Molecular & Cellular Proteomics最新文献

{"title":"Professor D.F. Hunt Relationship with Finnigan Corporation and His Impact on Mass Spectrometer Development.","authors":"Michael S Story, George C Stafford, John E P Syka","doi":"10.1016/j.mcpro.2025.101033","DOIUrl":"10.1016/j.mcpro.2025.101033","url":null,"abstract":"<p><p>Don Hunt's 50-year collaboration with Finnigan Instruments Corporation has resulted in many innovations in mass spectrometry that range from new instrumentation to new analytical methodologies which in turn enabled new applications. The fruits of this collaboration, directly and indirectly, have had a broad and enduring impact on the instrumentation and practice of modern mass spectrometry. The authors of this monograph were members of the research and development team at Finnigan over time frames that collectively encompass the entirety of the collaboration. This article provides a narrative history and chronology of the Hunt-Finnigan relationship based on their personal recollections as well as the recollections of other participants.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101033"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12419086/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increased EThcD Efficiency on the Hybrid Orbitrap Excedion Pro Mass Analyzer Extends the Depth in Identification and Sequence Coverage of HLA Class I Immunopeptidomes.","authors":"Amy L Kessler, Kyle L Fort, Hanno C Resemann, Peter Krüger, Cong Wang, Heiner Koch, Jan-Peter Hauschild, Fabio Marino, Albert J R Heck","doi":"10.1016/j.mcpro.2025.101049","DOIUrl":"10.1016/j.mcpro.2025.101049","url":null,"abstract":"<p><p>Gaining a complete and unbiased understanding of the nontryptic peptide repertoire presented by human leukocyte antigen class I (HLA-I) complexes by LC-MS/MS is indispensable for therapy design for cancer, autoimmunity, and infectious diseases. A serious concern in HLA peptide analysis is that the routinely used collision-based fragmentation methods [collision-induced dissociation (CID)/higher-energy collision-induced dissociation (HCD)] do not always render sufficiently informative MS2 spectra, whereby gaps in the fragmentation sequence coverage prevent unambiguous assignments. Electron-transfer/higher-energy collision dissociation (EThcD) can be utilized to generate complementary ion series, i.e., b/y ions and c/z ions, resulting in richer, more informative MS2 spectra, thereby filling in the gaps. Here, we present data generated on a novel hybrid orbitrap mass spectrometer, facilitating fast and efficient hybrid fragmentation due to the implementation of EThcD in the ion routing multipole. We hypothesized that this would enable more comprehensive and less error-prone analysis of immunopeptidomes at minimal costs in duty cycle. First, we optimized ETD/EThcD methods using an elastase-digested cell lysate, as this contains peptides of similar length and charge distributions to immunopeptides. Next, we compared HCD and EThcD on immunopeptidomes originating from three cell lines with distinct HLA-I complexes that present peptides with varying physicochemical properties. We demonstrate that the new instrument not only enables efficient and fast ETD reactions but, when combined with collision-based supplemental activation, i.e. EThcD, also consistently increases the sequence coverage and identification of peptide sequences, otherwise missed by using solely HCD. We reveal several of the biochemical properties that make HLA peptides preferably identifiable by EThcD, with internal Arg residues being one of the most dominant determinants. Finally, we demonstrate the power of EThcD for the identification and localization of HLA peptides harboring posttranslational modifications, focusing here on HLA Arg monomethylation/dimethylation. We foresee that this new instrument with efficient EThcD capabilities enhances not only immunopeptidomics analysis but also analysis of peptides harboring posttranslational modifications and de novo sequencing.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101049"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Turning Waste Into Insight: A Novel Proteomic Approach to Non-Invasive Wound Biomarker Discovery.","authors":"Victoria Soto, Veronika Jurczuk, Lilian Valadares Tose, Christian Alcalde Pretel, Victoria Garcia, Leah Farhadi, Sujad Younis, Natasa Strbo, Ahmed Hawash, Oliver Umland, Matthew Hardy, Carlos E Arteta Higgins, Jason Levine, Juan Bravo, Brian Eliceiri, Jennifer C Tang, Jose A Jaller, Hadar Lev-Tov, Vladimir Pozdin, Luis Rodriguez-Menocal, Evangelos Badiavas, Robert S Kirsner, Francisco A Fernandez Lima, Ivan Jozic","doi":"10.1016/j.mcpro.2025.101058","DOIUrl":"10.1016/j.mcpro.2025.101058","url":null,"abstract":"<p><p>Chronic wounds such as diabetic foot ulcers (DFUs) and venous leg ulcers (VLUs) are a growing public health burden, contributing to significant morbidity, healthcare costs, and mortality. Current management strategies are hampered by the inability to accurately predict