Journal article
Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods
Journal of Proteome Research, Vol.16(7), pp.2359-2369
2017
Abstract
Tandem mass spectrometry is one of the most popular techniques for quantitation of proteomes. There exists a large variety of options in each stage of data preprocessing that impact the bias and variance of the summarized protein-level values. Using a newly released data set satisfying a replicated Latin squares design, a diverse set of performance metrics has been developed and implemented in a web-based application, Quantitative Performance Evaluator for Proteomics (QPEP). QPEP has the flexibility to allow users to apply their own method to preprocess this data set and share the results, allowing direct and straightforward comparison of new methodologies. Application of these new metrics to three case studies highlights that (i) the summarization of peptides to proteins is robust to the choice of peptide summary used, (ii) the differences between iTRAQ labels are stronger than the differences between experimental runs, and (iii) the commercial software ProteinPilot performs equivalently well at between-sample normalization to more complicated methods developed by academics. Importantly, finding (ii) underscores the benefits of using the principles of randomization and blocking to avoid the experimental measurements being confounded by technical factors. Data are available via ProteomeXchange with identifier PXD003608.
Details
- Title
- Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods
- Authors/Creators
- D. Strbenac (Author/Creator)L. Zhong (Author/Creator)M.J. Raftery (Author/Creator)P. Wang (Author/Creator)S.R. Wilson (Author/Creator)N.J. Armstrong (Author/Creator)J.Y.H. Yang (Author/Creator)
- Publication Details
- Journal of Proteome Research, Vol.16(7), pp.2359-2369
- Publisher
- American Chemical Society
- Identifiers
- 991005543494507891
- Copyright
- © 2017 American Chemical Society
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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Source: InCites
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- Collaboration types
- Domestic collaboration
- Citation topics
- 2 Chemistry
- 2.211 Mass Spectrometry
- 2.211.497 Proteomics Mass Spectrometry
- Web Of Science research areas
- Biochemical Research Methods
- ESI research areas
- Biology & Biochemistry