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Title: Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics

Abstract

Advances in tandem mass spectrometry (MS/MS) acquisition rate have steadily led to increased performance in shotgun proteomics experiments. To that end, contemporary mass spectrometers are outfitted with multiple analyzers allowing for the simultaneous collection of survey (MS1) and MS/MS spectra. In the latest generation Orbitrap hybrid, MS/MS scans can be acquired at a high rate using the dual cell linear ion trap analyzer, all while the next precursor is being dissociated in a collision cell and a MS1 scan is occurring in the Orbitrap. Often overlooked in these experiments is that the ion trap scan duration is highly variable and dependent upon precursor mass. Here, we examine the use of various static mass-to-charge ratio scan ranges for ion trap MS/MS acquisition and determine performance relative to conventional dynamic mass-to-charge ratio range scanning. We demonstrate that a fixed mass-to-charge ratio scan range can generate 12% more MS/MS scans and more unique peptide identifications as compared to the standard dynamic approach, respectively.

Authors:
ORCiD logo [1];  [2];  [1]; ORCiD logo [3]
  1. Univ. of Wisconsin, Madison, WI (United States). Dept. of Chemistry
  2. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
  3. Univ. of Wisconsin, Madison, WI (United States). Dept. of Chemistry, and Dept. of Biomolecular Chemistry
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1569267
Grant/Contract Number:  
SC0018409
Resource Type:
Accepted Manuscript
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 91; Journal Issue: 20; Journal ID: ISSN 0003-2700
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English

Citation Formats

Trujillo, Edna A., Hebert, Alexander S., Brademan, Dain R., and Coon, Joshua J. Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics. United States: N. p., 2019. Web. doi:10.1021/acs.analchem.9b02979.
Trujillo, Edna A., Hebert, Alexander S., Brademan, Dain R., & Coon, Joshua J. Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics. United States. doi:10.1021/acs.analchem.9b02979.
Trujillo, Edna A., Hebert, Alexander S., Brademan, Dain R., and Coon, Joshua J. Wed . "Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics". United States. doi:10.1021/acs.analchem.9b02979.
@article{osti_1569267,
title = {Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics},
author = {Trujillo, Edna A. and Hebert, Alexander S. and Brademan, Dain R. and Coon, Joshua J.},
abstractNote = {Advances in tandem mass spectrometry (MS/MS) acquisition rate have steadily led to increased performance in shotgun proteomics experiments. To that end, contemporary mass spectrometers are outfitted with multiple analyzers allowing for the simultaneous collection of survey (MS1) and MS/MS spectra. In the latest generation Orbitrap hybrid, MS/MS scans can be acquired at a high rate using the dual cell linear ion trap analyzer, all while the next precursor is being dissociated in a collision cell and a MS1 scan is occurring in the Orbitrap. Often overlooked in these experiments is that the ion trap scan duration is highly variable and dependent upon precursor mass. Here, we examine the use of various static mass-to-charge ratio scan ranges for ion trap MS/MS acquisition and determine performance relative to conventional dynamic mass-to-charge ratio range scanning. We demonstrate that a fixed mass-to-charge ratio scan range can generate 12% more MS/MS scans and more unique peptide identifications as compared to the standard dynamic approach, respectively.},
doi = {10.1021/acs.analchem.9b02979},
journal = {Analytical Chemistry},
number = 20,
volume = 91,
place = {United States},
year = {2019},
month = {9}
}

Journal Article:
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This content will become publicly available on September 11, 2020
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