{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T13:48:29Z","timestamp":1764683309151,"version":"3.46.0"},"reference-count":47,"publisher":"Wiley","issue":"19","license":[{"start":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T00:00:00Z","timestamp":1756944000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2025,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:label\/>\n                    <jats:p>Mass spectrometry (MS)\u2010based single\u2010cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library\u2010based multiplex segmented selected ion monitoring (SLB\u2010msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single\u2010cell analysis. The single\u2010cell MS data is acquired by a multiplex segmented selected ion monitoring (msSIM) technique, which sequentially applies multiple isolation cycles with the quadrupole using a wide isolation window in each cycle to accumulate and store precursor ions in the C\u2010trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching using a well\u2010defined spectral library. We applied the SLB\u2010msSIM method to interrogate cellular heterogeneity in various pancreatic cancer cell lines, revealing common and distinct functional traits among PANC\u20101, MIA\u2010PaCa2, AsPc\u20101, HPAF, and normal HPDE cells. Furthermore, for the first time, our novel data revealed the diverse cell trajectories of individual PANC\u20101 cells during the induction and reversal of epithelial\u2010mesenchymal transition (EMT). Collectively, our results demonstrate that SLB\u2010msSIM is a highly sensitive and robust platform, applicable to a wide range of instruments for single\u2010cell proteomic studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>\n                      <jats:list list-type=\"bullet\">\n                        <jats:list-item>\n                          <jats:p>We present the SLB\u2010msSIM method, a conceptually unique approach in mass spectrometry\u2010based single\u2010cell proteomics that significantly enhances sensitivity and robustness.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>This innovative platform enables detailed analysis of the proteome landscape, capturing cellular heterogeneity, trajectories, and phenotypes at a single\u2010cell resolution.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Utilizing the SLB\u2010msSIM technique, we identified both common and distinct functional traits among various pancreatic cancer cell lines and normal cells. Moreover, our study unveiled new insights into the diverse cell trajectories of individual cancer cells during the induction and reversal of epithelial\u2010mesenchymal transition (EMT).<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>In summary, the SLB\u2010msSIM method offers a highly sensitive and robust platform for single\u2010cell proteomic studies, with broad applicability across different instruments.<\/jats:p>\n                        <\/jats:list-item>\n                      <\/jats:list>\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1002\/pmic.70037","type":"journal-article","created":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T07:03:19Z","timestamp":1756969399000},"page":"50-61","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["SLB\u2010msSIM: A Spectral Library\u2010Based Multiplex Segmented SIM Platform for Single\u2010Cell Proteomic Analysis"],"prefix":"10.1002","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0911-7320","authenticated-orcid":false,"given":"Lakmini","family":"Senavirathna","sequence":"first","affiliation":[{"name":"The Brown Foundation Institute of Molecular Medicine University of Texas Health Science Center at Houston  Houston Texas USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Ma","sequence":"additional","affiliation":[{"name":"The Brown Foundation Institute of Molecular Medicine University of Texas Health Science Center at Houston  Houston Texas USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4676-1804","authenticated-orcid":false,"given":"Van\u2010An","family":"Duong","sequence":"additional","affiliation":[{"name":"The Brown Foundation Institute of Molecular Medicine University of Texas Health Science Center at Houston  Houston Texas 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