Reference : Expanding the use of spectral libraries in proteomics.
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
Systems Biomedicine; Computational Sciences
http://hdl.handle.net/10993/37401
Expanding the use of spectral libraries in proteomics.
English
Deutsch, Eric W. [> >]
Perez-Riverol, Yasset [> >]
Chalkley, Robert J. [> >]
Wilhelm, Mathias [> >]
Tate, Stephen [> >]
Sachsenberg, Timo [> >]
Walzer, Mathias [> >]
Kall, Lukas [> >]
Delanghe, Bernard [> >]
Bocker, Sebastian [> >]
Schymanski, Emma mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Dorfer, Viktoria [> >]
Kuster, Bernhard [> >]
Volders, Pieter-Jan [> >]
Jehmlich, Nico [> >]
Vissers, Johannes P. C. [> >]
Wolan, Dennis W. [> >]
Wang, Ana Y. [> >]
Mendoza, Luis [> >]
Shofstahl, Jim [> >]
Dowsey, Andrew W. [> >]
Griss, Johannes [> >]
Salek, Reza M. [> >]
Neumann, Steffen [> >]
Binz, Pierre-Alain [> >]
Lam, Henry [> >]
Vizcaino, Juan Antonio [> >]
Bandeira, Nuno [> >]
Rost, Hannes [> >]
2018
Journal of proteome research
Yes (verified by ORBilu)
International
1535-3893
1535-3907
United States
[en] The 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 capture 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.
http://hdl.handle.net/10993/37401
10.1021/acs.jproteome.8b00485

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Limited access
Deutsch-Röst_2018_JPR_ExpandingSpecLibsProteomics.pdfAuthor postprint897.44 kBRequest a copy

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.