Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
نویسندگان
چکیده
منابع مشابه
Analyzing marginal cases in differential shotgun proteomics
SUMMARY We present an approach to statistically pinpoint differentially expressed proteins that have quantitation values near the quantitation threshold and are not identified in all replicates (marginal cases). Our method uses a Bayesian strategy to combine parametric statistics with an empirical distribution built from the reproducibility quality of the technical replicates. AVAILABILITY Th...
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The shotgun proteomic strategy based on digesting proteins into peptides and sequencing them using tandem mass spectrometry and automated database searching has become the method of choice for identifying proteins in most large scale studies. However, the peptide-centric nature of shotgun proteomics complicates the analysis and biological interpretation of the data especially in the case of hig...
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Proteomics technology is progressing at an incredible rate. The latest generation of tandem mass spectrometers can now acquire tens of thousands of fragmentation spectra in a matter of hours. Furthermore, quantitative proteomics methods have been developed that incorporate a stable isotope-labeled internal standard for every peptide within a complex protein mixture for the measurement of relati...
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A new result report for Mascot search results is described. A greedy set cover algorithm is used to create a minimal set of proteins, which is then grouped into families on the basis of shared peptide matches. Protein families with multiple members are represented by dendrograms, generated by hierarchical clustering using the score of the nonshared peptide matches as a distance metric. The pept...
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ژورنال
عنوان ژورنال: Current Protocols in Bioinformatics
سال: 2010
ISSN: 1934-3396,1934-340X
DOI: 10.1002/0471250953.bi1313s30