Journal of the American Society for Mass Spectrometry最新文献_第10页

Glycosaminoglycan Mass Spectrometry Imaging by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-03-03 DOI: 10.1021/jasms.4c0043510.1021/jasms.4c00435

Tana V. Palomino, and , David C. Muddiman*,

引用次数: 0

Top-Down Proteomic Profiling of Protein Corona by High-Throughput Capillary Isoelectric Focusing-Mass Spectrometry

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-03-02 DOI: 10.1021/jasms.4c0046310.1021/jasms.4c00463

Reyhane Tabatabaeian Nimavard, Seyed Amirhossein Sadeghi, Morteza Mahmoudi, Guijie Zhu* and Liangliang Sun*,

{"title":"Top-Down Proteomic Profiling of Protein Corona by High-Throughput Capillary Isoelectric Focusing-Mass Spectrometry","authors":"Reyhane Tabatabaeian Nimavard, Seyed Amirhossein Sadeghi, Morteza Mahmoudi, Guijie Zhu* and Liangliang Sun*, ","doi":"10.1021/jasms.4c0046310.1021/jasms.4c00463","DOIUrl":"https://doi.org/10.1021/jasms.4c00463https://doi.org/10.1021/jasms.4c00463","url":null,"abstract":"In the rapidly evolving field of nanomedicine, understanding the interactions between nanoparticles (NPs) and biological systems is crucial. A pivotal aspect of these interactions is the formation of a protein corona when NPs are exposed to biological fluids (e.g., human plasma), which significantly influences their behavior and functionality. This study introduces an advanced capillary isoelectric focusing tandem mass spectrometry (cIEF-MS/MS) platform designed to enable high-throughput and reproducible top-down proteomic analysis of protein corona. Our cIEF-MS/MS technique completed each analysis within 30 min. It produced reproducible proteoform measurements of protein corona for at least 50 runs regarding the proteoforms’ migration time [relative standard deviations (RSDs) <4%], the proteoforms’ intensity (Pearson’s correlation coefficients between any two runs >0.90), the number of proteoform identifications (71 ± 10), and the number of proteoform-spectrum matches (PrSMs) (196 ± 30). Of the 53 identified genes, 33 are potential biomarkers of various diseases (e.g., cancer, cardiovascular disease, and Alzheimer’s disease). We identified 1–102 proteoforms per potential protein biomarker, containing various sequence variations or post-translational modifications. Delineating proteoforms in protein corona by our cIEF-MS/MS in a reproducible and high-throughput fashion will benefit our understanding of nanobiointeractions and advance both diagnostic and therapeutic nanomedicine technologies.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 4","pages":"778–786 778–786"},"PeriodicalIF":3.1,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00463","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Impact of the Mass Analyzer and Tissue Section Thickness on Spatial N-Glycomics with MALDI-MSI

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-27 DOI: 10.1021/jasms.4c0049410.1021/jasms.4c00494

Dušan Veličković*, Marija Veličković, Christopher L. O’Connor, Markus Bitzer and Christopher Anderton,

{"title":"The Impact of the Mass Analyzer and Tissue Section Thickness on Spatial N-Glycomics with MALDI-MSI","authors":"Dušan Veličković*, Marija Veličković, Christopher L. O’Connor, Markus Bitzer and Christopher Anderton, ","doi":"10.1021/jasms.4c0049410.1021/jasms.4c00494","DOIUrl":"https://doi.org/10.1021/jasms.4c00494https://doi.org/10.1021/jasms.4c00494","url":null,"abstract":"We compared matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) spatial N-glycomics data sets from Fourier-transform ion cyclotron resonance (FTICR) and orthogonal accelerated time-of-flight (timsTOF) mass spectrometers of FFPE preserved human kidney samples. We also tested different tissue section thicknesses. In these analyses, we assessed the impact of the mass analyzer and tissue section thickness on N-glycan coverage, sensitivity, and histological alignment. Our results indicate negligible differences in N-glycan coverage between the two mass analyzers, where N-glycan annotation numbers remained consistent and were highly reproducible. The timsTOF-MS analyses demonstrated significant advantages with higher duty cycles and better lateral resolution, allowing for finer spatial resolution without compromising signal integrity. Specifically, timsTOF was able to generate detailed MALDI-MS images at 20 μm step size, accurately identifying N-glycan Hex:5 HexNAc:5 dHex:1 as a tubular-specific marker without observable delocalization. Despite minor annotation discrepancies, where only three species detected by FTICR were not detected by using timsTOF, and a few false-positive annotations from the timsTOF analysis attributed to lower mass resolving power, the overall consistency between the instruments was high. Importantly, tissue section thickness did not affect analysis sensitivity in the timsTOF analyses, with the average glycan signal intensity remaining stable between 7 and 2 μm sections. These findings demonstrate that 2 μm thick tissue slices can be effectively used in spatial N-glycomics workflows, maintaining sensitivity while enhancing confidence in pathohistological evaluations.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 4","pages":"823–828 823–828"},"PeriodicalIF":3.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-25 DOI: 10.1021/jasms.4c0043410.1021/jasms.4c00434

