Zhang, W. & Sun, W. MS-based Immunopeptidomics Analysis with PEAKS Studio X. (Application Note). 1/11/2018.

Workflows for immunopeptidomics are different from ones for more established shotgun proteomics. There are inherent challenges with the abundance and natural complexity when doing mass spectrometry analysis for the exploration of human immunopeptidome (e.g. HLA class-I and class-II peptides). A new approach harnessed by PEAKS Studio X was integrated with PEAKS’ de novo sequencing and database searching workflow for HLA peptide identifications, which increased peptide sequencing coverage and confidence. In addition, by introducing a feature-based identification method, PEAKS Studio X can also resolve the identification challenge of co-eluting peptides. Comparing with PEAKS Studio 8.5 and MaxQuant, PEAKS Studio X results show an increase of 13% and 73% more peptides identified, respectively.