{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T18:21:11Z","timestamp":1771266071795,"version":"3.50.1"},"posted":{"date-parts":[[2026,2,13]]},"group-title":"Systems Biology","reference-count":20,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T00:00:00Z","timestamp":1770940800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"crossref","award":["R35GM142502"],"award-info":[{"award-number":["R35GM142502"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,2,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Parallel Accumulation with Mobility-Aligned Fragmentation (PAMAF) achieves near-complete ion utilization and high spectral specificity by fragmenting all mobility-separated precursors without quadrupole isolation. Leveraging the ultrahigh mobility resolution of SLIM, this quadrupole-free strategy maximizes ion utilization efficiency and offers a promising approach in mass spectrometry\u2013based proteomics, particularly for low-abundance peptides or low-input samples. However, the unique data structure of PAMAF where precursor\u2013fragment relationships are encoded along the mobility dimension renders it incompatible with existing peptide identification tools. Here, we present xTracer, the first untargeted peptide identification algorithm developed specifically for PAMAF data. xTracer integrates correlations across both chromatographic and mobility dimensions to associate precursor and fragment ions, reconstruct pseudo-spectra, and enable database searching using well-established DDA search engines. Applied to datasets with varying sample loads and acquisition throughputs, xTracer consistently achieved robust and reproducible peptide identifications, outperforming single-domain correlation strategies. Overall, xTracer provides a versatile and high-efficiency computational framework for reconstructing pseudo-spectra from quadrupole-free, mobility-aligned fragmentation data, enhancing the analytical power of high-resolution ion mobility (HRIM)\u2013based proteomics.<\/jats:p>","DOI":"10.64898\/2026.02.11.705440","type":"posted-content","created":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T08:35:41Z","timestamp":1771058141000},"source":"Crossref","is-referenced-by-count":0,"title":["xTracer: Integrating chromatogram and mobiligram correlations for untargeted peptide identification in SLIM-based PAMAF data"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5841-6365","authenticated-orcid":false,"given":"Jian","family":"Song","sequence":"first","affiliation":[{"name":"Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3692-549X","authenticated-orcid":false,"given":"Liulin","family":"Deng","sequence":"additional","affiliation":[{"name":"MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-1148-9832","authenticated-orcid":false,"given":"Lauren","family":"Royer","sequence":"additional","affiliation":[{"name":"MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bennett","family":"Kalafut","sequence":"additional","affiliation":[{"name":"MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1143-1629","authenticated-orcid":false,"given":"Daniel","family":"DeBord","sequence":"additional","affiliation":[{"name":"MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2753-3926","authenticated-orcid":false,"given":"Jesse G.","family":"Meyer","sequence":"additional","affiliation":[{"name":"Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026021609301573000_2026.02.11.705440v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-08584-0"},{"key":"2026021609301573000_2026.02.11.705440v1.2","doi-asserted-by":"publisher","DOI":"10.1021\/acsmeasuresciau.3c00068"},{"key":"2026021609301573000_2026.02.11.705440v1.3","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20178126"},{"key":"2026021609301573000_2026.02.11.705440v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-02099-7"},{"key":"2026021609301573000_2026.02.11.705440v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-024-02129-y"},{"issue":"12","key":"2026021609301573000_2026.02.11.705440v1.6","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1038\/s41592-020-00998-0","article-title":"diaPASEF: parallel accumulation\u2013serial fragmentation combined with data-independent acquisition[J]","volume":"17","year":"2020","journal-title":"Nature methods"},{"key":"2026021609301573000_2026.02.11.705440v1.7","doi-asserted-by":"crossref","unstructured":"DeBord D , Rorrer L C , Deng L , et al. Abandoning the Quadrupole for Mass Spectrometry Fragmentation Analysis: Towards 1,000 Hz Speeds with 100% Ion Utilization Using High Resolution Ion Mobility Precursor Isolation[J]. bioRxiv, 2024: 2024.10. 18.619158.","DOI":"10.1101\/2024.10.18.619158"},{"key":"2026021609301573000_2026.02.11.705440v1.8","doi-asserted-by":"crossref","unstructured":"Uribe I R , Deng L , Rorrer III L , et al. High-Resolution Ion Mobility as an Alternative to Quadrupole-Based Precursor Isolation for Reducing Chimeric Fragmentation Spectra in Bottom-Up Proteomics[J]. Proteomics, 2025: e70084.","DOI":"10.1002\/pmic.70084"},{"key":"2026021609301573000_2026.02.11.705440v1.9","doi-asserted-by":"crossref","unstructured":"Schilling B , Rorrer III L , Royer L , et al. Novel high-resolution ion mobility mass spectrometry for sitespecific quantification of the sirtuin-5 regulated kidney succinylome[J]. bioRxiv, 2025: 2025.11. 01.686011.","DOI":"10.1101\/2025.11.01.686011"},{"key":"2026021609301573000_2026.02.11.705440v1.10","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.5b02481"},{"key":"2026021609301573000_2026.02.11.705440v1.11","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.6b01914"},{"key":"2026021609301573000_2026.02.11.705440v1.12","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.6b01915"},{"issue":"9","key":"2026021609301573000_2026.02.11.705440v1.13","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1074\/mcp.O114.047035","article-title":"Peptide-centric proteome analysis: an alternative strategy for the analysis of tandem mass spectrometry data[J]","volume":"14","year":"2015","journal-title":"Molecular & Cellular Proteomics"},{"key":"2026021609301573000_2026.02.11.705440v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2841"},{"issue":"1","key":"2026021609301573000_2026.02.11.705440v1.15","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput[J]","volume":"17","year":"2020","journal-title":"Nature methods"},{"issue":"3","key":"2026021609301573000_2026.02.11.705440v1.16","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1038\/nmeth.3255","article-title":"DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics[J]","volume":"12","year":"2015","journal-title":"Nature methods"},{"issue":"1","key":"2026021609301573000_2026.02.11.705440v1.17","doi-asserted-by":"crossref","first-page":"4154","DOI":"10.1038\/s41467-023-39869-5","article-title":"Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform[J]","volume":"14","year":"2023","journal-title":"Nature communications"},{"issue":"1","key":"2026021609301573000_2026.02.11.705440v1.18","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s41467-024-55448-8","article-title":"diaTracer enables spectrum-centric analysis of diaPASEF proteomics data[J]","volume":"16","year":"2025","journal-title":"Nature Communications"},{"key":"2026021609301573000_2026.02.11.705440v1.19","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.3c00486"},{"key":"2026021609301573000_2026.02.11.705440v1.20","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jproteome.7b00170"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.02.11.705440","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T17:30:26Z","timestamp":1771263026000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.02.11.705440"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,13]]},"references-count":20,"URL":"https:\/\/doi.org\/10.64898\/2026.02.11.705440","relation":{},"subject":[],"published":{"date-parts":[[2026,2,13]]},"subtype":"preprint"}}