PXD047261-2

PXD047261 is an original dataset announced via ProteomeXchange.

Title	CLIPPER 2.0: Peptide level annotation and data analysis for positional proteomics
Description	Positional proteomics methodologies have transformed protease research and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable generation of enormous positional proteomics datasets of protein termini and neo-termini of cleaved protease substrates. However, such progress has not been observed to the same extent in data analysis and post-processing steps, which arguably constitute the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms, and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:37:57.318.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Konstantinos Kalogeropoulos
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; dimethylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-27 02:31:18	ID requested
1	2024-05-02 04:05:10	announced
⏵ 2	2024-10-22 06:37:57	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: LC-MS, post-translational modification, positional proteomics, computational proteomics, degradomics

Konstantinos Kalogeropoulos
contact affiliation	DTU Bioengineering
contact email	konka@dtu.dk
lab head
Konstantinos Kalogeropoulos
contact affiliation	Technical University of Denmark
contact email	konskalogero@gmail.com
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/2024/05/PXD047261

PRIDE project URI

• PRIDE
  1. PXD047261
     1. Label: PRIDE project
     2. Name: CLIPPER 2.0: Peptide level annotation and data analysis for positional proteomics