healing trajectories or identify early treatment failures. Here, we present a novel, non-invasive proteomic approach that leverages routinely discarded wound dressings to profile the wound microenvironment across soluble, cellular, and extracellular vesicle (EV) compartments. Using a cohort of patients with DFU and VLU (n = 16), we performed spatially resolved, longitudinal sampling over 4 weeks and identified distinct proteomic signatures associated with healing versus non-healing outcomes. Mass spectrometry revealed more than 1000 unique proteins from viable cells and EVs as well as 489 proteins identified from soluble wound fluid. Our methodology captured immune cell phenotypes, enabling insight into tissue-specific immune responses without the need for biopsy. Longitudinal surveillance revealed patient-specific protein trajectories that correlated with wound size changes, supporting the feasibility of biomarker-based monitoring. Notably, differences in keratinocyte activation markers, acute-phase proteins, and EV-associated stress proteins distinguished healing from non-healing wounds. These findings demonstrate the utility of discarded dressings as a rich, untapped source of diagnostic and prognostic biomarkers. This platform has strong potential to inform future \"smart\" wound care technologies, including dressings capable of real-time biosensing or therapeutic EV delivery. Larger validation studies will be essential to translate these findings into clinical tools for precision wound care.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101058"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12475851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Restrained Wnt Signaling Pathway by Enhanced EsGSK3β Activity Facilitates the Infection of Spiroplasma and Leads to Neuropathic Diseases in Crustaceans.","authors":"Libo Hou, Yu Yao, Yubo Ma, Wei Gu, Wen Wang, Wei Sun, Qingguo Meng","doi":"10.1016/j.mcpro.2025.101059","DOIUrl":"10.1016/j.mcpro.2025.101059","url":null,"abstract":"<p><p>Spiroplasma eriocheiris has been identified as a lethal pathogen of Eriocheir sinensis tremor disease (TD), one neurological disease with typically paroxysmal tremors of the pereiopod. But, the pathogenic mechanism of TD was still unknown. First, in the current study, the phosphoproteomic changes of E. sinensis thoracic ganglion after S. eriocheiris infection were obtained using TMT labeling and affinity enrichment followed by high-resolution LC-MS/MS analysis. A total of 349 phosphorylation proteins are upregulated, and 331 phosphorylation proteins are downregulated when compared to the control sample with quantitative ratios above 1.5 or below 1/1.5 that are deemed significant. Bioinformatics analysis (Gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and domain analysis, etc.) showed that Wnt signaling pathways were restrained, corresponding to many nervous system developments, and signal transmission pathway was also disrupted. Neurotransmitter metabolite analysis showed metabolic dysregulation of four key neurotransmitters (5-Hydroxy-L-tryptophan, serotonin, acetylcholine, and γ-amino-butyric acid) in thoracic ganglion of E. sinensis following S. eriocheiris infection. Second, similar to its effects on the thoracic ganglion cells, S. eriocheiris infection of hemocytes (the primary target cells and most crucial immune cells in crabs) also suppressed the host Wnt pathway through enhanced EsGSK3β activity, both in vivo and in vitro. Co-immunoprecipitation analysis showed that EsGSK3β could directly interact with Esβ-catenin. Inhibited or enhanced EsGSK3β activity of hemocytes could reduce or facilitate S. eriocheiris infection by regulating the stability and nuclear translocation of Esβ-catenin. Finally, further analysis showed that Wnt-β-catenin pathway could functionally crosstalk with Toll pathway to positively regulate hemocytes antibacterial peptides transcription. Altogether, our results suggest that S. eriocheiris could restrain the crab Wnt pathway, reduce antibacterial peptides transcription to help its infection and disorder neurotransmitters to cause neuropathic TD at last.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101059"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144961695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CySP3-96 Enables Scalable, Streamlined, and Low-Cost Sample Preparation for Cysteine Chemoproteomic Applications.","authors":"Flowreen Shikwana, Beeta S Heydari, Samuel Ofori, Cindy Truong, Alexandra C Turmon, Joelle Darrouj, Lara Holoidovsky, Jeffrey L Gustafson, Keriann M Backus","doi":"10.1016/j.mcpro.2024.100898","DOIUrl":"10.1016/j.mcpro.2024.100898","url":null,"abstract":"<p><p>Cysteine chemoproteomic screening platforms are widely utilized for chemical probe and drug discovery campaigns. Chemoproteomic compound screens, which use a mass spectrometry-based proteomic readout, can interrogate the structure activity relationship for thousands of proteins in parallel across the proteome. The versatility of