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Phlairaharn, T.* ; Shannon, A.E.* ; Zeng, X.* ; Truong, D.J.J. ; Schoof, E.M.* ; Ye, Z.* ; Searle, B.C.*

Improving proteomic dynamic range with Multiple Accumulation Precursor Mass Spectrometry. 

J. Proteome Res. 24, 5116–5126 (2025)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
Orbitrap (OT)-based mass spectrometer platforms are a gold standard in high-resolution mass spectrometry, where their primary disadvantage is slower-scanning speed in comparison to time-of-flight or linear ion trap mass analyzers. In this study, we utilize long OT transients to extend the precursor dynamic range by modifying the selected ion monitoring method to multiplex several precursor m/z ranges into a single scan, which we call "multiple accumulation precursor mass spectrometry". Our approach requires no software or hardware modifications and hides the additional ion accumulation steps during the time it takes to make other Orbitrap measurements, producing precursor spectra with nearly 2× dynamic range and essentially no consequences. We collected data using both data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods to evaluate a range of approaches. With DDA, MAP-MS precursor quantification improves with higher quality measurements. At the same time, DIA detection is enhanced by up to 11% when combining precursor and tandem mass spectra for peptide detection.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Data-dependent Acquisition ; Data-independent Acquisition ; Mass Spectrometry ; Multiplexing ; Orbitrap Mass Analyzer ; Peptide Identification Optimization ; Peptide Quantification Optimization; Data-independent Acquisition; Peptide Identification; Selectivity; Ms/ms
ISSN (print) / ISBN 1535-3893
e-ISSN 1535-3907
Journal Journal of Proteome Research
Quellenangaben Volume: 24, Issue: 10, Pages: 5116–5126 Article Number: , Supplement: ,
Publisher American Chemical Society (ACS)
Publishing Place 1155 16th St, Nw, Washington, Dc 20036 Usa
Reviewing status Peer reviewed
Institute(s) Insitute of Synthetic Biomedicine (ISBM)
Grants NCTIB Fund for the R&D Platform for Cell and Gene Therapy
Suzhou Municipal Key Laboratory
Natural Science Foundation of Jiangsu Province
Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences
Nonprofit Central Research Institute Fund of the Chinese Academy of Medical Sciences
National Institutes of Health
Pelotonia Institute for Immuno-Oncology