The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires
peer-reviewed · Molecular & Cellular Proteomics · 2021
| Date | 2021-07-23 |
| Type | peer-reviewed |
| Venue | Molecular & Cellular Proteomics |
| Publisher | Elsevier BV |
| Contribution | benchmark |
| DOI | 10.1016/j.mcpro.2021.100124 |
| Citations (OpenAlex) | 36 |
| Venue 2-year citedness | 4.69 |
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. Utilizing data from single HLA allele expressing cell lines, we observed significant differences in amino acid frequency among the peptides reported, with a broadly higher representation of hydrophobic amino acids L, I, P, and V reported by Peaks. We validated these results using data generated with a synthetic library of 2000 HLA-associated peptides from four common HLA alleles with distinct anchor residues. Our investigation highlights that search engines create a bias in peptide sequence depth and peptide amino acid composition, and resulting data should be interpreted with caution.
Methods and tools
- Immunopeptidomics search engine comparison (PEAKS vs database engines): Compares the de novo-assisted PEAKS DB search with MaxQuant, Comet and MS-GF+ on HLA class I immunopeptidomics data and a synthetic peptide library. PEAKS reported substantially more peptides, with a bias towards hydrophobic residues.
Methods it uses
Data deposited
- The choice of search engine affects sequencing depth and HLA allele-specific peptide repertoires — as deposited · PXD025655
- The choice of search engine for interpretation of immunopeptidomics datasets affects the sequencing depth and the extent of detected HLA allele-specific peptide repertoires — as deposited · PXD023202