Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics Article Swipe
Devin K. Schweppe
,
Jimmy K. Eng
,
Derek J. Bailey
,
Ramin Rad
,
Qing Yu
,
Jose Navarrete‐Perea
,
Edward L. Huttlin
,
Brian K. Erickson
,
João A. Paulo
,
Steven P. Gygi
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/668533
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.1101/668533
Multiplexed quantitative analyses of complex proteomes enable deep biological insight. While a multitude of workflows have been developed for multiplexed analyses, the most quantitatively accurate method (SPS-MS3) suffers from long acquisition duty cycles. We built a new, real-time database search (RTS) platform, Orbiter, to combat the SPS-MS3 method’s longer duty cycles. RTS with Orbiter enables the elimination of SPS-MS3 scans if no peptide matches to a given spectrum. With Orbiter’s online proteomic analytical pipeline, which includes RTS and false discovery rate analysis, it was possible to process a single spectrum database search in less than 10 milliseconds. The result is a fast, functional means to identify peptide spectral matches using Comet, filter these matches, and more efficiently quantify proteins of interest. Importantly, the use of Comet for peptide spectral matching allowed for a fully featured search, including analysis of post-translational modifications, with well-known and extensively validated scoring. These data could then be used to trigger subsequent scans in an adaptive and flexible manner. In this work we tested the utility of this adaptive data acquisition platform to improve the efficiency and accuracy of multiplexed quantitative experiments. We found that RTS enabled a 2-fold increase in mass spectrometric data acquisition efficiency. Orbiter’s RTS was able to quantify more than 8000 proteins across 10 proteomes in half the time of an SPS-MS3 analysis (18 hours for RTS, 36 hours for SPS-MS3).
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/668533
- https://www.biorxiv.org/content/biorxiv/early/2019/06/12/668533.full.pdf
- OA Status
- green
- Cited By
- 30
- References
- 23
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2951544838
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Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W2951544838Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/668533Digital Object Identifier
- Title
-
Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomicsWork title
- Type
-
preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2019Year of publication
- Publication date
-
2019-06-12Full publication date if available
- Authors
-
Devin K. Schweppe, Jimmy K. Eng, Derek J. Bailey, Ramin Rad, Qing Yu, Jose Navarrete‐Perea, Edward L. Huttlin, Brian K. Erickson, João A. Paulo, Steven P. GygiList of authors in order
- Landing page
-
https://doi.org/10.1101/668533Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2019/06/12/668533.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2019/06/12/668533.full.pdfDirect OA link when available
- Concepts
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Orbiter, Computer science, Multiplexing, Comet, Proteome, Database search engine, Pipeline (software), Real-time database, Workflow, Data mining, Search engine, Database, Bioinformatics, Physics, Information retrieval, Biology, Telecommunications, Astronomy, Programming language, AstrophysicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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30Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 2, 2023: 5, 2022: 8, 2021: 4Per-year citation counts (last 5 years)
- References (count)
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23Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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