Improved Precursor Characterization for Data-Dependent Mass Spectrometry
Open accessAbstract
Modern ion trap mass spectrometers are capable of collecting up to 60 tandem MS (MS/MS) scans per second, in theory providing acquisition speeds that can sample every eluting peptide precursor presented to the MS system. In practice, however, the precursor sampling capacity enabled by these ultrafast acquisition rates is often underutilized due to a host of reasons (e.g., long injection times and wide analyzer mass ranges). One often overlooked reason for this underutilization is that the instrument exhausts all the peptide features it identifies as suitable for MS/MS fragmentation. Highly abundant features can prevent annotation of lower abundance precursor ions that occupy similar mass-to-charge (m/z) space, which ultimately inhibits the acquisition of an MS/MS event. Here, we present an advanced peak determination (APD) algorithm that uses an iterative approach to annotate densely populated m/z regions to increase the number of peptides sampled during data-dependent LC-MS/MS analyses. The APD algorithm enables nearly full utilization of the sampling capacity of a quadrupole-Orbitrap-linear ion trap MS system, which yields up to a 40% increase in unique peptide identifications from whole cell HeLa lysates (approximately 53 000 in a 90 min LC-MS/MS analysis). The APD algorithm maintains improved peptide and protein identifications across several modes of proteomic data acquisition, including varying gradient lengths, different degrees of prefractionation, peptides derived from multiple proteases, and phosphoproteomic analyses. Additionally, the use of APD increases the number of peptides characterized per protein, providing improved protein quantification. In all, the APD algorithm increases the number of detectable peptide features, which maximizes utilization of the high MS/MS capacities and significantly improves sampling depth and identifications in proteomic experiments.
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The Advanced Peak Determination algorithm was able to assign charge states of the most abundant proteoforms on-the-fly in the PTCR MS2 spectra.
“the Advanced Peak Determination algorithm44 was able to assign the charge states of the most abundant proteoforms on-the-fly.”
From Proton Transfer Charge Reduction Enables High-Throughput Top-Down Analysis of Large Proteoforms (2019) · cites this paper as [44]
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Self-citation
- Authors
- Hebert, A. S., Thöing, C., Riley, N. M., Kwiecien, N. W., Shiskova, E., Huguet, R., Cardasis, H. L., Kuehn, A., Eliuk, S., Zabrouskov, V., Westphall, M. S., McAlister, G. C., & Coon, J. J.
- Affiliations
- University of Wisconsin–Madison (US)
- Thermo Fisher Scientific (Germany) (DE)
- Thermo Fisher Scientific (United States) (US)
- Morgridge Institute for Research (US)
- Corresponding author
- Coon, Joshua J.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-01-11
- Volume
- 90
- Issue
- 3
- Pages
- 2333-2340
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC5803309
- OpenAlex
- W2778601930
- Cited by
- 67
- References
- 26
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 4 · 2023: 6 · 2022: 4 · 2021: 13 · 2020: 10 · 2019: 12 · 2018: 11
- FWCI
- 4.45
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (F99 CA212454)
- Thermo Fisher Scientific
- National Institute of General Medical Sciences (R35 GM118110)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- data-dependent acquisition, precursor ion selection, ion trap mass spectrometry, peptide identification, protein quantification, phosphoproteomics, prefractionation, proteomics
- MeSH terms
- Algorithms, HeLa Cells, Humans, Peptide Fragments, Protein Precursors, Proteome, Proteomics, Tandem Mass Spectrometry
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