PXD072997-1

PXD072997 is an original dataset announced via ProteomeXchange.

Title	Dimethyl Sulfoxide Enhances HLA Peptide Identification
Description	Immunopeptidomics relies on LC-MS/MS for comprehensive profiling of HLA-bound peptides, yet detection remains challenging due to their non-tryptic nature, variable lengths, and lack of basic residues, which limit ionisation and fragmentation efficiency. To address these limitations, we investigated the impact of incorporating 5% dimethyl sulfoxide (DMSO) into LC-MS/MS mobile phase buffers on immunopeptidomic workflows. Using B-lymphoblastoid cell lines expressing HLA class I and II alleles and elastase-digested HeLa lysates as a surrogate for non-tryptic peptides, we assessed peptide identification, ionisation efficiency, charge state distribution, and fragmentation quality. DMSO significantly increased peptide identifications across all sample types, with gains of ~1.33-fold for HLA class I, ~1.55-fold for HLA class II, and ~1.24-fold for elastase digests. Improvements were systematic and reproducible, driven by enhanced electrospray ionisation, higher charge states, and superior MS2 spectral quality, evidenced by a two-fold increase in b- and y-ion intensities. Importantly, DMSO did not introduce major sequence bias, preserving motif integrity and predicted binding characteristics. Overall, these findings establish DMSO as a robust additive for improving sensitivity and reliability in immunopeptidomics, particularly for low-input or clinically derived samples.
HostingRepository	PRIDE
AnnounceDate	2026-03-30
AnnouncementXML	Submission_2026-03-29_16:47:05.539.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Terry Lim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-13 01:30:22	ID requested
⏵ 1	2026-03-29 16:47:06	announced

10.3390/proteomes14010013;

Lim Kam Sian TCC, Ding Y, Blundell SA, Schittenhelm RB, Faridi P, Dimethyl Sulfoxide Enhances HLA Peptide Identification. Proteomes, 14(1):(2026) [pubmed]

submitter keyword: Immunopeptidomics, DMSO, supercharging

Pouya Faridi
contact affiliation	1 Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia. Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Australia. 2 Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Australia. 3 Monash Proteomics and Metabolomics Platform, Clinical Proteomics Node, School of Clinical Sciences, Monash University, Clayton, Australia
contact email	pouya.faridi@monash.edu
lab head
Terry Lim
contact affiliation	Monash University
contact email	terry.lim@monash.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD072997
     1. Label: PRIDE project
     2. Name: Dimethyl Sulfoxide Enhances HLA Peptide Identification