MS1Connect: a mass spectrometry run similarity measure.

Andy Lin, Brooke L Deatherage Kaiser, Janine R Hutchison, Jeffrey A Bilmes, William Stafford Noble

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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5 · Who and what money

Authors and funding

5 authors.

Andy LinChemical and Biological Signatures, Pacific Northwest National Laboratory, Richland, WA 99354, USA.

Brooke L Deatherage KaiserChemical and Biological Signatures, Pacific Northwest National Laboratory, Richland, WA 99354, USA.

Janine R HutchisonChemical and Biological Signatures, Pacific Northwest National Laboratory, Richland, WA 99354, USA.

Jeffrey A BilmesDepartment of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA.

William Stafford NobleDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.ORCID 0000-0001-7283-4715

Funding

Optimization and joint modeling for peptide detection by tandem mass spectrometryR01GM121818 · NIGMS · UNIVERSITY OF WASHINGTON · PI NOBLE, WILLIAM STAFFORD · 2017 to 2020

$1.3M

Battelle for the U.S. Department of EnergyBattelle Memorial Institute for the United States Department of Energy DE-AC06-76RLOLaboratory Directed Research and Development Program at Pacific Northwest National LaboratoryLinus Pauling Distinguished Postdoctoral FellowshipNIGMS NIH HHS R01 GM121818Pacific Northwest National Laboratory

6 · The paper itself

Abstract

motivationInterpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols.

resultsWe propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though these data are not used by MS1Connect. AVAILABILITY AND IMPLEMENTATION: The MS1Connect software is available at https://github.com/bmx8177/MS1Connect. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

PeptidesSoftwareMass SpectrometryProteomicsPeptides

Identifiers

PMID36702456

DOI10.1093/bioinformatics/btad058

PMCPMC9913042

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.