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Shedding light on black boxes in protein identification

(2014) PROTEOMICS. 14(9). p.1001-1005
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Bioinformatics: from nucleotids to networks (N2N)
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 . 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.
Keywords
PRIDE, TIME, METRICS, RESOURCES, QUALITY, MASS-SPECTROMETRY, SAMPLE PREPARATION, Tutorial, TOOL, SPECTROMETRY-BASED PROTEOMICS, Publication Guidelines, Protein Identification, Open Source, Bioinformatics

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Citation

Please use this url to cite or link to this publication:

Chicago
Vaudel, Marc, A Saskia Venne, Frode S Berven, René P Zahedi, Lennart Martens, and Harald Barsnes. 2014. “Shedding Light on Black Boxes in Protein Identification.” Proteomics 14 (9): 1001–1005.
APA
Vaudel, M., Venne, A. S., Berven, F. S., Zahedi, R. P., Martens, L., & Barsnes, H. (2014). Shedding light on black boxes in protein identification. PROTEOMICS, 14(9), 1001–1005.
Vancouver
1.
Vaudel M, Venne AS, Berven FS, Zahedi RP, Martens L, Barsnes H. Shedding light on black boxes in protein identification. PROTEOMICS. 2014;14(9):1001–5.
MLA
Vaudel, Marc, A Saskia Venne, Frode S Berven, et al. “Shedding Light on Black Boxes in Protein Identification.” PROTEOMICS 14.9 (2014): 1001–1005. Print.
@article{4397373,
  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 . 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.},
  author       = {Vaudel, Marc and Venne, A Saskia and Berven, Frode S and Zahedi, Ren{\'e} P and Martens, Lennart and Barsnes, Harald},
  issn         = {1615-9853},
  journal      = {PROTEOMICS},
  keyword      = {PRIDE,TIME,METRICS,RESOURCES,QUALITY,MASS-SPECTROMETRY,SAMPLE PREPARATION,Tutorial,TOOL,SPECTROMETRY-BASED PROTEOMICS,Publication Guidelines,Protein Identification,Open Source,Bioinformatics},
  language     = {eng},
  number       = {9},
  pages        = {1001--1005},
  title        = {Shedding light on black boxes in protein identification},
  url          = {http://dx.doi.org/10.1002/pmic.201300488},
  volume       = {14},
  year         = {2014},
}

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