TY - JOUR
T1 - ProteoClade
T2 - A taxonomic toolkit for multispecies and metaproteomic analysis
AU - Mooradian, Arshag D.
AU - Van Der Post, Sjoerd
AU - Naegle, Kristen M.
AU - Held, Jason M.
N1 - Publisher Copyright:
© 2020 Mooradian et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2020
Y1 - 2020
N2 - We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patientderived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.
AB - We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patientderived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.
UR - http://www.scopus.com/inward/record.url?scp=85082145304&partnerID=8YFLogxK
U2 - 10.1371/journal.pcbi.1007741
DO - 10.1371/journal.pcbi.1007741
M3 - Article
C2 - 32150535
AN - SCOPUS:85082145304
SN - 1553-734X
VL - 16
JO - PLoS computational biology
JF - PLoS computational biology
IS - 3
M1 - e1007741
ER -