chemoproteomic screens has been demonstrated across electrophilic, nucleophilic, and reversible classes of molecules. However, a key bottleneck that remains for these approaches is the low throughput nature of the most established sample preparation workflows, which rely on many time-intensive and often error prone steps. Addressing these challenges, here we establish a novel workflow, termed CySP3-96, that pairs single-pot, solid-phase-enhanced, sample preparation (SP3) with a customized 96-well sample cleanup workflow to achieve streamlined multiplexed sample preparation. Our CySP3-96 method addresses prior volume limitations of SP3, which allows for seamless 96-well chemoproteomic sample preparation, including for large input amounts that are incompatible with prior methods. By deploying CySP3-96 to screen a focused set of 16 cysteine-reactive compounds, we identify 2633 total ligandable cysteines, including 21 not captured in CysDB. Chemoproteomic analysis of a pair of atropisomeric electrophilic kinase inhibitors reveals striking stereoselective cysteine ligandability for 67 targets across the proteome. When paired with our innovative budget friendly magnetic resin, CySP3-96 represents a versatile, low cost, and highly reproducible screening platform with widespread applications spanning all types of chemoproteomic studies.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"100898"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872464","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}

{"title":"Localization of Organelle Proteins Using Data-Independent Acquisition (DIA-LOP).","authors":"Kieran McCaskie, Charlotte Hutchings, Renata Feret, Yong-In Kim, Lisa Breckels, Michael Deery, Kathryn Lilley","doi":"10.1016/j.mcpro.2025.101047","DOIUrl":"10.1016/j.mcpro.2025.101047","url":null,"abstract":"<p><p>Subcellular localization within the proteome fundamentally influences cellular processes; however, the development of high-throughput techniques to allow proteome-wide mapping of the cell has proven difficult. Here we present DIA-LOP, an approach capable of high-throughput spatial proteome mapping with in-depth subcellular resolution. This unified framework integrates differential-ultracentrifugation (DC) with ion-mobility-based data-independent acquisition mass spectrometry, alongside data processing using DIA-NN and spatial analysis within the pRoloc bioinformatics pipeline. We obtain the largest DIA-based subcellular proteomics map, with 8242 protein identifications across 13 organellar compartments in U-2 OS cells. Within the same experimental pipeline, we compare DC fractionation with an alternate detergent-based protocol using either DIA or data-dependent acquisition (DDA) mass spectrometry approaches, highlighting the increased subcellular resolution of the DC approach and the increased proteome coverage when DIA is applied. We demonstrate the ability of DIA-LOP to inform clinical studies by identifying and mapping disease-related proteins within our osteosarcoma cell model. With impressive coverage and resolution, DIA-LOP provides a straightforward, high-throughput tool for biochemical discovery. This study thus informs potential users of subcellular proteomics strategies that employ biochemical fractionation of the optimal workflows to achieve high proteome coverage and subcellular resolution.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101047"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-Treated Pancreatic Beta Cells.","authors":"Austin Gluth, Xiaolu Li, Marina A Gritsenko, Matthew J Gaffrey, Doo Nam Kim, Priscila M Lalli, Rosalie K Chu, Nicholas J Day, Tyler J Sagendorf, Matthew E Monroe, Song Feng, Tao Liu, Bin Yang, Wei-Jun Qian, Tong Zhang","doi":"10.1016/j.mcpro.2025.101056","DOIUrl":"10.1016/j.mcpro.2025.101056","url":null,"abstract":"","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":"24 9","pages":"101056"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058554","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}

{"title":"High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues.","authors":"Moe Haines, John R Thorup, Simone Gohsman, Claudia Ctortecka, Chelsea Newton, Dan C Rohrer, Galen Hostetter, D R Mani, Michael A Gillette, Shankha Satpathy, Steven A Carr","doi":"10.1016/j.mcpro.2025.101044","DOIUrl":"10.1016/j.mcpro.2025.101044","url":null,"abstract":"<p><p>Formalin-fixed, paraffin-embedded (FFPE) patient tissues are a valuable resource for proteomic studies with the potential to associate derived molecular insights with clinical annotations and outcomes. Here, we present an optimized, partially automated, plate-based workflow for FFPE proteomics combining pathology-guided macrodissection, xylene-free deparaffinization using Adaptive Focused Acoustics sonication for lysis and decrosslinking, optimized suspension trapping digestion and cleanup of peptides, and LC-MS/MS using Exploris 480, Orbitrap Astral, and timsTOF HT instrumentation. The workflow enables analysis of up to 96 dissected FFPE