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MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments, part 2

ABSTRACT: We propose a new pipeline for the refinement of spectrum-peptide assignment, designed specifically for MHC ligand identification. By modeling the peptidome as a collection of a limited number of specificities, corresponding to the MHC alleles of the cell line, our method achieves increased sequencing depth, while at the same time removing potential experimental outliers and contaminants.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Nicola Ternette

LAB HEAD: Nicola Ternette

PROVIDER: PXD011794 | Pride | 2019-01-02

REPOSITORIES: Pride

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MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments.

Andreatta Massimo M Nicastri Annalisa A Peng Xu X Hancock Gemma G Dorrell Lucy L Ternette Nicola N Nielsen Morten M

Proteomics 20190118 4

LC-MS/MS has become the standard platform for the characterization of immunopeptidomes, the collection of peptides naturally presented by major histocompatibility complex molecules to the cell surface. The protocols and algorithms used for immunopeptidomics data analysis are based on tools developed for traditional bottom-up proteomics that address the identification of peptides generated by tryptic digestion. Such algorithms are generally not tailored to the specific requirements of MHC ligand ...[more]

PMID: 30578603

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