. Whereas the more common application of grid electrodes leads to transmission reduction, severe trajectory deflections and blurring due to the non-point source geometry, these problems are avoided with open lens electrodes. A three-plate assembly with aperture electrodes has been tested and its properties are compared with those of grid electrodes. The photodissociation processes occurring in molecular oxygen following the two-photon 3dπ(3Σ1g −)(v=2, N=2)←X(3Σg −) Rydberg excitation around 225 nm are presented here to show the improvement in spatial resolution in the ion and electron images. Simulated trajectory calculations show good agreement with experiment and support the appealing properties of this velocity mapping technique.

Automated exploration of the low-energy chemical space with fast quantum chemical methods

2020-01-01

Philipp Pracht , Fabian Bohle , Stefan Grimme

We propose and discuss an efficient scheme for the<italic>in silico</italic>sampling for parts of the molecular low-energy chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. We propose and discuss an efficient scheme for the<italic>in silico</italic>sampling for parts of the molecular low-energy chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm.

Measurement of protein using bicinchoninic acid

1985-10-01

Pam Smith , Randall I. Krohn , Greg T. Hermanson +7 more

Physicochemical Hydrodynamics

1963-11-01

V. G. Levich , Raymond J. Seeger

First Page First Page

Nitrile-Imine-Mediated Cross-Linking of Peptides to Oligonucleotides in Gas-Phase Ion Complexes

2025-06-25

Jiahao Wan , Mikuláš Vlk , Chenyang Wei +1 more | Journal of the American Society for Mass Spectrometry

Gas-phase ion complexes of dinucleotides and trinucleotides with a diaryltetrazole-tagged peptide underwent covalent cross-linking upon UV photodissociation (UVPD) at 213 nm. The cross-linking reaction involved nitrile-imine intermediates produced by the … Gas-phase ion complexes of dinucleotides and trinucleotides with a diaryltetrazole-tagged peptide underwent covalent cross-linking upon UV photodissociation (UVPD) at 213 nm. The cross-linking reaction involved nitrile-imine intermediates produced by the loss of N2 from the tetrazole, whereby cross-linking between the complex components competed with internal cross-linking within the peptide. The propensity for UVPD-induced cross-linking of DNA nucleobases was established for complexes of dinucleotides dAA, dCC, dGG, and dTT, that gave cross-link yields of 5%, 15%, 40%, and <1%, respectively. Analysis of UVPD-produced nitrile-imine intermediates by collision-induced dissociation (CID-MS3) gave cross-link yields of 71%, 75%, 94%, and 8% for dAA, dCC, dGG, and dTT, respectively. UVPD-CID-MS3 of isomeric trinucleotide-peptide complexes of dCGA, dAGC, dCAG, dACG, and dGCA showed nearly quantitative cross-linking that favored guanine regardless of its position in the sequence. Binding energies for the gas-phase ion complexes were obtained by Born-Oppenheimer molecular dynamics and density functional theory calculations at the M06-2X/def2qzvpp level. These calculations showed similar binding energies for the dAA, dCC, and dCAG complexes that were in the 195-221 kJ mol-1 range, whereas binding to dGG and dTT was weaker. A mechanism for the novel cross-linking reaction between the nitrile imine and guanine was elucidated with a riboguanosine conjugate that was tagged with a diaryltetrazole group at 5'-O. Product analysis as well as the calculated structures and energies suggested that cross-links resulted from an attack on the aromatic ring of an imine intermediate by the guanine carbonyl oxygen, followed by proton migrations.

Nanospray Laser-Induced Plasma Ionization Mass Spectrometry for Analysis of Trace Short-Chain Chlorinated Paraffins in Single Cells

2025-06-24

Yunyun Yang , Junhao Lin , Yuehua Wu +5 more | Analytical Chemistry

Short-chain chlorinated paraffins (SCCPs) are a group of persistent organic pollutants that pose potential toxicity and health risks to biosystems and ecosystems. Analysis of trace SCCPs in single cells gives … Short-chain chlorinated paraffins (SCCPs) are a group of persistent organic pollutants that pose potential toxicity and health risks to biosystems and ecosystems. Analysis of trace SCCPs in single cells gives deeper insights into their cytotoxic, carcinogenic, and mutagenic investigations. Here a nanospray laser-induced plasma ionization mass spectrometry (nLIPI-MS) method was developed for accurate and sensitive analysis of trace SCCPs in single cells. An inner-wall molecularly imprinted polymer nanopipette was prepared, which allowed the exhaustive extraction of trace SCCPs from a single cell via molecular recognition. After extraction, the enriched SCCPs were desorbed using a methanol/chloroform (7:3, v/v) solvent. An alternating current high voltage was applied to the nanopipette to generate nanospray, and a laser beam was focused to create energetic plasma between the nanopipette and the MS inlet to ionize/secondary ionize SCCPs for mass spectrometric analysis. The method achieved fg-level detection sensitivity for the analysis of SCCPs in single cells, with limits of detection and quantitation of 0.2-0.4 and 0.6-1.0 fg/cell, respectively. Using the developed nLIPI-MS method, trace SCCPs accumulated in BEAS-2B cells following pollutant exposure were successfully detected. Significant heterogeneity in SCCP accumulation was observed among single BEAS-2B cells. Long-chain SCCPs accumulated at higher levels than short-chain SCCPs, and the cellular distribution patterns followed a gamma (γ) distribution.

Internal Cavity versus External Cavity: A Theoretical Study of Molecular Recognition of Biphenarene

2025-06-24

Zhe Zheng , Hanyu Lv , R. G. Liu +2 more | The Journal of Physical Chemistry A

Crystalline macrocyclic materials hold great promise for the efficient separation of compounds with similar structures and properties via selective molecular recognition. Notably, the crystal packing of the macrocycles creates new … Crystalline macrocyclic materials hold great promise for the efficient separation of compounds with similar structures and properties via selective molecular recognition. Notably, the crystal packing of the macrocycles creates new intermolecular external cavities capable of accommodating guest molecules in a manner distinct from molecular recognition in solution, thereby exhibiting different adsorption properties. This work focuses on the guest recognition mechanisms of MeBP3, a new type of macrocyclic arene, in a crystal environment. Density functional theory (DFT) calculations and wavefunction analyses are performed to elucidate the preferential encapsulation of CH3CN within the internal cavity of MeBP3. In contrast, cis-1,2-dichloroethene exhibits preferential encapsulation within the external cavity of MeBP3. This study provides insights into the selective molecular recognition of biphenarenes, particularly in solid-state environments, which is crucial for advancing the design and application of macrocyclic arenes in selective adsorption and separation.