Dennis D. Krutkin, Sydney Thomas, Simone Zuffa, Prajit Rajkumar, Rob Knight, Pieter C. Dorrestein and Scott T. Kelley*,

{"title":"To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question","authors":"Dennis D. Krutkin, Sydney Thomas, Simone Zuffa, Prajit Rajkumar, Rob Knight, Pieter C. Dorrestein and Scott T. Kelley*, ","doi":"10.1021/jasms.4c0043410.1021/jasms.4c00434","DOIUrl":"https://doi.org/10.1021/jasms.4c00434https://doi.org/10.1021/jasms.4c00434","url":null,"abstract":"Untargeted metabolomics often produce large datasets with missing values. These missing values are derived from biological or technical factors and can undermine statistical analyses and lead to biased biological interpretations. Imputation methods, such as k-Nearest Neighbors (kNN) and Random Forest (RF) regression, are commonly used, but their effects vary depending on the type of missing data, e.g., Missing Completely At Random (MCAR) and Missing Not At Random (MNAR). Here, we determined the impacts of degree and type of missing data on the accuracy of kNN and RF imputation using two datasets: a targeted metabolomic dataset with spiked-in standards and an untargeted metabolomic dataset. We also assessed the effect of compositional data approaches (CoDA), such as the centered log-ratio (CLR) transform, on data interpretation since these methods are increasingly being used in metabolomics. Overall, we found that kNN and RF performed more accurately when the proportion of missing data across samples for a metabolic feature was low. However, these imputations could not handle MNAR data and generated wildly inflated or imputed values where none should exist. Furthermore, we show that the proportion of missing values had a strong impact on the accuracy of imputation, which affected the interpretation of the results. Our results suggest imputation should be used with extreme caution even with modest levels of missing data and especially when the type of missingness is unknown.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 4","pages":"742–759 742–759"},"PeriodicalIF":3.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/jasms.4c00434","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Faces of Mass Spectrometry/Amanda Patrick

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-25 DOI: 10.1021/jasms.5c0004210.1021/jasms.5c00042

Anne Brenner, and , J. D. Brookbank,

引用次数: 0

Navigating the Postdoc Experience

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-20 DOI: 10.1021/jasms.4c0044810.1021/jasms.4c00448

Chae Kyung Jeon*, Daniel D. Vallejo and Michael T. Marty,

{"title":"Navigating the Postdoc Experience","authors":"Chae Kyung Jeon*, Daniel D. Vallejo and Michael T. Marty, ","doi":"10.1021/jasms.4c0044810.1021/jasms.4c00448","DOIUrl":"https://doi.org/10.1021/jasms.4c00448https://doi.org/10.1021/jasms.4c00448","url":null,"abstract":"There are many reasons to consider postdoctoral research after completing a Ph.D. For those interested in academic careers at all levels, a postdoctoral research associate (PDRA) position is often required or at least preferred. Even for those interested in industry, government, or alternative careers, postdoctoral research provides opportunities to expand your knowledge and skill sets beyond your Ph.D. training. It can be a wonderful time to focus on research with minimal distractions and interruptions. However, there has been little discussion about the challenges of the postdoc transition. The postdoc experience can vary widely, but common challenges include transitioning into a new environment, learning new skills, serving in multiple roles as a mentor and mentee, different and sometimes unclear positions in the institution, and competition for limited opportunities. In this Commentary, we draw on our personal experiences and interviews with postdocs of various backgrounds and intersectionalities (gender, race, first-gen, neurodiversity, etc.) to discuss how to successfully navigate various aspects of the postdoc experience. Our perspective comes primarily within mass spectrometry (MS) research, but the interviews include several experiences outside of the MS field to develop discussions applicable to a broad range of PDRA experiences.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 3","pages":"622–626 622–626"},"PeriodicalIF":3.1,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143547242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

HRMS-Viewer: Software for High Resolution Mass Spectrometry Formula Assignment and Data Visualization

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-19 DOI: 10.1021/jasms.4c0044210.1021/jasms.4c00442

Junyang Chen, Chen He, Jianxun Wu, Yahe Zhang and Quan Shi*,

{"title":"HRMS-Viewer: Software for High Resolution Mass Spectrometry Formula Assignment and Data Visualization","authors":"Junyang Chen, Chen He, Jianxun Wu, Yahe Zhang and Quan Shi*, ","doi":"10.1021/jasms.4c0044210.1021/jasms.4c00442","DOIUrl":"https://doi.org/10.1021/jasms.4c00442https://doi.org/10.1021/jasms.4c00442","url":null,"abstract":"Accurately assigning formulas to thousands of peaks generated by ultrahigh resolution mass spectrometry in a single analysis poses a significant challenge, especially when dealing with diverse molecular compositions across complex mixtures. This difficulty is further compounded by the lack of an established universal mass calibration and formula assignment method. We have developed HRMS-Viewer, a Python-based software tool designed for processing ultrahigh resolution mass spectrometry data specific to petroleum and natural organic matter (NOM). The software employs an efficient, experience-driven approach for small molecule formula assignment, offering a streamlined yet intuitive workflow. Key features include advanced noise reduction, automatic or manual recalibration, real-time visualization of formula assignment results, and options for manual correction. During the workflow, HRMS-Viewer enables the visualization and manual control of critical steps including noise reduction, recalibration, peak identification, and data review.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 3","pages":"565–572 565–572"},"PeriodicalIF":3.1,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143547494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling Readily Ionized and Robust Anionic Species: A Gateway to Enhanced Ionization Efficiency in ESI-MS Analysis

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-13 DOI: 10.1021/jasms.4c0040010.1021/jasms.4c00400

Benjamin B. Warnes, Jasmine Chihabi and Jeffrey M. Manthorpe*,

{"title":"Unveiling Readily Ionized and Robust Anionic Species: A Gateway to Enhanced Ionization Efficiency in ESI-MS Analysis","authors":"Benjamin B. Warnes, Jasmine Chihabi and Jeffrey M. Manthorpe*, ","doi":"10.1021/jasms.4c0040010.1021/jasms.4c00400","DOIUrl":"https://doi.org/10.1021/jasms.4c00400https://doi.org/10.1021/jasms.4c00400","url":null,"abstract":"Electrospray ionization mass spectrometry has long been a prevalent ionization method in the analysis of low volatility molecules with biological, environmental, and industrial relevance. To address analytical challenges associated with molecules suffering from low ionization efficiencies (IEs), chemical derivatization (CD) strategies have been developed and are frequently adopted into workflows. However, only a minute number of CD techniques have been developed for negative polarity. To address this disparity, we evaluated 27 anions based on three criteria: (1) IE relative to a sodium dodecyl sulfate (11 + Na+) internal standard; (2) stability to collision induced dissociation; (3) diagnostic tandem mass spectrometry behavior. Highly fluorous ions exhibiting weakly coordinating and hydrophobic properties displayed enhanced IE. Trifluoromethanesulfonyl-containing ions proved to be unexpectedly labile, while tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (23) and bis(nonafluoro-1-butane)sulfonimidate (25) were determined to be of optimal IE of 332% ± 25% and 939% ± 92%, respectively, and in tandem MS exhibited survival yields of 100% ± 0% and 72.6% ± 0.8% at −50 eV. 23 and 25 were also comparable in IE across several solvents, and combinations thereof, that are ubiquitous in liquid chromatography. Various salts of 25 were evaluated for cation effects, where the IE of 25 ranged from 939% ± 92% to 3195% ± 145% across K+, NH4+, Na+, and H+. Compared to tetra-n-butylammonium, tetra-n-butylphosphonium, and (4-methylphenyl)diphenylsulfonium cations, 25 displayed signal enhancements ranging from 136% ± 6% to 181% ± 14%, thereby making it an optimal candidate for CD development.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 3","pages":"524–533 524–533"},"PeriodicalIF":3.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143547398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection and Structural Elucidation of Copper Binding Tri- and Tetrapyrrole Ligands Produced by the Marine Diatom Phaeodactylum Tricornutum

