Limits...
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.


OpenSWATH analysis and PyProphet statistics of HLA peptidomic data acquired at Monash University, Australia.HLA-B27 peptides were isolated from C1R cells. Graphs showing ROC, d_score performance and d-score distributions were generated automatically using the iPortal workflow.DOI:http://dx.doi.org/10.7554/eLife.07661.026
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4507788&req=5

fig3s5: OpenSWATH analysis and PyProphet statistics of HLA peptidomic data acquired at Monash University, Australia.HLA-B27 peptides were isolated from C1R cells. Graphs showing ROC, d_score performance and d-score distributions were generated automatically using the iPortal workflow.DOI:http://dx.doi.org/10.7554/eLife.07661.026


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)

OpenSWATH analysis and PyProphet statistics of HLA peptidomic data acquired at Monash University, Australia.HLA-B27 peptides were isolated from C1R cells. Graphs showing ROC, d_score performance and d-score distributions were generated automatically using the iPortal workflow.DOI:http://dx.doi.org/10.7554/eLife.07661.026
© Copyright Policy
Related In: Results  -  Collection

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

fig3s5: OpenSWATH analysis and PyProphet statistics of HLA peptidomic data acquired at Monash University, Australia.HLA-B27 peptides were isolated from C1R cells. Graphs showing ROC, d_score performance and d-score distributions were generated automatically using the iPortal workflow.DOI:http://dx.doi.org/10.7554/eLife.07661.026
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.