PASS: De novo assembler for short peptide sequences

TL;DR

PASS is a novel de novo assembler that reconstructs large protein segments from short peptide sequences obtained via LC-MS, significantly aiding protein characterization with high accuracy.

Contribution

It introduces PASS, a new assembler capable of reconstructing large protein contigs from short peptides, enhancing protein analysis workflows.

Findings

Reconstructs protein sequences into large contigs over 100 amino acids.

Achieves high sequence identity (93.1-99.1%) with reference proteins.

Effective with minimal additional sequence processing.

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