Journal of Proteome Research最新文献

Candida albicans: A Comprehensive View of the Proteome.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-14 DOI: 10.1021/acs.jproteome.4c01020

Leticia Gomez-Artiguez, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, Lucía Monteoliva, Robert L Moritz, Eric W Deutsch, Concha Gil

{"title":"Candida albicans: A Comprehensive View of the Proteome.","authors":"Leticia Gomez-Artiguez, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, Lucía Monteoliva, Robert L Moritz, Eric W Deutsch, Concha Gil","doi":"10.1021/acs.jproteome.4c01020","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01020","url":null,"abstract":"We describe a new release of the Candida albicans PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. The C. albicans PeptideAtlas summary web page provides \"Build overview\", \"PTM coverage\", \"Experiment contribution\", and \"Data set contribution\" information. The protein and peptide information can also be accessed via the Candida Genome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments that identify each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyze PTM results is provided in the PeptideAtlas of this important pathogen. Candida albicans PeptideAtlas web page: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-13 DOI: 10.1021/acs.jproteome.4c00962

Ian Engels, Alexandra Burnett, Prudence Robert, Camille Pironneau, Grégory Abrams, Robbin Bouwmeester, Peter Van der Plaetsen, Kévin Di Modica, Marcel Otte, Lawrence Guy Straus, Valentin Fischer, Fabrice Bray, Bart Mesuere, Isabelle De Groote, Dieter Deforce, Simon Daled, Maarten Dhaenens

{"title":"Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline.","authors":"Ian Engels, Alexandra Burnett, Prudence Robert, Camille Pironneau, Grégory Abrams, Robbin Bouwmeester, Peter Van der Plaetsen, Kévin Di Modica, Marcel Otte, Lawrence Guy Straus, Valentin Fischer, Fabrice Bray, Bart Mesuere, Isabelle De Groote, Dieter Deforce, Simon Daled, Maarten Dhaenens","doi":"10.1021/acs.jproteome.4c00962","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00962","url":null,"abstract":"Liquid chromatography-mass spectrometry (LC-MS/MS) extends the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) Zooarcheology by Mass Spectrometry (ZooMS) \"mass fingerprinting\" approach to species identification by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse data containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. To ameliorate this issue, we present a ZooMS/MS data pipeline that builds on a manually curated Collagen database and comprises two novel algorithms: isoBLAST and ClassiCOL. isoBLAST first extends peptide ambiguity by generating all \"potential peptide candidates\" isobaric to the annotated precursor. The exhaustive set of candidates created is then used to retain or reject different potential paths at each taxonomic branching point from superkingdom to species, until the greatest possible specificity is reached. Uniquely, ClassiCOL allows for the identification of taxonomic mixtures, including contaminated samples, as well as suggesting taxonomies not represented in sequence databases, including extinct taxa. All considered ambiguity is then graphically represented with clear prioritization of the potential taxa in the sample. Using public as well as in-house data acquired on different instruments, we demonstrate the performance of this universal postprocessing and explore the identification of both genetic and sample mixtures. Diet reconstruction from 40,000-year-old cave hyena coprolites illustrates the exciting potential of this approach.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-13 DOI: 10.1021/acs.jproteome.4c00864

Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens

{"title":"Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.","authors":"Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens","doi":"10.1021/acs.jproteome.4c00864","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00864","url":null,"abstract":"Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident identification of bacterial immunopeptides. Immunopeptidomics data of cell cultures infected with Listeria monocytogenes were searched by four different search engines, PEAKS, Comet, Sage and MSFragger, followed by data-driven rescoring with MS2Rescore. Compared with individual search engine results, this integrated workflow boosted immunopeptide identification by an average of 27% and led to the high-confidence detection of 18 additional bacterial peptides (+27%) matching 15 different Listeria proteins (+36%). Despite the strong agreement between the search engines, a small number of spectra (<1%) had ambiguous matches to multiple peptides and were excluded to ensure high-confidence identifications. Finally, we demonstrate our workflow with sensitive timsTOF SCP data acquisition and find that rescoring, now with inclusion of ion mobility features, identifies 76% more peptides compared to Q Exactive HF acquisition. Together, our results demonstrate how integration of multiple search engine results along with data-driven rescoring maximizes immunopeptide identification, boosting the detection of high-confidence bacterial epitopes for vaccine development.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

dELTA-MS: A Mass Spectrometry-Based Proteomics Approach for Identifying ADP-Ribosylation Sites and Forms.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-13 DOI: 10.1021/acs.jproteome.4c00890

Isabel R Uribe, Emily Zahn, Richard Searfoss, Han-Byeol Kim, Morgan Dasovich, Jim Voorneveld, Sabrina R Hunt, Ugochi C Onuoha, Catherine Valadez, Dmitri V Filippov, Chan Hyun Na, Benjamin A Garcia, Benjamin C Orsburn, Anthony K L Leung

{"title":"dELTA-MS: A Mass Spectrometry-Based Proteomics Approach for Identifying ADP-Ribosylation Sites and Forms.","authors":"Isabel R Uribe, Emily Zahn, Richard Searfoss, Han-Byeol Kim, Morgan Dasovich, Jim Voorneveld, Sabrina R Hunt, Ugochi C Onuoha, Catherine Valadez, Dmitri V Filippov, Chan Hyun Na, Benjamin A Garcia, Benjamin C Orsburn, Anthony K L Leung","doi":"10.1021/acs.jproteome.4c00890","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00890","url":null,"abstract":"ADP-ribosylation, characterized by the addition of adenosine diphosphate ribose, can occur in both monomeric (MARylation) and polymeric (PARylation) forms. Little is known about the specific contributions of MARylation and PARylation to cellular processes due to a lack of tools for jointly investigating these individual forms. We present a novel mass spectrometry (MS)-based proteomics approach that preserves information about the native ADP-ribosylation form associated with the modification site within a single proteomics experiment. Our workflow enables the simplified, binary identification of ADP-ribosylation forms, avoiding some challenges typically presented by PARylated peptides during MS analysis. Our method uses the coronaviral enzyme NS2 to reverse our previous labeling approach, ELTA, which enzymatically labels the terminal ADP-ribose. NS2 deconjugates ELTA-labeled free or peptide-conjugated ADP-ribose monomers and polymers (thereby termed dELTA), leaving behind a signature phosphate. Our dELTA-MS workflow involves ELTA labeling, dELTA deconjugation, and further processing using Deinococcus radiodurans poly(ADP-ribose) glycohydrolase (DrPARG), resulting in two distinct mass shifts for MARylation and PARylation sites. We demonstrate the feasibility of this workflow for proteomics analyses using proof-of-principle peptide standards. dELTA-MS thus creates possibilities to reveal the fundamental biology of ADP-ribosylation and explore its dysregulation, in terms of both sites and forms, associated with disease progression.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discovery of RNA-Protein Molecular Clamps Using Proteome-Wide Stability Assays.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-12 DOI: 10.1021/acs.jproteome.4c01129

Stanley I Goldstein, Alice C Fan, Zihao Wang, Sai K Naineni, Regina Cencic, Steve B Garcia-Gutierrez, Kesha Patel, Sidong Huang, Lauren E Brown, Andrew Emili, John A Porco

{"title":"Discovery of RNA-Protein Molecular Clamps Using Proteome-Wide Stability Assays.","authors":"Stanley I Goldstein, Alice C Fan, Zihao Wang, Sai K Naineni, Regina Cencic, Steve B Garcia-Gutierrez, Kesha Patel, Sidong Huang, Lauren E Brown, Andrew Emili, John A Porco","doi":"10.1021/acs.jproteome.4c01129","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c01129","url":null,"abstract":"Uncompetitive inhibition is an effective strategy for suppressing dysregulated enzymes and their substrates, but discovery of suitable ligands depends on often-unavailable structural knowledge and serendipity. Hence, despite surging interest in mass spectrometry-based target identification, proteomic studies of substrate-dependent target engagement remain sparse. Herein, we describe a strategy for the discovery of substrate-dependent ligand binding. Using proteome integral solubility alteration (PISA) assays, we show that simple biochemical additives can enable detection of RNA-protein-small molecule complexes in native cell lysates. We apply our approach to rocaglates, molecules that specifically clamp RNA to eukaryotic translation initiation factor 4A (eIF4A), DEAD-box helicase 3X (DDX3X), and potentially other members of the DEAD-box (DDX) helicase family. To identify unexpected interactions, we used a target class-specific thermal window and compared ATP analog and RNA base dependencies for key rocaglate-DDX interactions. We report novel DDX targets of high-profile rocaglates-including the clinical candidate Zotatifin-and validate our findings using limited proteolysis-mass spectrometry and fluorescence polarization (FP) experiments. We also provide structural insight into divergent DDX3X affinities between synthetic rocaglates. Taken together, our study provides a model for screening uncompetitive inhibitors using a chemical proteomics approach and uncovers actionable DDX clamping targets, clearing a path toward characterization of novel molecular clamps and associated RNA helicases.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pilot Study of Metabolomic Biomarkers Associated with Outcomes in Patients with Lung Cancer Undergoing Radiation Therapy.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-12 DOI: 10.1021/acs.jproteome.4c00529

