The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires.

ABSTRACT: Standardization of immunopeptidomics experiments across laboratories is a pressing issue within the field, and currently a variety of different methods for sample preparation and data analysis tools are applied. Here, we compared different software packages to interrogate immunopeptidomics datasets and found that Peaks reproducibly reports substantially more peptide sequences (~30-70%) compared with Maxquant, Comet, and MS-GF+ at a global false discovery rate (FDR) of <1%. We noted that these differences are driven by search space and spectral ranking. Furthermore, we observed differences in the proportion of peptides binding the human leukocyte antigen (HLA) alleles present in the samples, indicating that sequence-related differences affected the performance of each tested engine. Utilizi

SUBMITTER: Parker R 

PROVIDER: S-EPMC8724928 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature