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Expanding the Use of Spectral Libraries in Proteomics
Inst Syst Biol, Seattle, WA 98109 USA..ORCID iD: 0000-0001-8732-0928
European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England..ORCID iD: 0000-0001-6579-6941
Univ Calif San Francisco, San Francisco, CA 94158 USA..ORCID iD: 0000-0002-9757-7302
Tech Univ Munich, Prote & Bioanalyt, D-85354 Freising Weihenstephan, Germany..ORCID iD: 0000-0002-9224-3258
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2018 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, no 12, p. 4051-4060Article in journal (Refereed) Published
Abstract [en]

The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on ABSTRACT: The 2017 Dagstuhl Seminar on Computational the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2018. Vol. 17, no 12, p. 4051-4060
Keywords [en]
mass spectrometry, spectral libraries, standards, formats, Dagstuhl Seminar, meeting report, Proteomics Standards Initiative
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-240749DOI: 10.1021/acs.jproteome.8b00485ISI: 000452930000004PubMedID: 30270626Scopus ID: 2-s2.0-85054995934OAI: oai:DiVA.org:kth-240749DiVA, id: diva2:1276551
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20190108

Available from: 2019-01-08 Created: 2019-01-08 Last updated: 2019-01-08Bibliographically approved

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Käll, Lukas

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Deutsch, Eric W.Perez-Riverol, YassetChalkley, Robert J.Wilhelm, MathiasKäll, LukasVolders, Pieter-JanSalek, Reza M.Vizcaino, Juan Antonio
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