tissue samples or 10 μm scrolls, identifying 8000 to 10,000 unique proteins per sample with median CVs <20%. Application to lung adenocarcinoma FFPE blocks confirms the platform's effectiveness in processing complex, clinically relevant samples, achieving deep proteome coverage and quantitative robustness comparable to tandem mass tagbased methods. Using the Orbitrap Astral with short, 24-min gradients, the workflow identifies up to 10,000 unique proteins and 11,000 fully localized phosphosites in lung adenocarcinoma FFPE tissue, demonstrating the ability to derive biologically relevant phosphoprotein/peptide results from clinically derived FFPE tumor samples. This high-throughput, scalable workflow advances biomarker discovery and proteomic research in archival tissue samples.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101044"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12450643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Hybrid High-Speed Mass Spectrometer Allows Rapid Translation From Biomarker Candidates to Targeted Clinical Tests Using ¹⁵N-Labeled Proteins.","authors":"Maria Wahle, Philip M Remes, Vincent Albrecht, Michael Baggio Lorenz, Johannes Mueller-Reif, Sophia Steigerwald, Tim Heymann, Lili Niu, Philip Lössl, Stevan Horning, Cristina C Jacob, Matthias Mann","doi":"10.1016/j.mcpro.2025.101050","DOIUrl":"10.1016/j.mcpro.2025.101050","url":null,"abstract":"<p><p>Recent developments in affinity binder or mass spectrometry (MS)-based plasma proteomics are now producing panels of potential biomarker candidates for diagnosis or prognosis. However, clinical validation and implementation of these biomarkers remain limited by the reliance on dated triple quadrupole MS technology. Here, we evaluate a novel hybrid high-speed mass spectrometer, Stellar MS, which integrates the robustness of triple quadrupoles with the enhanced capabilities of an advanced linear ion trap analyzer. This instrument allows for extremely rapid and sensitive parallel reaction monitoring (PRM) and MS3 targeting. The Stellar MS allowed targeting thousands of peptides originally measured on Orbitrap Astral MS, achieving high reproducibility and low coefficients of variation (CV) as well as sensitivity and specificity sufficient for many of the top 1000 plasma proteins. Furthermore, we developed targeted assays for alcohol-related liver disease (ALD) biomarkers, showcasing the potential of Stellar MS in clinical applications. Absolute quantification is typically a requirement for clinical assays, and we explore the use of ¹⁵N-labeled protein standards in a rapid, streamlined, and generic manner. Our results indicate that the Stellar MS can bridge the gap between proteomics discovery and routine clinical testing, enhancing the diagnostic and prognostic utility of protein biomarkers.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101050"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12455101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Automated Workflow to Address Proteome Complexity and the Large Search Space Problem in Proteomics and HLA-I Immunopeptidomics.","authors":"Yehor Horokhovskyi, Hanna P Roetschke, John A Cormican, Martin Pašen, Sina Garazhian, Michele Mishto, Juliane Liepe","doi":"10.1016/j.mcpro.2025.101039","DOIUrl":"10.1016/j.mcpro.2025.101039","url":null,"abstract":"<p><p>Antigenic noncanonical epitope and novel protein discovery are research areas with therapeutical applications, predominantly done via mass spectrometry. The latter should rely on a well-characterized proteogenomic search space. Its size is barely known for antigenic noncanonical peptides and novel proteins, and this could impact their identification. To address these issues, we here develop an automated workflow comprised of Sequoia for the creation of RNA sequencing-informed and exhaustive sequence search spaces for various noncanonical peptide origins, and SPIsnake for pre-filtering and exploration of sequence search space before mass spectrometry searches. We apply our workflow to characterize the exact sizes of tryptic and nonspecific peptide sequence search spaces in a variety of definitions, their reduction when using RNA expression, their inflation by post-translational modifications, and the frequency of peptide sequence multimapping to different noncanonical origins. Furthermore, we explore the application of Sequoia and SPIsnake on HLA-I immunopeptidomes, thereby rescuing sensitivity in peptide identification when confronted with inflated search spaces. Taken together, Sequoia and SPIsnake pave the way for an educated development of methods addressing large-scale exhaustive proteogenomic discovery by exposing the consequences of database size inflation and ambiguity of peptide and protein sequence identification.</p>","PeriodicalId":18712,"journal":{"name":"Molecular & Cellular Proteomics","volume":" ","pages":"101039"},"PeriodicalIF":5.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12397870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}