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J Proteome Res. 2010 Dec 3;9(12):6288-97. doi: 10.1021/pr1005586. Epub 2010 Nov 10.

The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics.

Author information

1
Department of Chemistry, School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States.

Abstract

Peptide detectability is defined as the probability that a peptide is identified in an LC-MS/MS experiment and has been useful in providing solutions to protein inference and label-free quantification. Previously, predictors for peptide detectability trained on standard or complex samples were proposed. Although the models trained on complex samples may benefit from the large training data sets, it is unclear to what extent they are affected by the unequal abundances of identified proteins. To address this challenge and improve detectability prediction, we present a new algorithm for the iterative learning of peptide detectability from complex mixtures. We provide evidence that the new method approximates detectability with useful accuracy and, based on its design, can be used to interpret the outcome of other learning strategies. We studied the properties of peptides from the bacterium Deinococcus radiodurans and found that at standard quantities, its tryptic peptides can be roughly classified as either detectable or undetectable, with a relatively small fraction having medium detectability. We extend the concept of detectability from peptides to proteins and apply the model to predict the behavior of a replicate LC-MS/MS experiment from a single analysis. Finally, our study summarizes a theoretical framework for peptide/protein identification and label-free quantification.

PMID:
21067214
PMCID:
PMC3006185
DOI:
10.1021/pr1005586
[Indexed for MEDLINE]
Free PMC Article
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