Expanding the Use of Spectral Libraries in Proteomics

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Expanding the Use of Spectral Libraries in Proteomics

Deutsch, Eric W. (författare): Inst Syst Biol, Seattle, WA 98109 USA.

Perez-Riverol, Yasset (författare): European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.

Chalkley, Robert J. (författare): Univ Calif San Francisco, San Francisco, CA 94158 USA.

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Wilhelm, Mathias (författare): Tech Univ Munich, Prote & Bioanalyt, D-85354 Freising Weihenstephan, Germany.

Tate, Stephen (författare): SCIEX Ltd, Concord, ON L4K4 V8, Canada.

Sachsenberg, Timo (författare): Univ Tubingen, Ctr Bioinformat, Dept Comp Sci, Sand 14, D-72076 Tubingen, Germany.

Walzer, Mathias (författare): European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.

Käll, Lukas, 1969- (författare): KTH,Science for Life Laboratory, SciLifeLab

Delanghe, Bernard (författare): Thermo Fisher Sci Bremen, Hanna Kunath Str 11, D-28199 Bremen, Germany.

Boecker, Sebastian (författare): Friedrich Schiller Univ Jena, Bioinformat, D-07743 Jena, Germany.

Schymanski, Emma L. (författare): Univ Luxembourg, Luxembourg Ctr Syst Biomed, 6 Ave Swing, L-4367 Belvaux, Luxembourg.

Wilmes, Paul (författare): Univ Luxembourg, Luxembourg Ctr Syst Biomed, 6 Ave Swing, L-4367 Belvaux, Luxembourg.

Dorfer, Viktoria (författare): Univ Appl Sci Upper Austria, Bioinformat Res Grp, A-4232 Hagenberg, Austria.

Kuster, Bernhard (författare): Tech Univ Munich, Prote & Bioanalyt, D-85354 Freising Weihenstephan, Germany.;Tech Univ Munich, Bavarian Biomol Mass Spectrometry Ctr, D-85354 Freising Weihenstephan, Germany.

Volders, Pieter-Jan (författare): Univ Gent VIB, Ctr Med Biotechnol, B-9000 Ghent, Belgium.

Jehmlich, Nico (författare): UFZ Helmholtz Ctr Environm Res, D-04318 Leipzig, Germany.

Vissers, Johannes P. C. (författare): Waters Corp, Wilmslow SK9 4AX, Cheshire, England.

Wolan, Dennis W. (författare): Scripps Res Inst, Dept Mol Med, La Jolla, CA 92037 USA.

Wang, Ana Y. (författare): Scripps Res Inst, Dept Mol Med, La Jolla, CA 92037 USA.

Mendoza, Luis (författare): Inst Syst Biol, Seattle, WA 98109 USA.

Shofstahl, Jim (författare): Thermo Fisher Sci, 355 River Oaks Pkwy, San Jose, CA 95134 USA.

Dowsey, Andrew W. (författare): Univ Bristol, Dept Populat Hlth Sci, Fac Hlth Sci, Bristol BS9 1BN, Avon, England.;Univ Bristol, Bristol Vet Sch, Fac Hlth Sci, Bristol BS9 1BN, Avon, England.

Griss, Johannes (författare): Med Univ Vienna, Div Immunol Allergy & Infect Dis, Dept Dermatol, Wahringer Gurtel 18-20, A-1090 Vienna, Austria.

Salek, Reza M. (författare): Int Agcy Res Canc, 150 Cours Albert Thomas, F-69372 Lyon 08, France.

Neumann, Steffen (författare): Leibniz Inst Plant Biochem, Dept Stress & Dev Biol, D-06120 Halle, Germany.;German Ctr Integrat Biodivers Res IDiv, D-04103 Leipzig, Germany.

Binz, Pierre-Alain (författare): CHU Vaudois, Clin Chem Serv, CH-1011 Lausanne, Switzerland.

Lam, Henry (författare): Hong Kong Univ Sci & Technol, Dept Chem & Biol Engn, Clear Water Bay, Hong Kong 999077, Peoples R China.

Vizcaino, Juan Antonio (författare): European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.

Bandeira, Nuno (författare): Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, Dept Comp Sci & Engn, Ctr Computat Mass Spectrometry, San Diego, CA 92093 USA.

Rost, Hannes (författare): Univ Toronto, Donnelly Ctr, 160 Coll St, Toronto, ON M5S 3E1, Canada.

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Inst Syst Biol, Seattle, WA 98109 USA European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England. (creator_code:org_t)

2018-10-01
2018
Engelska.
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 17:12, s. 4051-4060

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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.

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Expanding the Use of Spectral Libraries in Proteomics

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