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An open-source computational and data resource to analyze digital maps of immunopeptidomes.

Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R - Elife (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.

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.

No MeSH data available.


Related in: MedlinePlus

Heat map visualization of HLA-B27 and -C04 peptide ligands isolated from C1R cells.DOI:http://dx.doi.org/10.7554/eLife.07661.033
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fig4: Heat map visualization of HLA-B27 and -C04 peptide ligands isolated from C1R cells.DOI:http://dx.doi.org/10.7554/eLife.07661.033

Mentions: We updated the total number of unique peptides, alleles and transitions in the main text (Results and Discussion) and an HLA-C04-specific peptide assay library is now available in the SWATH Atlas repository: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetDIALibs?SBEAMSentrycode=HLASWATH2015. We also updated Figure 2—figure supplement 2 and Figure 2—source data 2. However, we did not modify the Figure 2 as the focus of this study is on HLA-A and -B alleles and because HLA-C04 peptide ligands would be poorly represented on the heat maps (see Author response image 1).10.7554/eLife.07661.033Author response image 1.


An open-source computational and data resource to analyze digital maps of immunopeptidomes.

Caron E, Espona L, Kowalewski DJ, Schuster H, Ternette N, Alpízar A, Schittenhelm RB, Ramarathinam SH, Lindestam Arlehamn CS, Chiek Koh C, Gillet LC, Rabsteyn A, Navarro P, Kim S, Lam H, Sturm T, Marcilla M, Sette A, Campbell DS, Deutsch EW, Moritz RL, Purcell AW, Rammensee HG, Stevanovic S, Aebersold R - Elife (2015)

Heat map visualization of HLA-B27 and -C04 peptide ligands isolated from C1R cells.DOI:http://dx.doi.org/10.7554/eLife.07661.033
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4507788&req=5

fig4: Heat map visualization of HLA-B27 and -C04 peptide ligands isolated from C1R cells.DOI:http://dx.doi.org/10.7554/eLife.07661.033
Mentions: We updated the total number of unique peptides, alleles and transitions in the main text (Results and Discussion) and an HLA-C04-specific peptide assay library is now available in the SWATH Atlas repository: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetDIALibs?SBEAMSentrycode=HLASWATH2015. We also updated Figure 2—figure supplement 2 and Figure 2—source data 2. However, we did not modify the Figure 2 as the focus of this study is on HLA-A and -B alleles and because HLA-C04 peptide ligands would be poorly represented on the heat maps (see Author response image 1).10.7554/eLife.07661.033Author response image 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.

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.

No MeSH data available.


Related in: MedlinePlus