PXD062213-1

PXD062213 is an original dataset announced via ProteomeXchange.

Title	CoMPaseD - Protease Score Prediction for the Analysis of Small Proteins
Description	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.
HostingRepository	PRIDE
AnnounceDate	2026-01-23
AnnouncementXML	Submission_2026-01-23_01:30:13.896.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juergen Bartel
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: NEWT:224308;
ModificationList	carbamoylated residue; monohydroxylated residue; iodoacetic acid derivatized residue; deamidated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-25 08:02:39	ID requested
⏵ 1	2026-01-23 01:30:14	announced

Bartel J, Kaulich PT, Ferrero-Bordera B, Gelhausen R, Backofen R, Tholey A, Maa, ß S, CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins. Microlife, 7():uqaf043(2026) [pubmed]

10.1093/femsml/uqaf043;

submitter keyword: Bacillus subtilis, Orbitrap Elite, alternative proteases, GluC, LysArgiNase

Dörte Becher
contact affiliation	University of Greifswald, Institute for Microbiology, Department for Microbial Proteomics
contact email	dbecher@uni-greifswald.de
lab head
Juergen Bartel
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	juergen.bartel@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD062213

PRIDE project URI

• PRIDE
  1. PXD062213
     1. Label: PRIDE project
     2. Name: CoMPaseD - Protease Score Prediction for the Analysis of Small Proteins