{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T12:48:16Z","timestamp":1793018896070,"version":"4.5.0"},"reference-count":94,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000646","name":"Japan Society for the Promotion of Science London","doi-asserted-by":"publisher","award":["23H04924"],"award-info":[{"award-number":["23H04924"]}],"id":[{"id":"10.13039\/501100000646","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000646","name":"Japan Society for the Promotion of Science London","doi-asserted-by":"publisher","award":["21H02459"],"award-info":[{"award-number":["21H02459"]}],"id":[{"id":"10.13039\/501100000646","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000646","name":"Japan Society for the Promotion of Science London","doi-asserted-by":"publisher","award":["23K18185"],"award-info":[{"award-number":["23K18185"]}],"id":[{"id":"10.13039\/501100000646","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP18gm1010010"],"award-info":[{"award-number":["JP18gm1010010"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020595","name":"National Science and Technology Council","doi-asserted-by":"publisher","award":["NSTC 112-2314-B-002-206"],"award-info":[{"award-number":["NSTC 112-2314-B-002-206"]}],"id":[{"id":"10.13039\/100020595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020595","name":"National Science and Technology Council","doi-asserted-by":"publisher","award":["111-2320-B-002-073"],"award-info":[{"award-number":["111-2320-B-002-073"]}],"id":[{"id":"10.13039\/100020595","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001695","name":"Japan Science and Technology Corporation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001695","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["mcponline.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular &amp; Cellular Proteomics"],"published-print":{"date-parts":[[2025,8]]},"DOI":"10.1016\/j.mcpro.2025.101019","type":"journal-article","created":{"date-parts":[[2025,6,24]],"date-time":"2025-06-24T11:41:23Z","timestamp":1750765283000},"page":"101019","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"title":["A Methanolic Urea-Enhanced Protein Extraction Enabling the Largest Bacterial Phosphorylation Resource"],"prefix":"10.1016","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-9482-8535","authenticated-orcid":false,"given":"Pei-Shan","family":"Wu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting-An","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo-Yu","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7714-203X","authenticated-orcid":false,"given":"Yasushi","family":"Ishihama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7079-4569","authenticated-orcid":false,"given":"Miao-Hsia","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.mcpro.2025.101019_bib1","first-page":"125","article-title":"Ser\/Thr\/Tyr protein phosphorylation in bacteria - for long time neglected, now well established","volume":"9","author":"Deutscher","year":"2005","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"10.1016\/j.mcpro.2025.101019_bib2","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1111\/j.1574-6976.2011.00314.x","article-title":"Impact of phosphoproteomics on studies of bacterial physiology","volume":"36","author":"Mijakovic","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.mcpro.2025.101019_bib3","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/s41579-019-0243-0","article-title":"Protein post-translational modifications in bacteria","volume":"17","author":"Macek","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib4","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1002\/1873-3468.13797","article-title":"Importance of protein Ser\/Thr\/Tyr phosphorylation for bacterial pathogenesis","volume":"594","author":"Bonne K\u00f8hler","year":"2020","journal-title":"FEBS Lett."},{"key":"10.1016\/j.mcpro.2025.101019_bib5","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00289-24","article-title":"More than two components: complexities in bacterial phosphosignaling","volume":"9","author":"Frando","year":"2024","journal-title":"mSystems"},{"key":"10.1016\/j.mcpro.2025.101019_bib6","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aau8645","article-title":"Illuminating the dark phosphoproteome","volume":"12","author":"Needham","year":"2019","journal-title":"Sci. Signal."},{"key":"10.1016\/j.mcpro.2025.101019_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.aca.2021.338857","article-title":"A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis","volume":"1199","author":"Urban","year":"2022","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.mcpro.2025.101019_bib8","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1021\/ac051896z","article-title":"Protein and proteome phosphorylation stoichiometry analysis by element mass spectrometry","volume":"78","author":"Kr\u00fcger","year":"2006","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2025.101019_bib9","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1074\/mcp.M600464-MCP200","article-title":"The serine\/threonine\/tyrosine phosphoproteome of the model bacterium Bacillus