PXD077371-1

PXD077371 is an original dataset announced via ProteomeXchange.

Title	qXL-MS of insulin resistance in C2C12 myotubes
Description	C2C12 myotubes were made insulin resistant with 0.5 mM palmitic acid for 24 h along with non-treated controls and then each group stimulated with or without 100 nM insulin for 30 min (n=4 each). Cells were then cross-linked with 2 mM of tPhoX for a further 30 min in the presence of insulin and the reaction quenched as previously described (Jiang et al., 2022). To increase the depth of analysis, each sample was subjected to a crude biochemical-based separation into four fractions (Wong et al., 2025) followed by digestion with trypsin/LysC. The 16 samples from each fraction were labelled with 16-plex Tandem Mass Tags (TMT) and pooled, followed by the depletion of phosphopeptides and enrichment of XL-peptides using immobilised metal-ion affinity chromatography (IMAC). Each of the four biochemical fractions underwent peptide-level size-exclusion chromatography (SEC) to partially fractionate larger XL-peptides from mono-/loop-linked peptides in 2-3 fractions which were further separated by high pH reversed-phase chromatography into 12 fractions and analysed by LC-MS/MS using data-dependent acquisition (DDA) resulting in the analysis of 132 individual runs. Data were analysed with pLink2 and searched against a skeletal muscle-specific mouse proteome database to limit the search space with filtering to 1% FDR followed by reporter-ion quantification and statistical analysis
HostingRepository	PRIDE
AnnounceDate	2026-05-29
AnnouncementXML	Submission_2026-05-28_18:16:13.786.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Benjamin Parker
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-19 23:29:22	ID requested
⏵ 1	2026-05-28 18:16:14	announced

Dataset with its publication pending

submitter keyword: TMT, C2C12,tPhoX

Benjamin Parker
contact affiliation	The University of Melbourne
contact email	ben.parker@unimelb.edu.au
lab head
Benjamin Parker
contact affiliation	The University of Melbourne
contact email	ben.parker@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/2026/05/PXD077371

PRIDE project URI

• PRIDE
  1. PXD077371
     1. Label: PRIDE project
     2. Name: qXL-MS of insulin resistance in C2C12 myotubes