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Updated: Mar 29, 2026
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Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis
Published on: October 15, 2021
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Dimethyl Sulfoxide Enhances HLA Peptide Identification.
Terry C C Lim Kam Sian1,2,3, Yue Ding2, Scott A Blundell4
1Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
Proteomes
|March 27, 2026
Summary
Dimethyl sulfoxide (DMSO) enhances mass spectrometry (MS)-based immunopeptidomics by improving peptide detection. This robust additive boosts sensitivity and reliability for HLA-bound peptide profiling, especially in challenging samples.
Area of Science:
- Proteomics
- Immunology
- Analytical Chemistry
Background:
- Mass spectrometry (MS)-based immunopeptidomics is crucial for profiling HLA-bound peptides.
- Detection challenges include non-tryptic nature, variable lengths, and poor ionization/fragmentation of peptides.
- Existing workflows struggle with sensitivity and reliability.
Purpose of the Study:
- To investigate the impact of dimethyl sulfoxide (DMSO) on LC-MS/MS immunopeptidomic workflows.
- To assess DMSO's effect on peptide identification, ionization, charge state, and fragmentation.
- To determine if DMSO introduces sequence bias.
Main Methods:
- Incorporated 5% DMSO into LC-MS/MS mobile-phase buffers.
- Utilized B-lymphoblastoid cell lines (HLA class I/II) and elastase-digested HeLa lysates.
- Assessed peptide identification rates, ionization efficiency, charge state distribution, and MS2 spectral quality.
Main Results:
- DMSO significantly increased peptide identifications (~1.33x for HLA class I, ~1.55x for HLA class II, ~1.24x for digests).
- Improvements attributed to enhanced electrospray ionization, higher charge states, and superior MS2 spectra (~2x b/y ion intensity).
- DMSO did not introduce significant sequence bias, preserving motif integrity.
Conclusions:
- DMSO is a robust additive for enhancing immunopeptidomics sensitivity and reliability.
- Particularly beneficial for low-input or clinically derived samples.
- Facilitates more comprehensive HLA-bound peptide profiling.
