2007
DOI: 10.1002/pmic.200601034
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Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry

Abstract: LC-MS/MS with certain labeling techniques such as isotope-coded affinity tag (ICAT) enables quantitative analysis of paired protein samples. However, current identification and quantification of differentially expressed peptides (and proteins) are not reliable for large proteomics screening of complex biological samples. The number of replicates is often limited because of the high cost of experiments and the limited supply of samples. Traditionally, a simple fold change cutoff is used, which results in a high… Show more

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Cited by 22 publications
(25 citation statements)
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“…is quickly becoming a major focus of investigation in quantitative proteomics studies (e.g. see Refs [23,40,41,68]). It is often the case that sample fractionation and enrichment strategies are necessary to provide greater depth of coverage.…”
Section: Discussionmentioning
confidence: 99%
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“…is quickly becoming a major focus of investigation in quantitative proteomics studies (e.g. see Refs [23,40,41,68]). It is often the case that sample fractionation and enrichment strategies are necessary to provide greater depth of coverage.…”
Section: Discussionmentioning
confidence: 99%
“…This is mainly due to the fact that the analysis is performed on the peptide products of the starting mixture en masse without any measurement of the intact proteins, such that isoforms remain unresolved and proteolytic products are masked by the intact species if both are present. The lower statistical power stems mainly from the fact that the mass spectrometer is sampling ions for tandem MS based on relative signal intensities that can vary from run to run [40,41], requiring many technical replicates for each independent sample to attain acceptable levels of statistical power.…”
Section: Multidimensional Lc/ms/ms Strategies: Procedures and Applicatmentioning
confidence: 99%
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“…It is now established that fold-change thresholds cannot be used for determining DRFs with high confidence [78]. Methods to estimate significant fold-changes from the ratio distribution rely on the assumptions that first only a tiny fraction of the proteins is regulated and second the variance of each protein is given by the distribution width, preventing a rigorous evaluation of statistical significance.…”
Section: Detection Of Differentially Regulated Ptm Proteoformsmentioning
confidence: 99%