MassIVE MSV000082184

Imported Reanalysis Dataset Public PXD006939

High-throughput MS-based immunopeptidomics

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Description

Comprehensive knowledge of the HLA class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their extraction for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential extraction of HLA-I and -II peptides from up to 96 samples in a plate format from cell lines or tissues. Our methodology drastically reduces sample-handling and can be completed within six hours. We report identification and quantification of thousands of peptides with excellent reproducibility (Pearson correlations reaching 0.98 and 0.97, class I and II, respectively). Due to improved sensitivity, as many as 1,846 HLA-I and 2,633 HLA-II peptides were accurately identified from only 107 B-cells. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma. This straightforward method is applicable for basic and clinical applications. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: HLA peptides ; HLA-I ; HLA-II ; affinity purification ; LC-MS/MS

Contact

Principal Investigators:
(in alphabetical order) 		Michal Bassani-Sternberg, Head / Immunopeptidomics unit Department of Oncology,CHUV Ludwig Cancer Research Center, N/A
Submitting User: ccms

Publications

Chong C, Marino F, Pak H, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M.
High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferon?-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome.
Mol. Cell Proteomics. 2018 Mar;17(3):533-548. Epub 2017 Dec 14.

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Experimental Design
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Identification Results
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Quantification Results
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When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.