Detection and Characterization of Water Radical Cations by Mass Spectrometry and Electron Paramagnetic Resonance Spectroscopy

2025-06-24

Xiaoping Zhang , Minmin Duan , Konstantin Chingin +4 more | Analytical Chemistry

Water radical cations (H2O+•) serve as key reactive intermediates in fundamental chemical processes, atmospheric chemistry, and energy-related applications due to their high reactivity and ability to initiate diverse chemical reactions. … Water radical cations (H2O+•) serve as key reactive intermediates in fundamental chemical processes, atmospheric chemistry, and energy-related applications due to their high reactivity and ability to initiate diverse chemical reactions. In this study, we investigated the generation of water dimer radical cations (m/z 36, (H2O)2+•) and their reaction products with different substrates using multiple soft ionization techniques. Our comprehensive analytical platform incorporates corona discharge ionization (CDI), electrospray ionization (ESI), dielectric barrier discharge ionization (DBDI), and microwave plasma torch (MPT), coupled with complementary mass analyzers, including ion trap, Orbitrap, and quadrupole time-of-flight (Q-TOF) mass spectrometers. To confirm the formation of (H2O)2+•, we employed a multitechnique verification strategy combining high-resolution mass spectrometry (MS), isotope labeling technique, tandem MS, and electron paramagnetic resonance (EPR) spectroscopy. The stabilization and reactivity of H2O+• were also examined by using different substrates.

Histone Analysis Using Mobility- and Mass-Selected Ultraviolet Photodissociation in Tandem with Ultra-High-Resolution Mass Spectrometry

2025-06-24

Cassandra N. Fuller , Md Shofiul Alam , Kévin Jeanne Dit Fouque +7 more | Analytical Chemistry

Ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (UHR FT-ICR MS) for top-down proteomics has shown the potential to resolve proteoforms and splice variants, particularly those with post-translational modifications. Here, … Ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (UHR FT-ICR MS) for top-down proteomics has shown the potential to resolve proteoforms and splice variants, particularly those with post-translational modifications. Here, we integrate trapped ion mobility and mass selection in tandem with ultraviolet photodissociation (UVPD) followed by FT-ICR MS measurements. The proposed method using mobility/mass-selected UVPD before FT-ICR MS allows for high protein sequence coverage and PTM localization with high mass accuracy (<1 ppm) and a better duty cycle (2×). When applied to the analysis of a bovine histone mixture, characteristic UVPD a/b/c/x/y/z ions led to the annotation of 51 proteoforms from H2B, H2A, and H4 core histones with high sequence coverages (up to 77%). Histone variants and PTM combinations, including acetylation, mono-, di-, and trimethylation, and phosphorylation, identified at the top-down level were confirmed using bottom-up analysis. This work provides the foundation for effective mobility and mass preselection of precursor ions and better annotation and spectral decongestion of UVPD fragments from protein mixtures, with general applicability for top-down proteoform analysis with minimal sample preparation.

An In Situ, Automated High-Explosives Aging Method Utilizing Two-Dimensional Gas Chromatography–Mass Spectrometry

2025-06-24

Colleen L. Ray , Chris E. Freye | ACS Omega

Temperature of Radicals Produced by Hydrogen Atom Attachment to Protonated Peptides in a Quadrupole Ion-Trap Mass Spectrometer

2025-06-24

Daiki Asakawa , Hidenori Takahashi , Shinichi Iwamoto +1 more | Journal of the American Society for Mass Spectrometry

Tandem mass spectrometry equipped with hydrogen attachment dissociation (HAD) has been developed for peptide and protein analysis. This study investigates gas-phase fragmentation induced by hydrogen-atom attachment to peptides containing S-carbamidomethylated … Tandem mass spectrometry equipped with hydrogen attachment dissociation (HAD) has been developed for peptide and protein analysis. This study investigates gas-phase fragmentation induced by hydrogen-atom attachment to peptides containing S-carbamidomethylated cysteine residues. The attachment of hydrogen atoms to peptides induces cleavage of either the N-Cα or Cα-C bond. The resulting α-carbon-centered radical intermediates undergo either side-chain loss or a further reaction with hydrogen atoms. Different precursor ions generate α-carbon-centered radical intermediates with varying stabilities, even when their chemical compositions are identical. This difference is due to the effective temperature of the resultant peptide cation radicals depending on the precursor ion. During hydrogen attachment to protonated peptides in the gas phase, the kinetic energy of the hydrogen atom and reaction enthalpy are converted to the internal energy of the resulting peptide cation radical. The effective temperature of the radicals is influenced by their number of degrees of freedom, as the excess energy from the reaction is distributed across these number of degrees of freedom. The fragmentation efficiency of HAD decreases with increasing peptide mass due to the reduced effective temperature. Supplemental activation through ion trap heating promoted fragmentation by HAD, which is especially useful for the analysis of large peptides.

Analysis of Drugs in Whole Blood by Paper Spray Mass Spectrometry with Integrated Solid-Phase Extraction

2025-06-24

Greta Ren , Brandon J. Bills , Nicholas E. Manicke | Analytical Chemistry

The continued rise in overdoses, driven by fentanyl and novel psychoactive substances (NPS), underscores the need for improved methods for drug screening. Traditional analytical techniques involving chromatography can be time-consuming … The continued rise in overdoses, driven by fentanyl and novel psychoactive substances (NPS), underscores the need for improved methods for drug screening. Traditional analytical techniques involving chromatography can be time-consuming and require sample preparation. Paper spray mass spectrometry (PS-MS) can rapidly detect analytes from complex matrices. However, challenges such as matrix effects can lead to higher detection limits, prompting improvements aimed at preconcentrating or cleaning up samples. While most methods focus on plasma analysis, there is a need to further simplify sample preparation, particularly for whole blood. Here, we report on three-dimensional (3D)-printed devices that preconcentrate drugs from whole blood for PS-MS analysis. An uncontrolled amount of blood was added to the blood reservoir part of the cartridge. The capillary fills and then rotates to sit on top of the SPE column. The blood wicks through the SPE to the waste pad, and the sample is left to dry until analysis. The dry SPE holder is "snapped" in the paper spray cartridge. A variety of parameters were optimized to improve manufacturing and the performance of the device, including waste pad substrates, SPE sorbents, and binders; the size of the SPE compartment; the amount of SPE; a water wash step; and blood volume. Performance was tested with 21 different drugs including opioids like fentanyl and isotonitazene, cathinones, designer and prescription benzodiazepines, cocaine, methamphetamine, and synthetic cannabinoids. Dried blood samples were found to be stable for at least 14 days. The detection limits were at single digit or subng/mL levels or lower for all analytes for 70 μL blood sample, with a median decrease of 9-fold compared to paper spray without SPE.

Development of Differential Ion Mobility Spectrometry Based Tandem Devices for Ion Separation Prior to Mass Spectrometry Analysis

2025-06-24

Simin Zhang , T.-Y Lui , Danna Hu +2 more | Rapid Communications in Mass Spectrometry

Differential ion mobility spectrometry (DMS) provides distinct potential in separation of gas phase ions. However, the resolving power still limits the widespread application of DMS technology and inspires to design … Differential ion mobility spectrometry (DMS) provides distinct potential in separation of gas phase ions. However, the resolving power still limits the widespread application of DMS technology and inspires to design tandem DMS for improvement of the performance. A robust tandem DMS module was fabricated to enhance the separation performance of the DMS system. To achieve the optimal separation, two carrier gas composition modulation strategies were carried out by adding different types of organic modifiers and by changing the modifier concentration in each DMS channel. The working performance of the home-made CaptiveSpray-tandem DMS-MS was evaluated by investigating the peak intensity and FWHM using reserpine and comparing the peak positions of peptide mixtures in two DMS channels. When carrier gas composition in two channels was controlled appropriately, the tandem DMS system could provide the DMS system with another dimension for ion separation and therefore enhance the separation ability. Two gas modification methods could be applied in this system for enhancing analytical performance. This tandem DMS platform allows precise control of the gap widths of the DMS channels and enables the modulation of carrier gas composition in two DMS channels separately. The developed method is capable of providing orthogonal separation behavior and achieving higher separation performance.

