PXD060854

PXD060854 is an original dataset announced via ProteomeXchange.

Title	Murine colon HUNTER N-terminomics
Description	The mammalian lysosomal protease legumain is often dysregulated in pathophysiological conditions including inflammation, neurodegeneration, and cancer, yet its proteolytic targets are poorly defined. To profile protease substrates degradomics techniques typically employ enrichment strategies to select for sub-stoichiometric and low abundant peptides generated from proteolytic cleavage. However, recent advancements in degradomics techniques have revealed N-termini enrichment can be circumvented if peptide-based fractionation is employed, enabling simultaneous proteome and N-terminome analysis. Herein, we compare the previously published enrichment free N-terminomics approach using high-field asymmetric waveform ion mobility spectrometry (FAIMS) to offline basic reverse-phase (bRP) fractionation to assess the complementarity of these fractionation methods for simultaneous proteomic and degradomic analysis. While at the protein levels FAIMS and bRP provide access to overlapping proteomic coverage, at the N-terminal level each fractionation technique reveals unique cleavage information. Combining fractionation approaches we identify 6,499 novel N-terminal peptides with N-terminal TMTpro labelling allowing the identification of cleavage events modulated in the context of Dextran Sulfate Sodium (DSS) induced colitis within wild type and legumain-deficient colons. Among these N-termini, we identify 35 putative legumain substrates in naïve and 41 in the DSS colons supporting legumain’s role in both pro-inflammatory and physiological conditions. Use of an additional negative selection method, High-efficiency Undecanal-based N-Termini EnRichment (HUNTER), further validated and supplemented this list of identified legumain substrates. Combined, this study identifies multiple putative substrates of legumain in healthy and inflamed murine colons as well as the utility of using complementary fractionation approaches for degradomics studies.
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-28_16:06:43.385.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexander Ziegler
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-16 17:41:33	ID requested
⏵ 1	2025-09-28 16:06:44	announced

10.1002/pro.70186;

Ziegler AR, Anderson BM, Latorre R, McQuade RM, Dufour A, Schmidt BL, Bunnett NW, Scott NE, Edgington-Mitchell LE, ve and inflamed murine colon reveals proteolytic signatures of legumain. J Cell Physiol, 240(1):e31466(2025) [pubmed]

Ziegler AR, Parker BL, Scott NE, Edgington-Mitchell LE, ve and inflamed colon tissue. Protein Sci, 34(10):e70186(2025) [pubmed]

10.1002/jcp.31466;

submitter keyword: legumain, mouse, colon, colitis,HUNTER

Laura Edgington-Mitchell
contact affiliation	Department of Biochemistry and Pharmacology Bio21 Institute, University of Melbourne
contact email	laura.edgingtonmitchell@unimelb.edu.au
lab head
Alexander Ziegler
contact affiliation	University of Melbourne
contact email	azzi@student.unimelb.edu.au
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/2025/09/PXD060854

PRIDE project URI

• PRIDE
  1. PXD060854
     1. Label: PRIDE project
     2. Name: Murine colon HUNTER N-terminomics