Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification.

ABSTRACT: Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here, we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between liquid chromatography-mass spectrometry runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in MS/MS spectra that can be used for quantification. Second

SUBMITTER: Yu SH 

PROVIDER: S-EPMC7586393 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature