PASS: De novo assembler for short peptide sequences
preprint · arXiv · 2022
| Date | 2022-08-11 |
| Type | preprint |
| Venue | arXiv |
| Contribution | post-processor |
| DOI | 10.48550/arxiv.2208.05598 |
| Citations (OpenAlex) | 0 |
Abstract
The ability to characterize proteins at sequence-level resolution is vital to biological research. Currently, the leading method for protein sequencing is by liquid chromatography mass spectrometry (LC-MS) whereas proteins are reduced to their constituent peptides by enzymatic digest and subsequently analyzed on an LC-MS instrument. The short peptide sequences that result from this analysis are used to characterize the original protein content of the sample. Here we present PASS, a de novo assembler for short peptide sequences that can be used to reconstruct large portions of protein targets, a step that can facilitate downstream sample characterization efforts. We show how, with adequate peptide sequence coverage and little-to-no additional sequence processing, PASS reconstructs protein sequences into relatively large (100 amino acid or longer) contigs having high (93.1 - 99.1%) sequence identity to reference antibody light and heavy chain proteins. Availability: PASS is released under the GNU General Public License Version 3 (GPLv3) and is publicly available from https://github.com/warrenlr/PASS
Methods and tools
- PASS: A de novo assembler for short peptide sequences that reconstructs protein targets into contigs of 100 residues or more from LC-MS/MS peptide reads.