Adaptive dynamic kinetic resolution enables alteration of chiral induction with ring sizes

2025-06-23

Bangkui Yu , Yao Huang , Haocheng Zhang +1 more | Nature Chemistry

From Solution to Gas Phase: Revealing Ligand-Dependent Conformations of Ribonuclease A with Tandem-Trapped Ion Mobility Spectrometry

2025-06-23

Fanny C. Liu , Mengqi Chai , Tao Qu +4 more | JACS Au

Probing Isomers and Conformers by Cryogenic Ion Vibrational Spectroscopy: Deprotonated States of Valine and Aminovaleric Acid

2025-06-23

Lane M. Terry , Maddie K. Klumb , Deacon Nemchick +2 more | The Journal of Physical Chemistry A

We present infrared photodissociation spectra of messenger-tagged, deprotonated valine and deprotonated aminovaleric acid, showing the difference in the vibrational spectra of isomers with the same functional groups. Through comparison of … We present infrared photodissociation spectra of messenger-tagged, deprotonated valine and deprotonated aminovaleric acid, showing the difference in the vibrational spectra of isomers with the same functional groups. Through comparison of experimental results and density functional theory calculations, we find that the deprotonated states of both valine and aminovaleric acid adopt a configuration in which the carboxylate group forms a hydrogen bond with the amine group. Despite the similarities of the intramolecular hydrogen bonding, the spectra of the two molecules under study are sufficiently different to use the infrared signatures of the carboxylate and amine functional groups as a means to distinguish between them. The conformational search in the case of aminovaleric acid is particularly challenging due to the large number of possible conformations induced by torsion around individual carbon-carbon bonds. For both valine and aminovaleric acid, their infrared spectra in their deprotonated states suggest that two of the lowest energy conformers are likely to be populated.

Synthesis of Silver Nanoparticles by Chemical Vapor Deposition Method and Its Application in Laser Desorption/Ionization Techniques

2025-06-23

Kinga Robotnik , Tomasz Zieliński , Justyna Walczak‐Skierska +5 more | Nanomaterials

Laser desorption/ionization techniques, such as matrix-assisted laser desorption/ionization (MALDI) and surface-assisted laser desorption/ionization (SALDI), are the basis of modern mass spectrometry, enabling the analysis of a wide range of chemical … Laser desorption/ionization techniques, such as matrix-assisted laser desorption/ionization (MALDI) and surface-assisted laser desorption/ionization (SALDI), are the basis of modern mass spectrometry, enabling the analysis of a wide range of chemical compounds, from small molecules to biopolymers. MALDI uses organic matrices to support ionization, while SALDI relies on inorganic surfaces or nanomaterials, which reduce background and improve measurement sensitivity. This review focuses on the potential of using silver nanoparticles (AgNPs) in LDI-MS, with particular emphasis on their synthesis from the gas phase (CVD, Chemical Vapor Deposition). The key role of nanostructures in increasing ionization efficiency and analytical selectivity is emphasized. The CVD technique enables precise control over the morphology, size, and distribution of nanoparticles, which translates into better repeatability and sensitivity of nanostructure-assisted laser desorption/ionization mass spectrometry (NALDI-MS) measurements. The latest achievements in this field are presented, as well as potential applications of CVD-produced AgNPs in analytical chemistry, environmental analysis, and the petrochemical industry.

Spatial profiling of carbonyl metabolites in diabetic cardiomyopathy by derivatization-assisted ambient mass spectrometry imaging

2025-06-23

Chang Jun Yin , Yanhua Liu , Shuohan Cheng +6 more | Analytical and Bioanalytical Chemistry

Resonance‐Enhanced Multiphoton Ionization Spectroscopy of Monocyclic and Polycyclic Aromatic Hydrocarbons in the Gas Phase

2025-06-21

Carolin Schwarz , Fabian Etscheidt , Christian Gehm +4 more | Rapid Communications in Mass Spectrometry

ABSTRACT Rationale Aromatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs) pose significant risks to human health and the environment due to their toxic and carcinogenic properties. These depend strongly on … ABSTRACT Rationale Aromatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs) pose significant risks to human health and the environment due to their toxic and carcinogenic properties. These depend strongly on molecular structure, with even isomers exhibiting different characteristics. Consequently, when conducting a risk assessment of a sample, a rapid and reliable detection technique capable of differentiating between isomers is crucial. Methods Time‐of‐flight mass spectrometry (TOFMS) combined with (1 + 1) resonance‐enhanced multiphoton ionization ((1 + 1)‐REMPI) has proven to be a promising approach due to its wavelength selectivity for different structures. An optical parametric oscillator generated UV radiation from 213 to 300 nm from the third harmonic (355 nm) of a Nd:YAG laser beam. A thermogravimetric system was applied to transfer the substances into the gas phase. Results We performed REMPI spectroscopy of 48 monocyclic and polycyclic aromatic hydrocarbons, including compounds with various substituents (alkyl groups, ‐OCH 3 , ‐SH, ‐OH, ‐Cl) and heteroatoms (N, O, S). The observed spectral shifts correlate with ring number as well as the type, number, and position of substituents and heteroatoms. While these shifts are comparable to trends observed in absorption spectra, variations in intensity arise due to differences in excited‐state lifetimes and the cross sections of both absorption steps. It was further demonstrated that the selected wavelength range, extending to a lower limit of 213 nm, is especially beneficial for the naphthalenes. The relative photoionization cross sections of the investigated compounds have been calculated, showing that the aforementioned structural dependencies also influence the ionization efficiency. Conclusions In common applications, these results may be used to determine a suitable laser wavelength for the substances of interest in order to achieve a higher level of sensitivity. For tunable laser applications, they serve as a reference for distinguishing and quantifying isomers in complex mixtures based on spectral shifts.

Modifying an Existing SIFT-MS Method (Procedure 7)

2025-06-20

| Royal Society of Chemistry eBooks

SIFT-MS, with its chromatography-free, soft chemical ionisation approach to the analysis of volatile compounds requires different procedures for modifying validated test methods compared to GC. This chapter provides procedures for … SIFT-MS, with its chromatography-free, soft chemical ionisation approach to the analysis of volatile compounds requires different procedures for modifying validated test methods compared to GC. This chapter provides procedures for modifying SIFT-MS methods involving addition or removal of analytes, modification to product ion selections, a change of matrix, a shift of the analytical range, and the use of different instrument configurations and specifications. It provides the method developer with the basic, practical steps for efficient method modification.

