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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

Selection of the 400-650 mass range. 3,079 manually validated HLA class I ligands from 15 renal cell carcinomas (RCCs) were used to define the mass range containing 99% of the ligands.DOI:http://dx.doi.org/10.7554/eLife.07661.034
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fig5: Selection of the 400-650 mass range. 3,079 manually validated HLA class I ligands from 15 renal cell carcinomas (RCCs) were used to define the mass range containing 99% of the ligands.DOI:http://dx.doi.org/10.7554/eLife.07661.034

Mentions: We thank the reviewers for this suggestion. To select the 400-650 mass range, we initially used 3,079 manually validated HLA peptide ligands isolated from 15 renal cell carcinomas (RCCs) and we define the range containing 99% of the ligands (see Author response image 2). Following the publication by Mommen et al. 2014, we re-evaluated the window by opening it up to 350-900m/z and we observed a decrease in unique peptides by ∼25%. The 400-650 mass range is therefore optimal in our hands using an Orbitrap-XL but might be influenced by the dynamic range and scan speeds of individual instruments and sample concentration. Using the Triple-TOF 5600, we observed that 98% of all class I peptide precursors fall within the 400-700 mass range. Thus, we now mention in the revised version of the manuscript: “Most class I peptide precursors (∼98%) fall within the range of 400-700 Th and were divided in 30 SWATH windows of 10 Da width each.”10.7554/eLife.07661.034Author response image 2.


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)

Selection of the 400-650 mass range. 3,079 manually validated HLA class I ligands from 15 renal cell carcinomas (RCCs) were used to define the mass range containing 99% of the ligands.DOI:http://dx.doi.org/10.7554/eLife.07661.034
© Copyright Policy
Related In: Results  -  Collection

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

fig5: Selection of the 400-650 mass range. 3,079 manually validated HLA class I ligands from 15 renal cell carcinomas (RCCs) were used to define the mass range containing 99% of the ligands.DOI:http://dx.doi.org/10.7554/eLife.07661.034
Mentions: We thank the reviewers for this suggestion. To select the 400-650 mass range, we initially used 3,079 manually validated HLA peptide ligands isolated from 15 renal cell carcinomas (RCCs) and we define the range containing 99% of the ligands (see Author response image 2). Following the publication by Mommen et al. 2014, we re-evaluated the window by opening it up to 350-900m/z and we observed a decrease in unique peptides by ∼25%. The 400-650 mass range is therefore optimal in our hands using an Orbitrap-XL but might be influenced by the dynamic range and scan speeds of individual instruments and sample concentration. Using the Triple-TOF 5600, we observed that 98% of all class I peptide precursors fall within the 400-700 mass range. Thus, we now mention in the revised version of the manuscript: “Most class I peptide precursors (∼98%) fall within the range of 400-700 Th and were divided in 30 SWATH windows of 10 Da width each.”10.7554/eLife.07661.034Author response image 2.

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