Use of de novo sequencing for proteins identification
peer-reviewed · Biomeditsinskaya Khimiya · 2017
| Date | 2017-07-01 |
| Type | peer-reviewed |
| Venue | Biomeditsinskaya Khimiya |
| Publisher | Institute of Biochemistry |
| Contribution | benchmark |
| DOI | 10.18097/pbmc20176304341 |
| Citations (OpenAlex) | 1 |
Abstract
Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) (“Sigma-Aldrich”, USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS was performed using pure UPS2 and UPS2 mixtures with E. coli extract and human plasma samples. Protein detection was based on identification of at least two peptides of 9 residues in length or one peptide containing at least 13 residues. Using these criteria 13 (Novor), 20 (PEAKS) and 11 (PepNovo+) proteins were detected in pure UPS2 sample. Protein identifications in mixed samples were comparable or worse. Better results (by ~20%) were obtained using prediction included high quality identified fragment (TAG) containing at least 7 residues and unidentified additional masses at N- and C-termini (PepNovo+). The latter approach confidently recognized mass-spectrometric artefacts (and probably PTM). Atypical mass changes missed in UNIMOD DB were found (PepNovo+) to be statistically significant at the C-terminus (+23.02, +26.04 and +27.03). Using peptides containing these modifications and milder detection threshold 41 of 48 UPS2 proteins were identified.
Methods and tools
- De novo protein identification comparison (UPS2): Compares Novor, PEAKS and PepNovo+ for identifying the 48 proteins of the UPS2 standard, pure and spiked into E. coli and human plasma.