  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
