Multibatch TMT Reveals False Positives, Batch Effects and Missing Values.

ABSTRACT: Multiplexing strategies for large-scale proteomic analyses have become increasingly prevalent, tandem mass tags (TMT) in particular. Here we used a large iPSC proteomic experiment with twenty-four 10-plex TMT batches to evaluate the effect of integrating multiple TMT batches within a single analysis. We identified a significant inflation rate of protein missing values as multiple batches are integrated and show that this pattern is aggravated at the peptide level. We also show that without normalization strategies to address the batch effects, the high precision of quantitation within a single multiplexed TMT batch is not reproduced when data from multiple TMT batches are integrated.Further, the incidence of false positives was studied by using Y chromosome peptides as an internal control.

SUBMITTER: Brenes A 

PROVIDER: S-EPMC6773557 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature