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PROTEOMICS
Article
License: CC BY SA
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PROTEOMICS
Other literature type . Article . 2014 . Peer-reviewed
License: Wiley Online Library User Agreement
PROTEOMICS
Article . 2013
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Shedding light on black boxes in protein identification

Authors: Marc Vaudel; A. Saskia Venne; Frode S. Berven; René P. Zahedi; Lennart Martens; Harald Barsnes;

Shedding light on black boxes in protein identification

Abstract

Performing a well thought‐out proteomics data analysis can be a daunting task, especially for newcomers to the field. Even researchers experienced in the proteomics field can find it challenging to follow existing publication guidelines for MS‐based protein identification and characterization in detail. One of the primary goals of bioinformatics is to enable any researcher to interpret the vast amounts of data generated in modern biology, by providing user‐friendly and robust end‐user applications, clear documentation, and corresponding teaching materials. In that spirit, we here present an extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics‐for‐proteomics. The material is completely based on freely available and open‐source tools, and has already been used and refined at numerous international courses over the past 3 years. During this time, it has demonstrated its ability to allow even complete beginners to intuitively conduct advanced bioinformatics workflows, interpret the results, and understand their context. This tutorial is thus aimed at fully empowering users, by removing black boxes in the proteomics informatics pipeline.

Country
Norway
Subjects by Vocabulary

Microsoft Academic Graph classification: Computer science media_common.quotation_subject Context (language use) Field (computer science) Task (project management) Documentation Software Quality (business) media_common business.industry Data science Pipeline (software) Informatics business

Keywords

Proteomics, Protein Identification, Bioinformatics, :Midical sciences: 700::Basic medical, dental and veterinary sciences: 710::Medical biochemistry: 726 [VDP], Biochemistry, :Medisinske fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk biokjemi: 726 [VDP], Tutorial, Databases, Protein, Molecular Biology, Open Source, Computational Biology, Proteins, Publication Guidelines, Database Management Systems, Software

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    impulse
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    Top 10%
  • citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    20
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
20
Average
Average
Top 10%
Green
hybrid