PASS: De novo assembler for short peptide sequences
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arXiv
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| Format: | Preprint |
| Published: |
2022
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| _version_ | 1866916835784392704 |
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| author | Warren, René L. |
| author_facet | Warren, René L. |
| contents | 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 |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2208_05598 |
| institution | arXiv |
| publishDate | 2022 |
| record_format | arxiv |
| spellingShingle | PASS: De novo assembler for short peptide sequences Warren, René L. Genomics Biomolecules 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 |
| title | PASS: De novo assembler for short peptide sequences |
| topic | Genomics Biomolecules |
| url | https://arxiv.org/abs/2208.05598 |