subtilis","volume":"6","author":"Macek","year":"2007","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib10","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1074\/mcp.M700311-MCP200","article-title":"Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser\/Thr\/Tyr phosphorylation","volume":"7","author":"Macek","year":"2008","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib11","doi-asserted-by":"crossref","first-page":"3486","DOI":"10.1002\/pmic.200800069","article-title":"The Ser\/Thr\/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins","volume":"8","author":"Soufi","year":"2008","journal-title":"Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib12","doi-asserted-by":"crossref","first-page":"2613","DOI":"10.1074\/mcp.M900276-MCP200","article-title":"Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence","volume":"8","author":"Lin","year":"2009","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib13","doi-asserted-by":"crossref","first-page":"5362","DOI":"10.1021\/pr300582p","article-title":"Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production","volume":"11","author":"Hu","year":"2012","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib14","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aaa3117","article-title":"Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation","volume":"8","author":"Lin","year":"2015","journal-title":"Sci. Signal."},{"key":"10.1016\/j.mcpro.2025.101019_bib15","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/nmeth.4580","article-title":"Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics","volume":"15","author":"Potel","year":"2018","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mcpro.2025.101019_bib16","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1074\/mcp.TIR117.000518","article-title":"Defeating major contaminants in Fe(3+)- immobilized metal ion affinity chromatography (IMAC) phosphopeptide enrichment","volume":"17","author":"Potel","year":"2018","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib17","doi-asserted-by":"crossref","first-page":"2529","DOI":"10.1021\/pr060682a","article-title":"Optimization of mass spectrometry-compatible surfactants for shotgun proteomics","volume":"6","author":"Chen","year":"2007","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib18","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1002\/elps.201400579","article-title":"Improved protease digestion conditions for membrane protein detection","volume":"36","author":"Min","year":"2015","journal-title":"Electrophoresis"},{"key":"10.1016\/j.mcpro.2025.101019_bib19","doi-asserted-by":"crossref","first-page":"10320","DOI":"10.1021\/acs.analchem.1c04200","article-title":"Solvent precipitation SP3 (SP4) enhances recovery for proteomics sample preparation without magnetic beads","volume":"94","author":"Johnston","year":"2022","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2025.101019_bib20","doi-asserted-by":"crossref","first-page":"4060","DOI":"10.1021\/acs.jproteome.7b00433","article-title":"Evaluation of FASP, SP3, and iST protocols for proteomic sample preparation in the low microgram range","volume":"16","author":"Sielaff","year":"2017","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib21","doi-asserted-by":"crossref","first-page":"757","DOI":"10.15252\/msb.20145625","article-title":"Ultrasensitive proteome analysis using paramagnetic bead technology","volume":"10","author":"Hughes","year":"2014","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.mcpro.2025.101019_bib22","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1074\/mcp.TIR118.001270","article-title":"Protein aggregation capture on microparticles enables multipurpose proteomics sample preparation","volume":"18","author":"Batth","year":"2019","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib23","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1074\/mcp.TIR119.001616","article-title":"Sample preparation by easy extraction and digestion (SPEED) - a universal, rapid, and detergent-free protocol for proteomics based on acid extraction","volume":"19","author":"Doellinger","year":"2020","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib24","doi-asserted-by":"crossref","first-page":"2917","DOI":"10.1021\/acs.jproteome.8b00505","article-title":"S-trap, an ultrafast sample-preparation approach for shotgun proteomics","volume":"17","author":"HaileMariam","year":"2018","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib25","doi-asserted-by":"crossref","first-page":"12232","DOI":"10.1021\/acs.analchem.3c00786","article-title":"Suspension trapping-based sample preparation workflow for in-depth plant phosphoproteomics","volume":"95","author":"Chen","year":"2023","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2025.101019_bib26","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1016\/j.ab.2007.10.002","article-title":"High-throughput tissue extraction protocol for NMR- and MS-based metabolomics","volume":"372","author":"Wu","year":"2008","journal-title":"Anal. Biochem."