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-13 DOI: 10.1021/jasms.4c0038010.1021/jasms.4c00380

Lydia Babcock-Adams, Jingxuan Li, Amy M. McKenna, Christopher L. Hendrickson and Daniel J. Repeta*,

{"title":"Detection and Structural Elucidation of Copper Binding Tri- and Tetrapyrrole Ligands Produced by the Marine Diatom Phaeodactylum Tricornutum","authors":"Lydia Babcock-Adams, Jingxuan Li, Amy M. McKenna, Christopher L. Hendrickson and Daniel J. Repeta*, ","doi":"10.1021/jasms.4c0038010.1021/jasms.4c00380","DOIUrl":"https://doi.org/10.1021/jasms.4c00380https://doi.org/10.1021/jasms.4c00380","url":null,"abstract":"In seawater, most dissolved copper (Cu) is complexed by organic ligands, many of which are thought to be produced by phytoplankton. Although very little is known about the composition and structure of these ligands, they play an important role in determining the reactivity and bioavailability of Cu. In this study, Phaeodactylum tricornutum, a marine diatom known to produce Cu ligands (CuLs), was grown in laboratory pure culture, and the CuLs were recovered from the growth media. Using liquid chromatography coupled to ultrahigh resolution tandem mass spectrometry, 11 Cu ligand complexes were identified and assigned molecular formulas. Molecular formulas were confirmed by comparing the expected and observed relative abundances of 15N, 13C, 65Cu, and 18O isotopologues. The CuLs had molecular weights from 520 to 719 Da and molecular formulas of C26–35H23–36O5–9N3–4Cu with an average assignment error of 56 ppb. High-resolution tandem mass spectrometry of the Cu-bound and metal-free ligands revealed these to be a suite of tri- and tetrapyrroles stabilized through complexation of Cu by N. The ligands share similar parent structures but differ in the number, type, and arrangement of functional groups that decorate the pyrroles. The similarity of CuL structures with known catabolites of chlorophyll suggests these ligands may be widely produced by marine photoautotrophs.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 4","pages":"713–720 713–720"},"PeriodicalIF":3.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143745872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PNGaseF-Generated N-Glycans Adduct onto Peptides in the Gas Phase

IF 3.1 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-02-12 DOI: 10.1021/jasms.4c0043110.1021/jasms.4c00431

Valentina Rangel-Angarita, Joann Chongsaritsinsuk, Keira E. Mahoney, Lea M. Kim, Ryan J. Chen, Akua A. Appah-Sampong, Isabella P. Tran, Alexandra D. Steigmeyer, Marie A. Hollenhorst and Stacy A. Malaker*,

{"title":"PNGaseF-Generated N-Glycans Adduct onto Peptides in the Gas Phase","authors":"Valentina Rangel-Angarita, Joann Chongsaritsinsuk, Keira E. Mahoney, Lea M. Kim, Ryan J. Chen, Akua A. Appah-Sampong, Isabella P. Tran, Alexandra D. Steigmeyer, Marie A. Hollenhorst and Stacy A. Malaker*, ","doi":"10.1021/jasms.4c0043110.1021/jasms.4c00431","DOIUrl":"https://doi.org/10.1021/jasms.4c00431https://doi.org/10.1021/jasms.4c00431","url":null,"abstract":"Glycoproteomics has recently increased in popularity due to instrumental and methodological advances. That said, O-glycoproteomic analysis is still challenging for various reasons, including signal suppression, search algorithm limitations, and co-occupancy of N- and O-glycopeptides. To decrease sample complexity and simplify analysis, most O-glycoproteomic workflows include PNGaseF digestion, which is an endoglycosidase that removes most N-glycan structures. Here, we report that N-glycans released from PNGaseF digestion were identified during data acquisition and hampered detection of O-glycopeptides. Importantly, we noted instances where free glycans adducted to unmodified peptides in the gas phase and were misidentified by search algorithms as O-glycopeptides. We confirmed the presence of free glycans in other experiments performed in our laboratory, as well as from data generated by other groups. To overcome this limitation, we demonstrated that released N-glycans can be removed using a molecular weight cut off filter prior to (glyco)protease digestion, which improves O-glycoproteomic coverage.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 3","pages":"542–552 542–552"},"PeriodicalIF":3.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143547391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0