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Adaptation of immunoaffinity protocol for the isolation of the cell line immunopeptides - immunopeptidomics part

ABSTRACT: BACKGROUND: The peptide repertoire presented by Human Leukocyte Antigens (HLA) provides a snapshot of intracellular proteins, which is monitored by the immune system. Although mass spectrometry is the gold standard for identification of these peptides, the upstream steps of the immunopeptidomics workflow, including immunoprecipitation and peptides purification, vary and critically impact the peptide yield.AIM: To optimize conditions for the isolation of a larger number of HLA I ligands.METHODS: Immunopeptidomes from cell lines were isolated using immunoaffinity followed by liquid chromatography-mass spectrometry analysis. Cell lines were lysed with various detergents (CHAPS, NP-40, SOD, Triton X-100) and eluted with TFA, urea, or thiocarbamate solutions.RESULTS: We optimized a protocol for immunoprecipitating peptide-HLA complexes and found that the number of identified peptides scales with the number of input cells, while being unaffected by the choice of lysis buffer.CONCLUSION: The optimized protocol allows the isolation of HLA I ligand peptides from suspension cell lines.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Georgij Arapidi

LAB HEAD: Georgij Arapidi

PROVIDER: PXD077041 | Pride | 2026-04-15

REPOSITORIES: Pride

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			Action	DRS
	070521P264.dat	Other
	070521P264.mgf	Mgf
	070521P264.mzid	Mzid
	070521P264.mzid_070521P264.MGF	Mzid
	070521P264.raw	Raw

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