Abstract
We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.
Highlights
Next-generation immune-based therapies are expected to facilitate the eradication of intractable pathogens, cancer and autoimmune diseases (Koff et al, 2013)
We recently introduced SWATH-mass spectrometry (MS), a new mass spectrometric technique that combines data-independent acquisition (DIA) with a targeted data extraction strategy (Gillet et al, 2012; Rost et al, 2014)
We developed a workflow to (1) generate a pilot repository of HLA allele-specific peptide spectral and assay libraries, and to (2) analyze SWATH-MS HLA peptidomic data acquired from multiple international laboratories (Figure 1)
Summary
Next-generation immune-based therapies are expected to facilitate the eradication of intractable pathogens, cancer and autoimmune diseases (Koff et al, 2013). We developed a workflow to (1) generate a pilot repository of HLA allele-specific peptide spectral and assay libraries, and to (2) analyze SWATH-MS HLA peptidomic data acquired from multiple international laboratories (Figure 1).
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