Wei Meng, Rui Xu, Eric Miller, Xiaowei Sun, Jennifer Thurmond, Amy Webb, Joseph McElroy, Joshua Palmer, Dominic J DiCostanzo, Shiqi Zhang, Hisashi Yamaguchi, Saikh Jaharul Haque, Jiangjiang Zhu, Arnab Chakravarti

{"title":"Pilot Study of Metabolomic Biomarkers Associated with Outcomes in Patients with Lung Cancer Undergoing Radiation Therapy.","authors":"Wei Meng, Rui Xu, Eric Miller, Xiaowei Sun, Jennifer Thurmond, Amy Webb, Joseph McElroy, Joshua Palmer, Dominic J DiCostanzo, Shiqi Zhang, Hisashi Yamaguchi, Saikh Jaharul Haque, Jiangjiang Zhu, Arnab Chakravarti","doi":"10.1021/acs.jproteome.4c00529","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00529","url":null,"abstract":"Lung cancer stands as the leading cause of cancer-related death worldwide, impacting both men and women in the United States and beyond. Radiation therapy (RT) serves as a key treatment modality for various lung malignancies. Our study aims to systematically assess the prognosis and influence of RT on metabolic reprogramming in patients diagnosed with nonsmall-cell lung cancer (NSCLC) through longitudinal metabolic profiling. A cohort of 54 NSCLC patients underwent thoracic radiotherapy, with 96% receiving a total radiation dose ranging from 40 to 70 Gy, averaging 56.3 Gy. Blood biospecimens were collected before RT, during RT, and at the first follow-up after RT, with a total of 126 serum samples randomized for liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis using a high-performance LC (HPLC)-Q-Exactive mass spectrometry system. Our results indicated that the serum metabolite coumarin derivatives prior to radiotherapy exhibited the strongest unfavorable outcome with overall survival in these NSCLC cases. The metabolites in the blood samples can reflect the responses during RT. Notably, over half of the metabolites (12/23) were found to be fatty acids in the longitudinal analysis. This pilot study indicated that metabolic profiling of biofluids from NSCLC patients undergoing RT has the potential to assess the patient outcomes during and after treatment.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeted Lipidomics and Transcriptomics Unveil Aberrant Lipid Metabolic Remodeling in Visceral and Subcutaneous Adipose Tissue under ER Stress.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-11 DOI: 10.1021/acs.jproteome.4c00952

Ping He, Li Zhang, Peng Ma, Tianshu Xu, Zijing Wang, Li Li, Guanhua Du, Guifen Qiang, Cuiqing Liu

{"title":"Targeted Lipidomics and Transcriptomics Unveil Aberrant Lipid Metabolic Remodeling in Visceral and Subcutaneous Adipose Tissue under ER Stress.","authors":"Ping He, Li Zhang, Peng Ma, Tianshu Xu, Zijing Wang, Li Li, Guanhua Du, Guifen Qiang, Cuiqing Liu","doi":"10.1021/acs.jproteome.4c00952","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00952","url":null,"abstract":"Endoplasmic reticulum (ER) stress is known to impair the function of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT), disrupting lipid metabolism. Despite the crucial role lipid plays in regulating adipose tissue function, the specific lipidomic alterations in VAT and SAT under ER stress remain unclear. In this study, ER stress was induced in VAT and SAT, and targeted lipidomic and transcriptomic approaches were used to analyze lipid metabolism and gene expression profiles. The results revealed that VAT exhibited a stronger ER stress response, characterized by a significant increase in binding immunoglobulin protein (BiP) expression and notable lipidomic disruptions, especially in glycerides and sterols. These disruptions were marked by a decrease in protective polyunsaturated fatty acyl species and the accumulation of lipotoxic molecules. In contrast, SAT displayed less severe lipidomic alterations. Transcriptomic analysis indicated that VAT was more susceptible to immune activation, inflammation, and metabolic dysfunction, while SAT primarily showed alterations in protein folding processes. These findings underscore the tissue-specific mechanisms of ER stress adaptation in VAT and SAT. In conclusion, VAT appears to be a critical target for addressing metabolic dysfunction in obesity and related disorders, with potential therapeutic implications for managing ER stress-induced metabolic diseases.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-10 DOI: 10.1021/acs.jproteome.4c00943

