{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,7]],"date-time":"2026-11-07T02:49:16Z","timestamp":1794019756725,"version":"4.8.0"},"reference-count":35,"publisher":"American Chemical Society (ACS)","issue":"12","license":[{"start":{"date-parts":[[2015,12,2]],"date-time":"2015-12-02T00:00:00Z","timestamp":1449014400000},"content-version":"vor","delay-in-days":27,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/na","name":"Max-Planck Society for the Advancement of Sciences","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>In liquid chromatography-mass spectrometry (LC-MS)-based proteomics, many precursors elute from the column simultaneously. In data-dependent analyses, these precursors are fragmented one at a time, whereas the others are discarded entirely. Here we employ trapped ion mobility spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF) mass spectrometer to remove this limitation. In TIMS, all precursor ions are accumulated in parallel and released sequentially as a function of their ion mobility. Instead of selecting a single precursor mass with the quadrupole mass filter, we here implement synchronized scans in which the quadrupole is mass positioned with sub-millisecond switching times at the m\/z values of appropriate precursors, such as those derived from a topN precursor list. We demonstrate serial selection and fragmentation of multiple precursors in single 50 ms TIMS scans. Parallel accumulation\u2013serial fragmentation (PASEF) enables hundreds of MS\/MS events per second at full sensitivity. Modeling the effect of such synchronized scans for shotgun proteomics, we estimate that about a 10-fold gain in sequencing speed should be achievable by PASEF without a decrease in sensitivity.<\/jats:p>","DOI":"10.1021\/acs.jproteome.5b00932","type":"journal-article","created":{"date-parts":[[2015,11,5]],"date-time":"2015-11-05T05:10:03Z","timestamp":1446700203000},"page":"5378-5387","source":"Crossref","is-referenced-by-count":466,"title":["Parallel Accumulation\u2013Serial\nFragmentation\n(PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized\nScans in a Trapped Ion Mobility Device"],"prefix":"10.1021","volume":"14","author":[{"given":"Florian","family":"Meier","sequence":"first","affiliation":[{"name":"Max-Planck-Institute of Biochemistry , , Am Klopferspitz 18 , ,","place":["Martinsried, Germany, 82152"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scarlet","family":"Beck","sequence":"additional","affiliation":[{"name":"Max-Planck-Institute of Biochemistry , , Am Klopferspitz 18 , ,","place":["Martinsried, Germany, 82152"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niklas","family":"Grassl","sequence":"additional","affiliation":[{"name":"Max-Planck-Institute of Biochemistry , , Am Klopferspitz 18 , ,","place":["Martinsried, Germany, 82152"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Lubeck","sequence":"additional","affiliation":[{"name":"Bruker Daltonik GmbH , Fahrenheitstrasse 4 , ,","place":["Bremen, Germany, 28359"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melvin A.","family":"Park","sequence":"additional","affiliation":[{"name":"Bruker Daltonics Inc. , 40 Manning Road , , Massachusetts ,","place":["Billerica, United States, 01821"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Raether","sequence":"additional","affiliation":[{"name":"Bruker Daltonik GmbH , Fahrenheitstrasse 4 , ,","place":["Bremen, Germany, 28359"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Mann","sequence":"additional","affiliation":[{"name":"Max-Planck-Institute of Biochemistry , , Am Klopferspitz 18 , ,","place":["Martinsried, Germany, 82152"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2015,11,5]]},"reference":[{"issue":"6928","key":"2026090119340954600_cit1","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1038\/nature01511","article-title":"Mass spectrometry-based\nproteomics","volume":"422","author":"Aebersold","year":"2003","journal-title":"Nature"},{"issue":"7172","key":"2026090119340954600_cit2","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1038\/nature06525","article-title":"The biological\nimpact of mass-spectrometry-based proteomics","volume":"450","author":"Cravatt","year":"2007","journal-title":"Nature"},{"issue":"1","key":"2026090119340954600_cit3","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/nrg3356","article-title":"Next-generation proteomics: towards\nan integrative view of proteome dynamics","volume":"14","author":"Altelaar","year":"2013","journal-title":"Nat.\nRev. 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Proteomics"},{"issue":"6","key":"2026090119340954600_cit7","doi-asserted-by":"publisher","first-page":"1696","DOI":"10.1002\/pmic.200800564","article-title":"Database\nsearching and accounting of multiplexed precursor\nand product ion spectra from the data independent analysis of simple\nand complex peptide mixtures","volume":"9","author":"Li","year":"2009","journal-title":"Proteomics"},{"key":"2026090119340954600_cit8","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.O111.016717","article-title":"Targeted data\nextraction of the MS\/MS spectra generated by data-independent acquisition:\na new concept for consistent and accurate proteome analysis","author":"Gillet","year":"2012","journal-title":"Mol. Cell. 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Soc.\nMass Spectrom."},{"key":"2026090119340954600_cit31","unstructured":"R Development Core Team. \n          R: A Language and Environment for Statistical Computing; 2014."},{"issue":"5","key":"2026090119340954600_cit32","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1038\/nprot.2009.36","article-title":"A practical\nguide to the MaxQuant\ncomputational platform for SILAC-based quantitative proteomics","volume":"4","author":"Cox","year":"2009","journal-title":"Nat. Protoc."},{"issue":"8","key":"2026090119340954600_cit33","doi-asserted-by":"publisher","first-page":"4152","DOI":"10.1021\/pr1003856","article-title":"Quantifying the impact of chimera\nMS\/MS spectra on peptide identification in large-scale proteomics\nstudies","volume":"9","author":"Houel","year":"2010","journal-title":"J. Proteome Res."},{"issue":"7","key":"2026090119340954600_cit34","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1021\/ac60357a043","article-title":"Theory of Plasma\nChromatography Gaseous Electrophoresis\n- Review","volume":"47","author":"Revercomb","year":"1975","journal-title":"Anal. 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