Validation of De Novo Peptide Sequences with Bottom-Up Tag Convolution
peer-reviewed · Proteomes · 2021
| Date | 2021-12-29 |
| Type | peer-reviewed |
| Venue | Proteomes |
| Publisher | MDPI AG |
| Contribution | post-processor |
| DOI | 10.3390/proteomes10010001 |
| Citations (OpenAlex) | 3 |
Abstract
De novo sequencing is indispensable for the analysis of proteins from organisms with unknown genomes, novel splice variants, and antibodies. However, despite a variety of methods developed to this end, distinguishing between the correct interpretation of a mass spectrum and a number of incorrect alternatives often remains a challenge. Tag convolution is computed for a set of peptide sequence tags of a fixed length k generated from the input tandem mass spectra and can be viewed as a generalization of the well-known spectral convolution. We demonstrate its utility for validating de novo peptide sequences by using a set of those generated by the algorithm PepNovo+ from high-resolution bottom-up data sets for carbonic anhydrase 2 and the Fab region of alemtuzumab and indicate its further potential applications.
Methods and tools
- Bottom-up tag convolution: Tells a correct spectrum interpretation from its plausible alternatives by convolving the set of length-k sequence tags a candidate implies, attacking the step de novo sequencing is weakest at: not producing a sequence but choosing between the ones it produced.
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