{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/pass-de-novo-assembler-for-short-peptide","title":"PASS: De novo assembler for short peptide sequences","arxiv_id":"2208.05598","date":"2022-08-11","proceeding":null,"authors":["René L. Warren"],"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","url_abs":"https://arxiv.org/abs/2208.05598v1","url_pdf":"https://arxiv.org/pdf/2208.05598v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"pass-de-novo-assembler-for-short-peptide","repo_url":"https://github.com/warrenlr/pass","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}