Safety, Maintenance, and Troubleshooting

2025-06-20

| Royal Society of Chemistry eBooks

Selected ion flow tube mass spectrometry (SIFT-MS) instruments, like any analytical instrumentation, have safety and maintenance requirements that ensure users and the instrument itself are protected. Additionally, performance issues occasionally … Selected ion flow tube mass spectrometry (SIFT-MS) instruments, like any analytical instrumentation, have safety and maintenance requirements that ensure users and the instrument itself are protected. Additionally, performance issues occasionally arise with complex analytical instrumentation. After providing a high-level overview of SIFT-MS instrumentation, together with the preferred ‘xyz’ robotic automation technology, this chapter provides general guidelines for safety, maintenance, and troubleshooting.

Native Top-Down Proteomics of Endogenous Protein Complexes Enabled by Online Two-Dimensional Liquid Chromatography

2025-06-20

Matthew S. Fischer , Holden T. Rogers , Emily A. Chapman +2 more | Analytical Chemistry

Protein complexes are essential for virtually all biological processes, yet their structural characterization remains a major challenge due to their heterogeneous, dynamic nature and the complexity of the proteome. Native … Protein complexes are essential for virtually all biological processes, yet their structural characterization remains a major challenge due to their heterogeneous, dynamic nature and the complexity of the proteome. Native top-down mass spectrometry (nTDMS) has emerged as a powerful tool for comprehensive structural characterization of purified protein complexes, but its application to endogenous protein complexes in the proteome is challenging and typically requires labor-intensive and time-consuming prefractionation. Here, for the first time, we develop a nondenaturing online two-dimensional liquid chromatography (2D-LC) method for native top-down proteomics (nTDP), enabling high-throughput structural analysis of endogenous protein complexes. The automated, online interfacing of size-exclusion and mixed-bed ion-exchange chromatography achieves high coverage of endogenous protein complexes. We further develop a multistage nTDMS approach that enables comprehensive structural characterization within the chromatographic time scale, capturing intact noncovalent complexes, released subunits/cofactors, and backbone fragments. Our analysis detected 133 native proteoforms and endogenous protein complexes (up to 350 kDa) from human heart tissue in less than 2 h. This work represents a significant technical advancement toward direct, high-throughput structural characterization of endogenous protein complexes from biological mixtures.

Radio-frequency pseudo-null induced by light in an ion trap

2025-06-20

NULL AUTHOR_ID | Physical review. A/Physical review, A

Standards for MicroED

2025-06-20

Johan Unge , Brent L. Nannenga , Allen G. Oliver +1 more | Acta Crystallographica Section C Structural Chemistry

As the electron diffraction technique MicroED gains momentum and is increasingly embraced by researchers in both academia and industry, we have the opportunity to familiarize ourselves with the characteristics of … As the electron diffraction technique MicroED gains momentum and is increasingly embraced by researchers in both academia and industry, we have the opportunity to familiarize ourselves with the characteristics of MicroED data and results. The number of refined structures and their associated data is steadily growing and becoming more accessible to the scientific community, offering valuable insights into the significance and quality of MicroED-derived structures. Additionally, the growing body of experience is helping to identify best practices for the technique. In this summary, we highlight key lessons learned from these data and propose gold standards for the community to consider adopting.

Complete Workflows for Routine Headspace Approaches

2025-06-20

| Royal Society of Chemistry eBooks

Automated selected ion flow tube mass spectrometry (SIFT-MS) instruments can be applied to routine headspace analysis based on static headspace analysis (SHA), multiple headspace extraction (MHE), and the method of … Automated selected ion flow tube mass spectrometry (SIFT-MS) instruments can be applied to routine headspace analysis based on static headspace analysis (SHA), multiple headspace extraction (MHE), and the method of standard additions (MoSA). For each of these approaches, this chapter provides complete workflows from the early stages of method development through to setting up for routine analysis.

Identification of Proteins Associated with Ovarian Cancer Chemotherapy Resistance Using MALDI-MSI

2025-06-19

Tannith M. Noye , Parul Mittal , Zoe K. Price +7 more | International Journal of Molecular Sciences

Ovarian cancer is the most lethal gynecological cancer. Up to 75% of cases are high-grade serous ovarian cancer (HGSOC) that have high chemosensitivity to first-line platinum-based therapies. However, 75% of … Ovarian cancer is the most lethal gynecological cancer. Up to 75% of cases are high-grade serous ovarian cancer (HGSOC) that have high chemosensitivity to first-line platinum-based therapies. However, 75% of patients will become chemoresistant following relapse. The underlying mechanism for developing resistance to chemotherapy in HGSOC is poorly understood. In this study, we employed Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging (MALDI-MSI) on matching formalin-fixed paraffin-embedded (FFPE) HGSOC tissues at the time of diagnosis and following relapse with chemotherapy-resistant disease (n = 4). We identified m/z values that were differentially abundant in the matching diagnosis and relapse HGSOC tissues. These were matched to proteins using nano-liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified upregulated proteins in the HGSOC relapse tissues, including COL12A1, FUBP1, PLEC, SLC4A1, and TKT. These proteins were validated by immunohistochemistry (IHC) and gene expression using online databases. IHC showed COL12A1, FUBP1, PLEC, SLC4A1, and TKT protein abundance were significantly elevated in HGSOC relapse tissues compared to matching tissues at diagnosis. COL12A1, FUBP1, PLEC, and TKT mRNA expression levels were significantly increased in HGSOC compared to normal ovary and associated with poor prognosis in HGSOC. We confirmed that higher protein abundance of both COL12A1 and PLEC correlated with reduced progression-free survival in HGSOC patients. Furthermore, both COL12A1 and PLEC mRNA and protein levels were significantly associated with chemotherapy resistance. In summary, using MALDI-MSI, we have identified proteins, including COL12A1 and PLEC, associated with chemotherapy resistance to be further evaluated as HGSOC biomarkers and/or therapeutic targets.

OpenDMS: An Open-Source Approach to Differential Mobility Spectrometry

2025-06-19

Dylan T. Koch , Yevgeniy Belous , Bradley S. Chew +6 more | Analytical Chemistry

Differential mobility spectrometry (DMS) is a powerful gas-phase chemical analysis technique that separates ions based on their differential mobility in an asymmetric electric field, offering high sensitivity and rapid analysis … Differential mobility spectrometry (DMS) is a powerful gas-phase chemical analysis technique that separates ions based on their differential mobility in an asymmetric electric field, offering high sensitivity and rapid analysis crucial for fields such as proteomics, metabolomics, and environmental monitoring. Despite its advantages, the widespread adoption of DMS technology has been hindered by the high cost, proprietary nature, and lack of flexibility of commercial systems. In this study, we introduce OpenDMS, an open-source differential mobility spectrometry system designed to be accessible, customizable, and cost-effective. OpenDMS is constructed using readily available components with fully documented designs and open-source software for data processing and visualization. We demonstrate the system's performance through detailed dispersion plots and sensitivity analyses, achieving a theoretical limit of detection of 38 ppt and a resolving power of 1.57 at 10 ppb and 836 SV for an ethylbenzene monomer. The ability to interchange ionization sources, such as plasma and UV ionization, highlights the system's versatility. Importantly, we demonstrate that doping is compatible with the OpenDMS with the use of acetone shifting the DMMP monomer peak. By providing an open-source platform, OpenDMS aims to provide a solid foundation for access to DMS technology, fostering innovation and collaboration within the scientific community and accelerating advancements in various scientific fields.

Broadband Collision-Induced Dissociation Mass Spectrometry Imaging

2025-06-19

S. Krupa , Wiktoria Szuberla , Joanna Nizioł +3 more | Journal of the American Society for Mass Spectrometry

This study demonstrates the first application of broadband collision-induced dissociation (bbCID) to mass spectrometry imaging (MSI) for the identification of untargeted metabolites in human tissues. The methodology integrates bbCID with … This study demonstrates the first application of broadband collision-induced dissociation (bbCID) to mass spectrometry imaging (MSI) for the identification of untargeted metabolites in human tissues. The methodology integrates bbCID with laser ablation-remote atmospheric pressure photoionization/chemical ionization (LARAPPI/CI), enabling the simultaneous acquisition of precursor and fragment ion distributions during MSI for many compounds simultaneously. In this approach, an infrared (IR) laser is used to ablate biological material, which is then ionized in the gas phase by a combination of photoionization and chemical ionization at atmospheric pressure. The method was validated using reference compounds, including thymidine and commonly used synthetic dyes, to assess ionization efficiency, fragmentation behavior, and spatial colocalization of precursor and fragment ions. Subsequently, bbCID-MSI was applied to clinical tissue samples of human bladder and kidney cancer. For the bladder cancer tissue, higher intensities of heptadecanoic acid, docosahexaenoic acid (FA(22:6)), docosapentaenoic acid (FA(22:5)), and FA(16:0) were observed in tumor regions, whereas proline was more abundant in adjacent nontumorous area. In renal cell carcinoma, cancerous regions exhibited elevated levels of polyunsaturated fatty acids such as arachidonic acid (FA(20:4)) and adrenic acid (FA(22:4)), while creatine and serine were enriched in healthy tissue zones. These findings highlight the utility of bbCID-MSI for spatially resolved metabolite analysis and its potential to reveal biologically relevant metabolic alterations associated with cancer.

Enhanced SALDI-MS sensitivity via Schottky and p-n junction engineering in Ag/TiO₂/Si nanohybrids: Leveraging charge separation and plasmonic thermal effects

2025-06-18

Jiaxin Lü , Chunning Chen , Jingtong Zhai +1 more | Microchemical Journal

All-Ions Laser Induced Dissociation (AI-LID) in the C-Trap of a Q Exactive: Data Independent Identification and Quantification directly from ultra-high resolution differential mass spectra

2025-06-18

Luke MacAleese , Xavier Dagany , Lény Garcia +3 more | International Journal of Mass Spectrometry

Energetic Materials as Matrices for MALDI-TOFMS Analysis of High-Molecular-Weight Polyvinylidene Fluoride-co-chlorotrifluoroethylene

2025-06-17

Colleen L. Ray , Chris E. Freye | Analytical Chemistry

Since the invention of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS), this method has lent itself well to the analysis of a wide range of macromolecules including synthetic polymers. … Since the invention of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOFMS), this method has lent itself well to the analysis of a wide range of macromolecules including synthetic polymers. However, MALDI sources and the matrices commonly used in polymer analysis have proven to be incapable of ionizing certain families of polymers. One particularly challenging polymer for MALDI-TOFMS analysis is linear copolymers of vinylidene fluoride and chlorotrifluoroethylene (VDF-co-CTFE), the analysis of which has not previously been demonstrated via this method. During this work, it was discovered that analysis of VDF-co-CTFE via MALDI-TOFMS is a problem that can be solved through the application of high explosives, albeit in quite a nontraditional manner. This study investigated the use of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) and triaminotrinitrobenzene (TATB), two high explosives, as MALDI matrices in combination with various trifluoroacetate salts. The use of these explosives as a matrix allows for the first demonstration of the ionization, detection, and analysis of various lots of a VDF-co-CTFE polymer using MALDI-TOFMS.

Distinct binding strategies of plasma proteins on gold surfaces: flexibility versus stability in the protein corona formation

2025-06-17

Beatrice Cipriani , Hender López , Giorgia Brancolini | Frontiers in Nanotechnology

When in contact with biological matrices, gold nanoparticles (AuNPs) become coated with a protein corona, which governs their biological identity and mediates interactions with cells and tissues. This study explores … When in contact with biological matrices, gold nanoparticles (AuNPs) become coated with a protein corona, which governs their biological identity and mediates interactions with cells and tissues. This study explores the adsorption behavior and conformational dynamics of two key plasma proteins, human serum albumin (HSA) and transferrin (TRF), on AuNP surfaces using Brownian Dynamics (BD) and atomistic Molecular Dynamics (MD) simulations. The results reveal multiple binding mechanisms for HSA and TRF on Au (111) surfaces. HSA exhibits significant reorientations during binding, initiated by negatively charged residues and stabilized by hydrophilic amino acids, with its structural rigidity requiring multiple reversible anchoring attempts before achieving more energetically favorable interactions. In contrast, TRF demonstrates rapid and stable binding due to its intrinsic local flexibility, retaining docked orientations with minimal reorientation. While both proteins utilize electrostatic interactions to approach the surface, TRF’s disordered structure enables swift adaptation, whereas HSA’s rigidity supports strong interactions upon relaxation. These findings highlight contrasting binding strategies, with TRF prioritizing speed and flexibility, and HSA exploiting domain rearrangements for sustained stability. Importantly, the results obtained at the all-atom level of resolution are critical for the development of coarse-grained and mesoscale models. The approach in classifying protein orientation enhances our understanding of the protein corona’s shape and morphology and could advance its effective representation in lower-resolution models. The insights gained from these simulations enable us to analyze the different adsorption behavior of TRF and HSA, providing a deeper understanding of how their structural properties influence protein corona formation.

Metal Ion Isotope Ratio Using ESI-Orbitrap HRMS: Proof of Concept and Initial Performance Evaluation for Lead Isotopic Ratios

2025-06-17

G Roncoroni , Davide Spanu , Gilberto Binda +1 more | Analytical Chemistry

This study introduces a novel approach using an electrospray source coupled to an Orbitrap MS instrument to determine metal isotope ratios. The procedure involves forming a complex between the ion … This study introduces a novel approach using an electrospray source coupled to an Orbitrap MS instrument to determine metal isotope ratios. The procedure involves forming a complex between the ion of interest and an appropriate ligand, generating gas-phase ions via electrospray ionization, selecting the complex mass by quadrupole filtering, and performing collisional fragmentation to yield free metal ions. The isotopic pattern of the free ion is then analyzed by high-resolution MS. The approach ensures high selectivity and interference-free spectra. A proof-of-concept study was conducted to determine Pb isotope ratios, focusing on identifying the factors that influence the accuracy and precision of the procedure. At this early stage, optimal accuracy was achieved even in the presence of matrix components by applying mass bias correction methods originally developed for other isotope ratio techniques; precision is comparable to that achieved by single-collector ICP-MS instrumentation. This approach may complement conventional methods that suffer from limited mass resolution and usually require extensive sample preparation.

