Proteomics

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CoMPaseD - Protease Score Prediction for the Analysis of Small Proteins

ABSTRACT: In proteome studies, the application of alternative proteases, exclusively or in addition to trypsin, often increases protein sequence or proteome coverage. It has recently been shown that, in particular, the analysis of small proteins benefits from such multi-protease approaches. In the accompanying manuscript, we present a protease score that enables the objective comparison of multiple-protease digestions and a Python-based tool named CoMPaseD (Comparison of Multiple Protease Digestions), that utilises Monte-Carlo simulations to predict this score for a user-defined set of proteases and any combination of these. This tool was validated by comparing CoMPaseD-predicted protease scores with experimentally derived protease scores for Bacillus subtilis total protein extracts. While data for three proteases (trypsin, Lys-C, chymotrypsin) were obtained from the dataset with the PRIDE identifier PXD017416, this submission contains additional data for the proteases Glu-C and LysArgiNase.

INSTRUMENT(S):

ORGANISM(S): Bacillus Subtilis Subsp. Subtilis Str. 168

SUBMITTER: Juergen Bartel  

LAB HEAD: Dörte Becher

PROVIDER: PXD062213 | Pride | 2026-01-23

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
201102_VE1_PM4_ToK_SPP_BSubt_LysArginase_1.raw Raw
201102_VE1_PM4_ToK_SPP_BSubt_LysArginase_2.raw Raw
201102_VE1_PM4_ToK_SPP_BSubt_LysArginase_3.raw Raw
201103_VE1_PM4_ToK_SPP_BSubt_GlutC_1.raw Raw
201103_VE1_PM4_ToK_SPP_BSubt_GlutC_2.raw Raw
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Publications

CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.

Bartel Jürgen J   Kaulich Philipp T PT   Ferrero-Bordera Borja B   Gelhausen Rick R   Backofen Rolf R   Tholey Andreas A   Maaß Sandra S  

microLife 20260106

In proteome studies, the application of alternative proteases, exclusively or in addition to trypsin, often increases protein sequence or proteome coverage. It has recently been shown that, in particular, the analysis of small proteins benefits from such multi-protease approaches. However, selecting the most optimal combination of proteases either requires laboursome experiments or the decision of an experienced user, which might be biased. In this manuscript, we present a protease score that en  ...[more]

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