Taojunfeng Su, Ryan T Fellers, Joseph B Greer, Richard D LeDuc, Paul M Thomas, Neil L Kelleher

{"title":"Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics.","authors":"Taojunfeng Su, Ryan T Fellers, Joseph B Greer, Richard D LeDuc, Paul M Thomas, Neil L Kelleher","doi":"10.1021/acs.jproteome.4c00943","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00943","url":null,"abstract":"Proteoforms are distinct molecular forms of proteins that act as building blocks of organisms, with post-translational modifications (PTMs) being one of the key changes that generate these variations. Mass spectrometry (MS)-based top-down proteomics (TDP) is the leading technology for proteoform identification due to its preservation of intact proteoforms for analysis, making it well-suited for comprehensive PTM characterization. A crucial step in TDP is searching MS data against a database of candidate proteoforms. To extend the reach of TDP to organisms with limited PTM annotations, we developed Proteoform-predictor, an open-source tool that integrates homology-based PTM site prediction into proteoform database creation. The new tool creates databases of proteoform candidates after registration of homologous sequences, transferring PTM sites from well-characterized species to those with less comprehensive proteomic data. Our tool features a user-friendly interface and intuitive workflow, making it accessible to a wide range of researchers. We demonstrate that Proteoform-predictor expands proteoform databases with tens of thousands of proteoforms for three bacterial strains by comparing them to the reference proteome of Escherichia coli (E. coli) K12. Subsequent TDP analysis for Serratia marcescens (S. marcescens) and Salmonella typhimurium (S. typhimurium) demonstrated significant improvement in protein and proteoform identification, even for proteins with variant sequences. As TDP technology advances, Proteoform-predictor will become an important tool for expanding the applicability of proteoform identification and PTM biology to more diverse species across the phylogenetic tree of life.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143583948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer.

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 Epub Date: 2025-02-12 DOI: 10.1021/acs.jproteome.4c01107

Xinyue Liu, Shane L Dawson, Steven P Gygi, Joao A Paulo

{"title":"Isobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometer.","authors":"Xinyue Liu, Shane L Dawson, Steven P Gygi, Joao A Paulo","doi":"10.1021/acs.jproteome.4c01107","DOIUrl":"10.1021/acs.jproteome.4c01107","url":null,"abstract":"Comprehensive global proteome profiling that is amenable to high throughput processing will broaden our understanding of complex biological systems. Here, we evaluate two leading mass spectrometry techniques, Data Independent Acquisition (DIA) and Tandem Mass Tagging (TMT), for extensive protein abundance profiling. DIA provides label-free quantification with a broad dynamic range, while TMT enables multiplexed analysis using isobaric tags for efficient cross-sample comparisons. We analyzed 18 samples, including four cell lines (IHCF, HCT116, HeLa, MCF7) under standard growth conditions, in addition to IHCF treated with two H2O2 concentrations, all in triplicate. Experiments were conducted on an Orbitrap Astral mass spectrometer, employing Field Asymmetric Ion Mobility Spectrometry (FAIMS). Despite utilizing different acquisition strategies, both the DIA and TMT approaches achieved comparable proteome depth and quantitative consistency, with each method quantifying over 10,000 proteins across all samples, with marginally higher protein-level precision for the TMT strategy. Relative abundance correlation analysis showed strong agreement at both peptide and protein levels. Our findings highlight the complementary strengths of DIA and TMT for high-coverage proteomic studies, providing flexibility in method selection based on specific experimental needs.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":" ","pages":"1414-1424"},"PeriodicalIF":3.8,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Special Software Issue in Celebration of Margaret Dayhoff’s 100th Birthday

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2025-03-07 DOI: 10.1021/acs.jproteome.5c0014710.1021/acs.jproteome.5c00147

Magnus Palmblad*, Michael R. Hoopmann* and Viktoria Dorfer*,

引用次数: 0