publication . Article . 2017

A community proposal to integrate proteomics activities in ELIXIR

Juan Antonio Vizcaíno; Mathias Walzer; Rafael C. Jiménez; Wout Bittremieux; David Bouyssié; Christine Carapito; Fernando Corrales; Myriam Ferro; Albert J.R. Heck; Peter Horvatovich; ...
Open Access English
  • Published: 13 Jun 2017
Abstract
We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).
Subjects
free text keywords: Biology and Life Sciences, Chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV]Life Sciences [q-bio], To be checked by Faculty, Opinion Article, Articles, Protein Chemistry & Proteomics, Science & Medical Policies, mass spectrometry, computational proteomics, databases, bioinformatics infrastructure, data standards, training, multi-omics approaches., White paper, Portfolio, Elixir, Bioinformatics, Proteomics, Data science, Medicine, business.industry, business
Funded by
EC| ELIXIR-EXCELERATE
Project
ELIXIR-EXCELERATE
ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
  • Funder: European Commission (EC)
  • Project Code: 676559
  • Funding stream: H2020 | RIA
21 references, page 1 of 2

Mallick P, Kuster B: Proteomics: a pragmatic perspective. Nat Biotechnol. 2010; 28(7): 695-709.

PubMed Abstract | Publisher Full Text Aebersold R, Mann M: Mass-spectrometric exploration of proteome structure and function. Nature. 2016; 537(7620): 347-55.

PubMed Abstract | Publisher Full Text Menschaert G, Fenyö D: Proteogenomics from a bioinformatics angle: A growing ifeld. Mass Spectrom Rev. 2015.

PubMed Abstract | Publisher Full Text Cox J, Mann M: MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008; 26(12): 1367-72.

PubMed Abstract | Publisher Full Text Röst HL, Sachsenberg T, Aiche S, et al.: OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016; 13(9): 741-8.

PubMed Abstract | Publisher Full Text Barsnes H, Vaudel M, Colaert N, et al.: compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinformatics. 2011; 12: 70.

PubMed Abstract | Publisher Full Text | Free Full Text Vaudel M, Burkhart JM, Zahedi RP, et al.: PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nat Biotechnol. 2015; 33(1): 22-4.

PubMed Abstract | Publisher Full Text Vizcaino JA, Csordas A, del-Toro N, et al.: 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016; 44(D1): D447-56.

PubMed Abstract | Publisher Full Text | Free Full Text Deutsch EW, Csordas A, Sun Z, et al.: The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Nucleic Acids Res. 2017; 45(D1): D1100-D6.

PubMed Abstract | Publisher Full Text | Free Full Text Deutsch EW, Albar JP, Binz PA, et al.: Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Inform Assoc. 2015; 22(3): 495-506.

PubMed Abstract | Publisher Full Text | Free Full Text Uhlén M, Fagerberg L, Hallström BM, et al.: Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220): 1260419.

PubMed Abstract | Publisher Full Text 13. Lane L, Argoud-Puy G, Britan A, et al.: neXtProt: a knowledge platform for human proteins. Nucleic Acids Res. 2012; 40(Database issue): D76-83.

PubMed Abstract | Publisher Full Text | Free Full Text 15. Ison J, Rapacki K, Ménager H, et al.: Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res.

2016; 44(D1): D38-47.

21 references, page 1 of 2
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publication . Article . 2017

A community proposal to integrate proteomics activities in ELIXIR

Juan Antonio Vizcaíno; Mathias Walzer; Rafael C. Jiménez; Wout Bittremieux; David Bouyssié; Christine Carapito; Fernando Corrales; Myriam Ferro; Albert J.R. Heck; Peter Horvatovich; ...