In-depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values.

ABSTRACT: Considering as one of the major goals in quantitative proteomics, detection of the differentially expressed proteins (DEPs) plays an important role in biomarker selection and clinical diagnostics. There have been plenty of algorithms and tools focusing on DEP detection in proteomics research. However, due to the different application scopes of these methods, and various kinds of experiment designs, it is not very apparent about the best choice for large-scale proteomics data analyses. Moreover, given the fact that proteomics data usually contain high percentage of missing values (MVs), but few replicates, a systematic evaluation of the DEP detection methods combined with the MV imputation methods is essential and urgent. Here, we analyzed a total of four representative imputation methods a

SUBMITTER: Wang J 

PROVIDER: S-EPMC5469784 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature