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Expanding the Use of Spectral Libraries in Proteomics
journal contribution
posted on 2018-10-01, 00:00 authored by Eric W. Deutsch, Yasset Perez-Riverol, Robert J. Chalkley, Mathias Wilhelm, Stephen Tate, Timo Sachsenberg, Mathias Walzer, Lukas Käll, Bernard Delanghe, Sebastian Böcker, Emma L. Schymanski, Paul Wilmes, Viktoria Dorfer, Bernhard Kuster, Pieter-Jan Volders, Nico Jehmlich, Johannes P. C. Vissers, Dennis W. Wolan, Ana Y. Wang, Luis Mendoza, Jim Shofstahl, Andrew W. Dowsey, Johannes Griss, Reza M. Salek, Steffen Neumann, Pierre-Alain Binz, Henry Lam, Juan Antonio Vizcaíno, Nuno Bandeira, Hannes RöstThe 2017 Dagstuhl
Seminar on Computational Proteomics provided
an opportunity for a broad discussion on 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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future directionsmetadata requirementssignature ionspeptide tandem mass spectrometryas-yet-unidentified spectrapeptide ionSpectral LibrariesProteomics Standards Initiative-approvedlibrary formatrepresentative spectraproteomics datasets2017 Dagstuhl SeminarComputational Proteomicslibrary formatspeak annotation levelfragment ionencoding mass modifications
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