Comet Fragment-Ion Indexing for Enhanced Peptide Sequencing

2025-06-17

Christopher D. McGann , Erik J. Bergstrom , Vagisha Sharma +4 more | Journal of Proteome Research

Fragment ion indexing has significantly improved the efficiency of proteomics database search tools. This work implements fragment ion indexing in Comet, a widely used, open-source search engine. We demonstrate that … Fragment ion indexing has significantly improved the efficiency of proteomics database search tools. This work implements fragment ion indexing in Comet, a widely used, open-source search engine. We demonstrate that this enhancement maintains scoring and identification accuracy while substantially increasing peptide spectral matching speeds across multiple applications, including open modification searches, immunopeptidomics, and real-time searches. Comet-FI reduced search speeds by up to 94%, enabling the rapid analysis of complex data types like immunopeptidomes. Fragment-ion indexing enables Comet to keep pace with modern instrumentation and expanding applications in proteomics, reinforcing its utility in diverse proteomics workflows and its integration with a wide range of proteomics tools and platforms.

An investigation of the dynamics of the ionization/dissociation in SF6 with femtosecond pulses

2025-06-17

Guoqiang Shi , Yingbo Shi , Yun Wang +3 more | The Journal of Chemical Physics

We systematically investigated the ionization and dissociation of SF6 in strong laser fields. The dependence of ion yield on laser intensity and the kinetic energy distributions and angular distributions of … We systematically investigated the ionization and dissociation of SF6 in strong laser fields. The dependence of ion yield on laser intensity and the kinetic energy distributions and angular distributions of fragment ions were also measured. The observed sequence of fragment ions is consistent with the predictions of strong-field ionization theory. The kinetic energy distributions of the Fq+ (q = 1–3) fragment ions are presented. Using a point charge model, we propose that the structure-symmetric dissociation (SSD) explains the origin of the kinetic energy of Fq+ ions. Furthermore, we identify the relevant channels and the kinetic energies of the Fq+ fragment ions produced by these channels. These results are in excellent agreement with the experimental data. The angular distributions of the Fq+ and Sq+ (q = 3, 5) ions are all anisotropic and isotropic, respectively. This is the result of the SSD process of the parent ion. However, the anisotropic component in the angular distribution of SFn+ (n = 1–4), SFn2+ (n = 2, 4), and Sq+ (q = 1, 2) suggests that the molecular structure has undergone deformation by the presence of the laser field. A comparison of the time-of-flight (TOF) spectra of fragment ions under linearly polarized and circularly polarized laser fields reveals that the SF6 molecule exhibits negligible dynamic alignment in the laser field, with geometric alignment being the dominant mechanism. Furthermore, the rescattering process plays a significant role in the production of SFn2+ (n = 2, 4) ions. The dynamics of the ionization/dissociation mechanism are discussed in the context of the TOF mass spectra, kinetic energies, and angular distributions recorded for SF6.

Extend m/z Range of External Ion Injection Into Ion Trap/TOFMS: SIMION Analysis

2025-06-16

Yixue Cao , Ping Chen , Xuesong Zhang +5 more | Journal of Mass Spectrometry

ABSTRACT Ion trap usually serves as a TOF pusher region in ion trap time‐of‐flight mass spectrometer (IT/TOF), achieving benefits of high duty cycle, MS/MS capability, and high mass resolution. While … ABSTRACT Ion trap usually serves as a TOF pusher region in ion trap time‐of‐flight mass spectrometer (IT/TOF), achieving benefits of high duty cycle, MS/MS capability, and high mass resolution. While a short ion trap rod length improves TOF resolution, it limits the mass range in coaxial IT/TOF. Through a computational study based on SIMION simulations, this work systematically investigates the influence of geometric parameters (trap rod length) and voltage parameters (bias DC voltage, end‐cap electrode voltage) on the mass range of coaxial IT‐TOF systems. By optimizing length of trap rod, over 90% injection efficiency was achieved within a m/z 400–1400 without sacrificing mass resolution. By implementing DC bias voltage adjustments for low‐m/z ions and step voltage optimization on end‐cap electrodes for high‐ m/z ions, the simulated mass range is extended to m/z 200–1400 with minimal mass discrimination. All above these findings are derived solely from simulation analysis.

Mechanical squeezed Kerr oscillator based on a tapered ion trap

2025-06-16

NULL AUTHOR_ID | Physical review. A/Physical review, A

Quantitative Mass Spectrometry Imaging by Targeted‐DESI‐MSI in MRM Mode Provides Higher Sensitivity and Specificity for Fast Quantification of Chloroquine Drug in Mice Kidney

2025-06-16

Md. Muedur Rahman , Mst. Sayela Afroz , Md. Al Mamun +7 more | Journal of Mass Spectrometry

ABSTRACT Quantitative mass spectrometry imaging (QMSI) is being applied for spatial quantification of drugs and metabolites using mass spectrometry imaging (MSI) tools. DESI‐MSI is ideally suited to QMSI as a … ABSTRACT Quantitative mass spectrometry imaging (QMSI) is being applied for spatial quantification of drugs and metabolites using mass spectrometry imaging (MSI) tools. DESI‐MSI is ideally suited to QMSI as a soft and ambient ionization technique. However, some challenging issues of QMSI include extraction efficiency, matrix effect, sensitivity, and specificity, which need to be addressed. Here, we applied targeted DESI‐MSI in multiple reaction monitoring (MRM) mode for QMSI of chloroquine, an antimalarial drug, as a model in mice kidneys and carefully addressed those challenging issues. A triple quadrupole mass spectrometer coupled with a DESI source was used to quantify the chloroquine (transition m/z 320.2 → 247.1) drug. A deuterated internal standard chloroquine‐d 5 (transition m/z 325.2 → 147.1), was used to normalize the data from pixel to pixel. A mimetic in‐tissue model was employed to constract a calibration curve demonstrating good linearity (y = 0.0041x, R 2 = 0.9953) and precision (RSD < 15%). The calibration curve was validated by back‐calculation, with results falling within acceptable ranges (accuracy error< ±15%). Finally, the dosed (30 mg/kg) chloroquine was quantified in three spatial regions (cortex, medulla, and pelvis) in the mice kidneys. The highest concentrations of chloroquine in the pelvis (399.85 and 436.28 ng/mg of kidney tissue at 30 and 60 min intervals) region is consistent with the previous report that a portion of the drug is eliminated from the kidney as unchanged forms. This study provides valuable insights into using DESI‐MSI in MRM mode for the QMSI of drugs in biological tissues and will have implications for future research on pharmacology and toxicology.