},{"key":"10.1016\/j.mcpro.2025.101019_bib27","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.aca.2018.07.034","article-title":"Evaluation of two-step liquid-liquid extraction protocol for untargeted metabolic profiling of serum samples to achieve broader metabolome coverage by UPLC-Q-TOF-MS","volume":"1035","author":"Liu","year":"2018","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.mcpro.2025.101019_bib28","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2022.101302","article-title":"Polar metabolomics in human muscle biopsies using a liquid-liquid extraction and full-scan LC-MS","volume":"3","author":"Schomakers","year":"2022","journal-title":"STAR Protoc."},{"key":"10.1016\/j.mcpro.2025.101019_bib29","doi-asserted-by":"crossref","first-page":"2035","DOI":"10.1021\/acs.jproteome.9b00867","article-title":"Rapid and quantitative protein precipitation for proteome analysis by mass spectrometry","volume":"19","author":"Nickerson","year":"2020","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib30","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/S0304-4157(96)00010-X","article-title":"Adaptation mechanisms of microorganisms to the toxic effects of organic solvents on membranes","volume":"1286","author":"Weber","year":"1996","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.mcpro.2025.101019_bib31","doi-asserted-by":"crossref","first-page":"3225","DOI":"10.1007\/s11033-019-04782-y","article-title":"The effect of organic solvents on selected microorganisms and model liposome membrane","volume":"46","author":"Dyrda","year":"2019","journal-title":"Mol. Biol. Rep."},{"key":"10.1016\/j.mcpro.2025.101019_bib32","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/s42003-022-04400-x","article-title":"A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics","volume":"6","author":"Tsai","year":"2023","journal-title":"Commun. Biol."},{"key":"10.1016\/j.mcpro.2025.101019_bib33","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences","volume":"428","author":"Kanehisa","year":"2016","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.mcpro.2025.101019_bib34","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/nmeth.2646","article-title":"pLogo: a probabilistic approach to visualizing sequence motifs","volume":"10","author":"O'Shea","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.mcpro.2025.101019_bib35","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1002\/jssc.202100452","article-title":"Homogeneous liquid-liquid extraction as an alternative sample preparation technique for biomedical analysis","volume":"45","author":"Hammad","year":"2022","journal-title":"J. Sep. Sci."},{"key":"10.1016\/j.mcpro.2025.101019_bib36","series-title":"Western Blotting for the Non-expert","first-page":"117","article-title":"Dissolving proteins using lysis buffer","author":"Kurien","year":"2021"},{"key":"10.1016\/j.mcpro.2025.101019_bib37","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1038\/s41596-018-0014-9","article-title":"High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform","volume":"13","author":"Humphrey","year":"2018","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.mcpro.2025.101019_bib38","doi-asserted-by":"crossref","first-page":"2215","DOI":"10.1021\/pr700575m","article-title":"The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage","volume":"7","author":"Ham","year":"2008","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib39","doi-asserted-by":"crossref","first-page":"2828","DOI":"10.1021\/pr300242w","article-title":"Improve the coverage for the analysis of phosphoproteome of HeLa cells by a tandem digestion approach","volume":"11","author":"Bian","year":"2012","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib40","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/s41467-020-14609-1","article-title":"Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries","volume":"11","author":"Bekker-Jensen","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101019_bib41","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/s41467-018-03309-6","article-title":"Benchmarking common quantification strategies for large-scale phosphoproteomics","volume":"9","author":"Hogrebe","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.mcpro.2025.101019_bib42","doi-asserted-by":"crossref","first-page":"3407","DOI":"10.3390\/cells10123407","article-title":"Phosphoproteomics sample preparation impacts biological interpretation of phosphorylation signaling outcomes","volume":"10","author":"Sampadi","year":"2021","journal-title":"Cells"},{"key":"10.1016\/j.mcpro.2025.101019_bib43","doi-asserted-by":"crossref","first-page":"2370","DOI":"10.1021\/acs.jproteome.9b00054","article-title":"Perspective and guidelines for metaproteomics in microbiome studies","volume":"18","author":"Zhang","year":"2019","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib44","doi-asserted-by":"crossref","first-page":"100612","DOI":"10.1016\/j.mcpro.2023.100612","article-title":"Unified workflow for the rapid and in-depth characterization of bacterial proteomes","volume":"22","author":"Abele","year":"2023","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib45","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.jprot.2017.07.001","article-title":"Assessing the impact of protein extraction methods for human gut metaproteomics","volume":"180","author":"Zhang","year":"2018","journal-title":"J. Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib46","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1021\/acs.jproteome.6b00450","article-title":"Development of an integrated pipeline for profiling microbial proteins from mouse fecal samples by LC-MS\/MS","volume":"15","author":"Wu","year":"2016","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib47","doi-asserted-by":"crossref","first-page":"5379","DOI":"10.1021\/acs.analchem.0c00062","article-title":"Differential lysis approach enables selective extraction of taxon-specific proteins for gut metaproteomics","volume":"92","author":"Wang","year":"2020","journal-title":"Anal. Chem."},{"key":"10.1016\/j.mcpro.2025.101019_bib48","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/s12275-023-00036-6","article-title":"Bacterial regulatory mechanisms for the control of cellular processes: simple organisms\u2019 complex regulation","volume":"61","author":"Lee","year":"2023","journal-title":"J. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib49","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1111\/1462-2920.16123","article-title":"The importance of understanding the regulation of bacterial metabolism","volume":"25","author":"Moreno","year":"2023","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib50","series-title":"Industrial Microbiology and Biotechnology: An Insight into Current Trends","first-page":"327","article-title":"Two-component regulatory systems in microbial pathogenesis","author":"Jagtap","year":"2024"},{"key":"10.1016\/j.mcpro.2025.101019_bib51","doi-asserted-by":"crossref","DOI":"10.1016\/j.micres.2024.127995","article-title":"Decoding bacterial communication: intracellular signal transduction, quorum sensing, and cross-kingdom interactions","volume":"292","author":"Liu","year":"2025","journal-title":"Microbiol. Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib52","series-title":"Antimicrobial Resistance in the 21st Century","first-page":"461","article-title":"Bacterial signal transduction systems in antimicrobial resistance","author":"Ulijasz","year":"2018"},{"key":"10.1016\/j.mcpro.2025.101019_bib53","doi-asserted-by":"crossref","first-page":"4886","DOI":"10.1021\/acs.jproteome.1c00364","article-title":"Automated phosphopeptide enrichment for gram-positive bacteria","volume":"20","author":"Birk","year":"2021","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib54","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1074\/mcp.RA118.000880","article-title":"A new tool to reveal bacterial signaling mechanisms in antibiotic treatment and resistance","volume":"17","author":"Lin","year":"2018","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib55","doi-asserted-by":"crossref","first-page":"6297","DOI":"10.1007\/s00216-014-8045-8","article-title":"Potential of liquid-isoelectric-focusing protein fractionation to improve phosphoprotein characterization of Pseudomonas aeruginosa PA14","volume":"406","author":"Ouidir","year":"2014","journal-title":"Anal. Bioanal. Chem."},{"key":"10.1016\/j.mcpro.2025.101019_bib56","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.RA120.002232","article-title":"In-depth characterization of the Staphylococcus aureus phosphoproteome reveals new targets of Stk1","volume":"20","author":"Prust","year":"2021","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib57","doi-asserted-by":"crossref","first-page":"6046","DOI":"10.1021\/pr500929u","article-title":"Quantitative proteome analyses identify PrfA-responsive proteins and phosphoproteins in Listeria monocytogenes","volume":"13","author":"Misra","year":"2014","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib58","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1038\/s41597-020-0506-7","article-title":"dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes","volume":"7","author":"Shi","year":"2020","journal-title":"Sci. Data"},{"key":"10.1016\/j.mcpro.2025.101019_bib59","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1016\/j.tim.2021.11.005","article-title":"Recent advances in bacterial signaling by serine\/threonine protein kinases","volume":"30","author":"Nagarajan","year":"2022","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib60","doi-asserted-by":"crossref","first-page":"931","DOI":"10.3390\/microorganisms11040931","article-title":"A review of the bacterial phosphoproteomes of beneficial microbes","volume":"11","author":"Lim","year":"2023","journal-title":"Microorganisms"},{"key":"10.1016\/j.mcpro.2025.101019_bib61","doi-asserted-by":"crossref","first-page":"5481","DOI":"10.1021\/pr200762y","article-title":"Phosphoproteome analysis of streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation","volume":"10","author":"Manteca","year":"2011","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib62","doi-asserted-by":"crossref","first-page":"2764","DOI":"10.1002\/pmic.200800655","article-title":"Ser\/Thr\/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species","volume":"9","author":"Ravichandran","year":"2009","journal-title":"Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib63","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/S0167-4889(96)00083-3","article-title":"How do protein kinases recognize their substrates?","volume":"1314","author":"Pinna","year":"1996","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.mcpro.2025.101019_bib64","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1073\/pnas.0609836104","article-title":"Large-scale phosphorylation analysis of mouse liver","volume":"104","author":"Vill\u00e9n","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.mcpro.2025.101019_bib65","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1080\/1040841X.2021.1911930","article-title":"Listeria monocytogenes: review of pathogenesis and virulence determinants-targeted immunological assays","volume":"47","author":"Lopes-Luz","year":"2021","journal-title":"Crit. Rev. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib66","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3389\/fcimb.2014.00009","article-title":"Listeria monocytogenes: survival and adaptation in the gastrointestinal tract","volume":"4","author":"Gahan","year":"2014","journal-title":"Front. Cell Infect. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib67","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1099\/jmm.0.049742-0","article-title":"Proteomic analysis of the response of Listeria monocytogenes to bile salts under anaerobic conditions","volume":"62","author":"Payne","year":"2013","journal-title":"J. Med. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib68","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1007\/s13213-012-0452-5","article-title":"Comparative proteomic analysis of Listeria monocytogenes tolerance to bile stress","volume":"63","author":"Zhou","year":"2013","journal-title":"Ann. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib69","first-page":"107","article-title":"The effect of oxygen on bile resistance in Listeria monocytogenes","volume":"9","author":"Wright","year":"2016","journal-title":"J. Proteomics Bioinform."},{"key":"10.1016\/j.mcpro.2025.101019_bib70","doi-asserted-by":"crossref","first-page":"396","DOI":"10.3389\/fmicb.2013.00396","article-title":"Bile resistance mechanisms in lactobacillus and bifidobacterium","volume":"4","author":"Ruiz","year":"2013","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib71","article-title":"The classification of bacterial survival strategies in the presence of antimicrobials","volume":"155","author":"Chebotar","year":"2021","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.mcpro.2025.101019_bib72","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1021\/pr300794y","article-title":"Proteomic and transcriptional analysis of Lactobacillus johnsonii PF01 during bile salt exposure by iTRAQ shotgun proteomics and quantitative RT-PCR","volume":"12","author":"Lee","year":"2013","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib73","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.ijfoodmicro.2013.03.001","article-title":"Listeria monocytogenes dairy isolates show a different proteome response to sequential exposure to gastric and intestinal fluids","volume":"163","author":"Melo","year":"2013","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib74","doi-asserted-by":"crossref","first-page":"6757","DOI":"10.1128\/AEM.00637-07","article-title":"Adaptation and response of Bifidobacterium animalis subsp. lactis to bile: a proteomic and physiological approach","volume":"73","author":"S\u00e1nchez","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib75","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1111\/j.1365-2958.2004.04454.x","article-title":"A PrfA-regulated bile exclusion system (BilE) is a novel virulence factor in Listeria monocytogenes","volume":"55","author":"Sleator","year":"2005","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib76","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1128\/IAI.00330-10","article-title":"Investigation of the mechanisms by which Listeria monocytogenes grows in porcine gallbladder bile","volume":"79","author":"Dowd","year":"2011","journal-title":"Infect. Immun."},{"key":"10.1016\/j.mcpro.2025.101019_bib77","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.ijfoodmicro.2010.12.028","article-title":"SigB plays a major role in Listeria monocytogenes tolerance to bile stress","volume":"145","author":"Zhang","year":"2011","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib78","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/S1097-2765(02)00470-7","article-title":"Structure of the bacterial RNA polymerase promoter specificity sigma subunit","volume":"9","author":"Campbell","year":"2002","journal-title":"Mol. Cell"},{"key":"10.1016\/j.mcpro.2025.101019_bib79","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1128\/IAI.73.2.894-904.2005","article-title":"Contribution of three bile-associated loci, bsh, pva, and btlB, to gastrointestinal persistence and bile tolerance of Listeria monocytogenes","volume":"73","author":"Begley","year":"2005","journal-title":"Infect. Immun."},{"key":"10.1016\/j.mcpro.2025.101019_bib80","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1007\/s002530000330","article-title":"Protective effect of the bile salt hydrolase-active Lactobacillus reuteri against bile salt cytotoxicity","volume":"53","author":"De Boever","year":"2000","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"10.1016\/j.mcpro.2025.101019_bib81","doi-asserted-by":"crossref","first-page":"1742","DOI":"10.1002\/pro.3484","article-title":"Bile salt hydrolases: structure and function, substrate preference, and inhibitor development","volume":"27","author":"Dong","year":"2018","journal-title":"Protein Sci."