{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T10:05:43Z","timestamp":1784023543148,"version":"3.55.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T00:00:00Z","timestamp":1783987200000},"content-version":"vor","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Predictive Phenomics Initiative at Pacific Northwest National Laboratory"},{"DOI":"10.13039\/100007000","name":"Laboratory Directed Research and Development Program","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007000","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC05-76RL01830"],"award-info":[{"award-number":["DE-AC05-76RL01830"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Systemic perturbations trigger extensive changes across the proteome\u2013altering protein abundance, post-translational modifications (PTMs), conformational states, and complex assembly. Interpreting these effects demands computational pipelines capable of integrating diverse proteomics modalities, such as multi-PTM profiling, limited proteolysis mass spectrometry (LiP-MS), and cross-linking mass spectrometry (XL-MS), within a unified and interoperable framework. Because instrument data are quantified at the peptide level, mapping these measurements to individual residues or modification sites is essential for biologically meaningful interpretation. We introduce ProteoMeter, an open-source Python library designed to integrate multi-modal proteomics datasets and map them to single-residue resolution using a standardized coordinate framework. We showcase its capabilities in a combined multi-PTM and LiP-MS analysis profiling the proteomic response to human coronavirus 229e (HCoV-229E) infection. ProteoMeter is actively maintained and is freely available\u2013including all source code and figure-generation scripts\u2013at the following repository: https:\/\/github.com\/PNNL-Predictive-Phenomics\/ProteoMeter.<\/jats:p>","DOI":"10.1093\/nargab\/lqag073","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T11:54:54Z","timestamp":1783684494000},"source":"Crossref","is-referenced-by-count":0,"title":["ProteoMeter: a pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4356-9809","authenticated-orcid":false,"given":"Jordan C","family":"Rozum","sequence":"first","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy C","family":"Sims","sequence":"additional","affiliation":[{"name":"Nuclear, Chemical, and Biological Technologies Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9845-1584","authenticated-orcid":false,"given":"Xiaolu","family":"Li","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4551-0314","authenticated-orcid":false,"given":"Snigdha","family":"Sarkar","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2540-2017","authenticated-orcid":false,"given":"Tong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3781-2566","authenticated-orcid":false,"given":"John T","family":"Melchior","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0190-4530","authenticated-orcid":false,"given":"Danielle","family":"Ciesielski","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7627-4214","authenticated-orcid":false,"given":"David D","family":"Pollock","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine , Aurora, CO 80045 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0232-6867","authenticated-orcid":false,"given":"H Steven","family":"Wiley","sequence":"additional","affiliation":[{"name":"Environmental Molecular Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5393-2827","authenticated-orcid":false,"given":"Wei-Jun","family":"Qian","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3983-9009","authenticated-orcid":false,"given":"Song","family":"Feng","sequence":"additional","affiliation":[{"name":"Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99354 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,14]]},"reference":[{"key":"2026071405162642600_B1","doi-asserted-by":"publisher","first-page":"100881","DOI":"10.1016\/j.mcpro.2024.100881","article-title":"Integrative multi-PTM proteomics reveals dynamic global, redox, phosphorylation, and acetylation regulation in cytokine-treated pancreatic beta cells","volume":"23","author":"Gluth","year":"2024","journal-title":"Mol Cell Proteomics"},{"key":"2026071405162642600_B2","doi-asserted-by":"publisher","first-page":"2391","DOI":"10.1038\/nprot.2017.100","article-title":"Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry","volume":"12","author":"Schopper","year":"2017","journal-title":"Nat Protoc"},{"key":"2026071405162642600_B3","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1038\/s41596-022-00771-x","article-title":"Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications","volume":"18","author":"Malinovska","year":"2022","journal-title":"Nat Protoc"},{"key":"2026071405162642600_B4","doi-asserted-by":"crossref","first-page":"5026","DOI":"10.1021\/acs.jproteome.5c00400","article-title":"Human coronavirus-229E hijacks key host-cell RNA-processing complexes for replication","volume":"24","author":"Sarkar","year":"2025","journal-title":"J Proteome Res"},{"key":"2026071405162642600_B5","doi-asserted-by":"publisher","first-page":"100477","DOI":"10.1016\/j.mcpro.2022.100477","article-title":"MSstatsPTM: statistical relative quantification of posttranslational modifications in bottom-up mass spectrometry-based proteomics","volume":"22","author":"Kohler","year":"2023","journal-title":"Mol Cell Proteomics"},{"key":"2026071405162642600_B6","doi-asserted-by":"publisher","first-page":"btad526","DOI":"10.1093\/bioinformatics\/btad526","article-title":"DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data","volume":"39","author":"Feng","year":"2023","journal-title":"Bioinformatics"},{"key":"2026071405162642600_B7","doi-asserted-by":"publisher","first-page":"vbab041","DOI":"10.1093\/bioadv\/vbab041","article-title":"protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data","volume":"2","author":"Quast","year":"2022","journal-title":"Bioinform Adv"},{"key":"2026071405162642600_B8","doi-asserted-by":"publisher","first-page":"2332","DOI":"10.1021\/acs.jproteome.3c00887","article-title":"FLiPPR: a processor for Limited Proteolysis (LiP) mass spectrometry data sets built on FragPipe","volume":"23","author":"Manriquez-Sandoval","year":"2024","journal-title":"J Proteome Res"},{"key":"2026071405162642600_B9","article-title":"MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments","author":"Kohler","year":"2025"},{"key":"2026071405162642600_B10","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.cell.2020.12.021","article-title":"Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ","volume":"184","author":"Cappelletti","year":"2021","journal-title":"Cell"},{"key":"2026071405162642600_B11","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1038\/s41594-022-00837-0","article-title":"Global, in situ analysis of the structural proteome in individuals with Parkinson\u2019s disease to identify a new class of biomarker","volume":"29","author":"Mackmull","year":"2022","journal-title":"Nat Struct Mol Biol"},{"key":"2026071405162642600_B12","doi-asserted-by":"publisher","first-page":"100934","DOI":"10.1016\/j.mcpro.2025.100934","article-title":"Analysis of limited proteolysis-coupled mass spectrometry data","volume":"24","author":"Nagel","year":"2025","journal-title":"Mol Cell Proteomics"},{"key":"2026071405162642600_B13","doi-asserted-by":"publisher","article-title":"A phosphoproteomics data resource for systems-level modeling of kinase signaling networks","author":"Feng","DOI":"10.1101\/2023.08.03.551714"},{"key":"2026071405162642600_B14","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/j.molcel.2015.09.013","article-title":"Functional dynamics within the human ribosome regulate the rate of active protein synthesis","volume":"60","author":"Ferguson","year":"2015","journal-title":"Mol Cell"},{"key":"2026071405162642600_B15","doi-asserted-by":"publisher","first-page":"12666","DOI":"10.1074\/jbc.M113.546481","article-title":"C-terminal Src Kinase (Csk)-mediated phosphorylation of eukaryotic elongation factor 2 (eEF2) promotes proteolytic cleavage and nuclear translocation of eEF2*","volume":"289","author":"Yao","year":"2014","journal-title":"J Biol Chem"},{"key":"2026071405162642600_B16","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/nature12104","article-title":"Structures of the human and Drosophila 80S ribosome","volume":"497","author":"Anger","year":"2013","journal-title":"Nature"},{"key":"2026071405162642600_B17","doi-asserted-by":"publisher","first-page":"eaaz7651","DOI":"10.1126\/sciadv.aaz7651","article-title":"Cryo-EM structure of NPF-bound human Arp2\/3 complex and activation mechanism","volume":"6","author":"Zimmet","year":"2020","journal-title":"Sci Adv"},{"key":"2026071405162642600_B18","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/s41586-018-0237-5","article-title":"Nuclear ARP2\/3 drives DNA break clustering for homology-directed repair","volume":"559","author":"Schrank","year":"2018","journal-title":"Nature"},{"key":"2026071405162642600_B19","doi-asserted-by":"publisher","first-page":"4490","DOI":"10.1128\/iai.67.9.4490-4498.1999","article-title":"Legionella pneumophila invasion of MRC-5 cells induces tyrosine protein phosphorylation","volume":"67","author":"Susa","year":"1999","journal-title":"Infect Immun"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag073\/68769198\/lqag073.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag073\/68769198\/lqag073.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T09:16:36Z","timestamp":1784020596000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag073\/8733747"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,27]]},"references-count":19,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,6,27]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag073","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,6,27]]},"article-number":"lqag073"}}