Dynamic assessment of the allocation of copper to cytochrome c oxidase using size-exclusion chromatography (SEC) combined with inductively coupled plasma mass spectrometry (ICP-MS)

2025-06-16

Dina Secic , Megan E. Bischoff , L. Ph. H. Schmidt +4 more | bioRxiv (Cold Spring Harbor Laboratory)

Copper (Cu) is an essential trace element required for mitochondrial respiration via its incorporation into cytochrome c oxidase (CuCOX), the terminal enzyme of the electron transport chain. In this study, … Copper (Cu) is an essential trace element required for mitochondrial respiration via its incorporation into cytochrome c oxidase (CuCOX), the terminal enzyme of the electron transport chain. In this study, we employed size-exclusion chromatography coupled with inductively coupled plasma mass spectrometry (SEC-ICP-MS), UV-Vis spectroscopy, and immunoblotting to identify and validate a high-molecular-weight Cu-containing peak in SEC-ICP-MS chromatogram as representative of CuCOX activity. We demonstrate that this CuCOX peak is enhanced under metabolic conditions favoring oxidative phosphorylation, such as high Cu supplementation or galactose-containing media, and correlates with increased mitochondrial respiration. By tracing exogenously supplied 63Cu, we characterized the time- and dose-dependent incorporation of newly acquired Cu into CuCOX. Functional RNA interference (RNAi) experiments targeting key Cu transporters revealed that CuCOX formation is independent of the high-affinity Cu importer CTR1, but instead relies on alternative transporters including DMT1, LAT1, and the mitochondrial carrier SLC25A3. These findings offer new insight into the cellular pathways governing Cu trafficking and allocation to mitochondria under physiologically relevant conditions. Furthermore, our work establishes SEC-ICP-MS as a sensitive and specific method for quantifying CuCOX and assessing mitochondrial metabolism. This platform holds promise for the identification of Cu-related biomarkers and therapeutic targets, particularly in the context of diseases such as renal cell carcinoma (RCC), where dysregulated Cu homeostasis plays a critical role.

Multiplexed Targeted Spatial Mass Spectrometry Imaging Assays to monitor lipids and NAD+ metabolites in CD38 knockout mice exhibiting improved metabolism

2025-06-16

Birgit Schilling , Charles A. Schurman , Joanna Bons +7 more | Research Square (Research Square)

<title>Abstract</title> Mass spectrometry imaging (MSI) is a rapidly advancing technology that provides mapping of the spatial molecular landscape of tissues for a variety of analytes. Matrix-assisted laser desorption/ionization (MALDI)-MSI is … <title>Abstract</title> Mass spectrometry imaging (MSI) is a rapidly advancing technology that provides mapping of the spatial molecular landscape of tissues for a variety of analytes. Matrix-assisted laser desorption/ionization (MALDI)-MSI is commonly employed, however, confident <italic>in situ</italic> identification and accurate quantification of analytes remain challenging. We present a novel imaging methodology combining trapped ion mobility spectrometry (TIMS)-based parallel accumulation-serial fragmentation (PASEF) with MALDI ionization for targeted imaging parallel reaction monitoring (iprm-PASEF). We investigated the spatial distribution of lipids and metabolites in liver tissues from wild-type and CD38 knockout mice (CD38−/−). CD38, an enzyme involved in nicotinamide adenine dinucleotide (NAD⁺) metabolism, significantly influences liver metabolic function and contributes to age-related NAD⁺ decline. Although CD38 deletion previously was linked to improved metabolic phenotypes, the underlying spatial metabolic mechanisms are poorly understood. The spatial iprm-PASEF workflow enabled confident identification and differentiation of lipid isomers at the MS2 fragment ion level and revealed increased NAD+ and decreased adenosine diphosphate ribose (ADPR), a by-product of NAD+ hydrolysis, in CD38−/− livers. This approach provided confident, specific, and robust MS2-based identification and quantification of fragment ions in spatial MSI experiments. Additionally, the innovative iprm-PASEF opens unprecedented opportunities for spatial metabolomics and lipidomics, offering spatially resolved insights into molecular mechanisms.

P52 Morphological and biophysical profile of bladder cancer cells for label-free detection

2025-06-16

Rosário Monteiro , C.C. de Azevedo , C.N. Fernandes +5 more | European Urology Open Science

Structure Elucidation for MALDI Mass Spectrometry Imaging Using Infrared Ion Spectroscopy

2025-06-16

Jelle L. Schuurman , Lara van Tetering , Kas J. Houthuijs +7 more | Analytical Chemistry

Infrared ion spectroscopy (IRIS) is a tandem mass spectrometry (MS) technique that generates structurally diagnostic vibrational spectra for mass-selected ions trapped in a mass spectrometer. Until now, IRIS applications for … Infrared ion spectroscopy (IRIS) is a tandem mass spectrometry (MS) technique that generates structurally diagnostic vibrational spectra for mass-selected ions trapped in a mass spectrometer. Until now, IRIS applications for biological samples have primarily focused on solution-based analyses, such as body fluids (e.g., plasma and urine) and tissue homogenates, using electrospray ionization (ESI) coupled with liquid chromatography-mass spectrometry (LC-MS). In this study, we have combined matrix-assisted laser desorption/ionization (MALDI) with IRIS for the direct analysis of small molecules from biological tissues on a Fourier-transform ion cyclotron resonance mass spectrometer. We applied this technique alongside MALDI mass spectrometry imaging to analyse brain tissue from two knockout mouse models of l-lysine catabolism disorders: pyridoxine-dependent epilepsy (ALDH7A1) and glutaric aciduria type 1 (GCDH). The MALDI-IRIS platform, now available for users at HFML-FELIX, represents a significant advance in the direct structural characterization of metabolites in complex biological tissues and opens new possibilities for structure elucidation in the field of MALDI mass spectrometry imaging.

Advancing Peptide and Protein Stereoisomer Analysis with Conformation‐based Chiral Separation via Liquid Chromatography and Ion Mobility‐Mass Spectrometry

2025-06-16

Juan Liu , Gongyu Li | Analysis & Sensing

Peptides and proteins with D‐amino acids and other stereoisomers in their sequences are now considered to be widespread in different organisms. Their significance is attributed to the altered functions of … Peptides and proteins with D‐amino acids and other stereoisomers in their sequences are now considered to be widespread in different organisms. Their significance is attributed to the altered functions of these molecules, such as having some pathological significance or enhancing biological activity. Only slight shifts in structural and other biophysical parameters make their full characterization and complete distinction technically challenging for traditional tools like mass spectrometry (MS). Ion mobility spectrometry (IMS) in conjunction with liquid chromatography (LC) adds an extra dimension to the separation in space as it depends on the mobility of ions, being determined by their overall shape and the orientation of the molecules. Thus, peptide isomers having measurable mobility and collisional cross‐section (CCS) values can thus be resolved by IM‐MS. In addition, by combining with tandem MS techniques, IM‐MS with adequate conformation‐resolving capability is likely to localize the isomerization sites. In this review, we briefly introduce the basic principles of conformation‐based chiral separation through LC and CE, in conjunction with IM‐MS for enhanced peptide/protein stereoisomer differentiation, and then comprehensively summarize the recent advancements in IM‐MS‐based peptide/protein stereoisomer analysis, focusing on the development of conformation‐based chiral separation strategies, including instrumental modifications, chemical modifications and computational tools.