},{"key":"10.1016\/j.mcpro.2025.101019_bib82","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1111\/1462-2920.12491","article-title":"Bile-induced peptidoglycan remodelling in Salmonella enterica","volume":"17","author":"Hern\u00e1ndez","year":"2015","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib83","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1111\/j.1574-6968.2007.00854.x","article-title":"Cell envelope changes in Bifidobacterium animalis ssp. lactis as a response to bile","volume":"274","author":"Ruiz","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.mcpro.2025.101019_bib84","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2022.100232","article-title":"Widespread arginine phosphorylation in Staphylococcus aureus","volume":"21","author":"Prust","year":"2022","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib85","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.mib.2010.01.003","article-title":"Use of two-component signal transduction systems in the construction of synthetic genetic networks","volume":"13","author":"Ninfa","year":"2010","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib86","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.ceb.2016.12.010","article-title":"pHisphorylation: the emergence of histidine phosphorylation as a reversible regulatory modification","volume":"45","author":"Fuhs","year":"2017","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.mcpro.2025.101019_bib87","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1038\/s41564-022-01313-7","article-title":"The Mycobacterium tuberculosis protein O-phosphorylation landscape","volume":"8","author":"Frando","year":"2023","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib88","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1139\/y59-099","article-title":"A rapid method of total lipid extraction and purification","volume":"37","author":"Bligh","year":"1959","journal-title":"Can. J. Biochem. Physiol."},{"key":"10.1016\/j.mcpro.2025.101019_bib89","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S0021-9258(18)64849-5","article-title":"A simple method for the isolation and purification of total lipides from animal tissues","volume":"226","author":"Folch","year":"1957","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.mcpro.2025.101019_bib90","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1194\/jlr.D700041-JLR200","article-title":"Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics","volume":"49","author":"Matyash","year":"2008","journal-title":"J. Lipid Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib91","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1039\/C6AN02486F","article-title":"MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling","volume":"142","author":"Burnum-Johnson","year":"2017","journal-title":"Analyst."},{"key":"10.1016\/j.mcpro.2025.101019_bib92","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1074\/mcp.M115.053702","article-title":"Simultaneous metabolite, protein, lipid extraction (SIMPLEX): a combinatorial multimolecular omics approach for systems biology","volume":"15","author":"Coman","year":"2016","journal-title":"Mol. Cell Proteomics"},{"key":"10.1016\/j.mcpro.2025.101019_bib93","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1021\/acs.jproteome.2c00758","article-title":"Proteome coverage after simultaneous proteo-metabolome liquid-liquid extraction","volume":"22","author":"van Pijkeren","year":"2023","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.mcpro.2025.101019_bib94","doi-asserted-by":"crossref","first-page":"D1218","DOI":"10.1093\/nar\/gky899","article-title":"The jPOST environment: an integrated proteomics data repository and database","volume":"47","author":"Moriya","year":"2019","journal-title":"Nucleic Acids Res."}],"container-title":["Molecular &amp; Cellular Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947625001185?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947625001185?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T20:25:29Z","timestamp":1778617529000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535947625001185"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":94,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2025,8]]}},"alternative-id":["S1535947625001185"],"URL":"https:\/\/doi.org\/10.1016\/j.mcpro.2025.101019","relation":{},"ISSN":["1535-9476"],"issn-type":[{"value":"1535-9476","type":"print"}],"subject":[],"published":{"date-parts":[[2025,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A Methanolic Urea-Enhanced Protein Extraction Enabling the Largest Bacterial Phosphorylation Resource","name":"articletitle","label":"Article Title"},{"value":"Molecular & Cellular Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.mcpro.2025.101019","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology\u00e9","name":"copyright","label":"Copyright"}],"article-number":"101019"}}