Practical Tips for the Application of HDX-MS to Membrane Proteins, Biomolecular Condensates, and Weak Protein Binders

2025-06-16

Xiaoxuan Lin , Andrew V. Molina , Julia Shangguan +2 more | Journal of the American Society for Mass Spectrometry

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) has emerged as a powerful biophysical tool to study protein thermodynamics, dynamics, and function. Despite its increasing use, effective implementation of HDX-MS requires knowledge of … Hydrogen-deuterium exchange mass spectrometry (HDX-MS) has emerged as a powerful biophysical tool to study protein thermodynamics, dynamics, and function. Despite its increasing use, effective implementation of HDX-MS requires knowledge of protein chemistry, folding, liquid chromatography, MS, and automation. Whereas method development for soluble globular proteins is often easily generalizable, HDX-MS on more complex systems is challenging. Published method sections are usually concise, and available step-by-step protocols typically only provide generalized procedures. Here, we offer tips for applying HDX-MS to three complex systems: integral membrane proteins, biomolecular condensates, and weak protein binders. These practices have yielded high sequence coverage and high-quality data, allowing for free energy quantification and, importantly, mechanistic understanding of protein functions. We believe that sharing our methodologies will help others apply and develop HDX-MS methods for these and similar systems.

Evaluating the impact of chaotropic salts on protein corona formation on polyethylene glycol-b-polylactic acid polymersomes

2025-06-15

Owen Tabah , D. I. Nichols , A. R. Blake +3 more | Journal of Colloid and Interface Science

Polymersomes (PS) are a class of hollow polymeric nanoparticle vesicles made of amphiphilic block co-polymers that self-assemble via hydrophobic interactions. One of the significant unsung challenges for their translation is … Polymersomes (PS) are a class of hollow polymeric nanoparticle vesicles made of amphiphilic block co-polymers that self-assemble via hydrophobic interactions. One of the significant unsung challenges for their translation is the uncontrolled formation of the protein corona, which can influence PS biodistribution, cellular uptake, and immune recognition. Despite the major benefits associated with PS, no studies have yet explored engineering their protein corona. Evidence suggests that the confirmation of polyethylene glycol (PEG) chains, which can vary in response to Hofmeister series salts, can affect protein corona composition. Here, we investigated the impact of different Hofmeister series salt ions, focusing on increasing chaotropic salts [NaCl (Na+) < CaCl2 (Ca2+) < MgCl2 (Mg2+)] on the biomolecular identity of PEG-b-polylactic acid (PLA) PS after incubation in serum. We observed that the ionic environment significantly influences the protein corona formation on PEG-b-PLA PS. The presence of different salt ions, particularly divalent cations like calcium and magnesium, can change the size and surface chemistry of PEG-b-PLA PS, leading to alterations in the specific protein composition of the corona. We propose that these protein corona differences are driven by both (1) charge-based and (2) biologically driven interactions. This knowledge could be leveraged to engineer nanoparticles with tailored protein coronas. While this research focused primarily on PS made of one polymer, PEG-b-PLA, other polymers and polyelectrolytes in PSs need to be investigated. We've shown that a surface coated with low molecular weight PEG can be impacted by ions, despite not having any ionizable groups.

Gaussian Process Regression for Mapping Free EnergyLandscape of Mg2+-Cl− Ion Pairing in Aqueous Solution: Molecular Insights and Computational Efficiency

2025-06-15

Wasut Pornpatcharapong | Molecules

Free energy landscapes are pivotal for understanding molecular interactions in solution, yet their reconstruction in complex systems remains computationally demanding. In this study, we integrated Gaussian process regression (GPR) with … Free energy landscapes are pivotal for understanding molecular interactions in solution, yet their reconstruction in complex systems remains computationally demanding. In this study, we integrated Gaussian process regression (GPR) with well-tempered metadynamics (WT-MTD) to efficiently map the free energy landscape of the Mg2+-Cl− ion pairing in an aqueous solution, a system central to biological processes such as magnesium hydration and ligand exchange. We compared traditional umbrella sampling (WHAM) with WT-MTD-derived free energy profiles, identifying critical discrepancies attributed to insufficient sampling in barrier regions. WT-MTD captures two distinct minima corresponding to the contact ion pair (CIP: 0.23 nm) and solvent-separated ion pair (SSIP: 0.47 nm) configurations, consistent with previous computational and experimental studies. GPR, trained on free energy gradients from WT-MTD trajectories, reconstructs smooth landscapes with small datasets (5000 points) while reducing computational costs via grid sparsification. Our results demonstrate that GPR hyperparameters can be optimized based on the insights from WT-MTD simulations, enabling accurate reconstructions even in sparse data regimes. This approach bridges computational efficiency with molecular-level resolution, offering a robust framework for studying ion solvation dynamics and hydration effects in complex systems, where this work is the first application of GPR in ionic solvation environments. The methodology’s scalability to multidimensional landscapes further underscores its potential for advancing molecular simulations in biochemistry and material science.

Determination of Copolymer Block-Length Distributions Using Fragmentation Data Obtained from Tandem Mass Spectrometry

2025-06-15

Tijmen S. Bos , Rick S. van den Hurk , Ynze Mengerink +4 more | Macromolecules

Revealing Anisotropic Growth of Liraglutide Oligomers by Native Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

2025-06-15

Zhenyu Xi , Syuan‐Ting Kuo , Xiao Cong +2 more | ACS Central Science

Screening of Protein Carbonylation Sites in Human Serum by Ion Mobility Mass Spectrometry

2025-06-14

Juan Camilo Rojas Echeverri , Sanja Milkovska‐Stamenova , Ulf Wagner +1 more | Journal of Proteome Research

Excessive oxidative stress, associated with various diseases, can induce protein carbonylation-nonenzymatic modifications involving aldehyde or keto group formation. These modifications are structurally diverse and low in abundance, which complicates their … Excessive oxidative stress, associated with various diseases, can induce protein carbonylation-nonenzymatic modifications involving aldehyde or keto group formation. These modifications are structurally diverse and low in abundance, which complicates their detection and quantitation. Here, we developed a strategy to identify and quantify protein carbonylation in human serum proteins from 39 rheumatoid arthritis patients and 29 healthy donors. Reactive carbonyl groups were derivatized with an aldehyde reactive probe (ARP), digested with trypsin, enriched via avidin affinity chromatography, and analyzed using RP-HPLC-ESI-IMS-MS/MS. Ion mobility spectrometry (IMS) was applied in both data-dependent (DDA) and data-independent acquisition (DIA) modes. DDA generated spectral libraries of ARP-derivatized peptides (ARP-peptides), which enabled peptide-centric detection in DIA data. We manually confirmed 86 ARP-peptides, with 93.8% of peak areas showing signal-to-background ratios >3. Among the 32 unique carbonylation sites, 28 were on human serum albumin, with hotspots at Cys58, Lys214, Lys219, Lys223, Lys456, Lys543, Lys549, and Lys565. Six previously unreported species were identified using IMS, DIA, ARP-reporter ions, and de novo sequencing. The ARP-peptides were quantified with ≥ 75% intrabatch reproducibility (coefficient of variation <20%). Similar modification levels were observed in both groups, suggesting basal, disease-independent carbonylation in abundant serum proteins.