The SysteMHC Atlas project

Wenguang Shao, Patrick G.A. Pedrioli, Witold Wolski, Cristian Scurtescu, Emanuel Schmid, Juan A. Vizcaíno, Mathieu Courcelles, Heiko Schuster, Daniel Kowalewski, Fabio Marino, Cecilia S.L. Arlehamn, Kerrie Vaughan, Bjoern Peters, Alessandro Sette, Tom H.M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H.E. Kaufmann, Ralph Schlapbach, John C. Castle & 26 others Alexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. Van Veelen, Cécile A.C.M. Van Els, Albert J.R. Heck, Gustavo A. De Souza, Ludvig M. Sollid, Arie Admon, Stefan Stevanovic, Hans Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron

Research output: Contribution to journalArticleOtherpeer-review

25 Citations (Scopus)

Abstract

Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.

Original languageEnglish
Pages (from-to)D1237-D1247
Number of pages11
JournalNucleic Acids Research
Volume46
Issue numberD1
DOIs
Publication statusPublished - 1 Jan 2018

Cite this

Shao, W., Pedrioli, P. G. A., Wolski, W., Scurtescu, C., Schmid, E., Vizcaíno, J. A., ... Caron, E. (2018). The SysteMHC Atlas project. Nucleic Acids Research, 46(D1), D1237-D1247. https://doi.org/10.1093/nar/gkx664
Shao, Wenguang ; Pedrioli, Patrick G.A. ; Wolski, Witold ; Scurtescu, Cristian ; Schmid, Emanuel ; Vizcaíno, Juan A. ; Courcelles, Mathieu ; Schuster, Heiko ; Kowalewski, Daniel ; Marino, Fabio ; Arlehamn, Cecilia S.L. ; Vaughan, Kerrie ; Peters, Bjoern ; Sette, Alessandro ; Ottenhoff, Tom H.M. ; Meijgaarden, Krista E. ; Nieuwenhuizen, Natalie ; Kaufmann, Stefan H.E. ; Schlapbach, Ralph ; Castle, John C. ; Nesvizhskii, Alexey I. ; Nielsen, Morten ; Deutsch, Eric W. ; Campbell, David S. ; Moritz, Robert L. ; Zubarev, Roman A. ; Ytterberg, Anders Jimmy ; Purcell, Anthony W. ; Marcilla, Miguel ; Paradela, Alberto ; Wang, Qi ; Costello, Catherine E. ; Ternette, Nicola ; Van Veelen, Peter A. ; Van Els, Cécile A.C.M. ; Heck, Albert J.R. ; De Souza, Gustavo A. ; Sollid, Ludvig M. ; Admon, Arie ; Stevanovic, Stefan ; Rammensee, Hans Georg ; Thibault, Pierre ; Perreault, Claude ; Bassani-Sternberg, Michal ; Aebersold, Ruedi ; Caron, Etienne. / The SysteMHC Atlas project. In: Nucleic Acids Research. 2018 ; Vol. 46, No. D1. pp. D1237-D1247.
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abstract = "Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.",
author = "Wenguang Shao and Pedrioli, {Patrick G.A.} and Witold Wolski and Cristian Scurtescu and Emanuel Schmid and Vizca{\'i}no, {Juan A.} and Mathieu Courcelles and Heiko Schuster and Daniel Kowalewski and Fabio Marino and Arlehamn, {Cecilia S.L.} and Kerrie Vaughan and Bjoern Peters and Alessandro Sette and Ottenhoff, {Tom H.M.} and Meijgaarden, {Krista E.} and Natalie Nieuwenhuizen and Kaufmann, {Stefan H.E.} and Ralph Schlapbach and Castle, {John C.} and Nesvizhskii, {Alexey I.} and Morten Nielsen and Deutsch, {Eric W.} and Campbell, {David S.} and Moritz, {Robert L.} and Zubarev, {Roman A.} and Ytterberg, {Anders Jimmy} and Purcell, {Anthony W.} and Miguel Marcilla and Alberto Paradela and Qi Wang and Costello, {Catherine E.} and Nicola Ternette and {Van Veelen}, {Peter A.} and {Van Els}, {C{\'e}cile A.C.M.} and Heck, {Albert J.R.} and {De Souza}, {Gustavo A.} and Sollid, {Ludvig M.} and Arie Admon and Stefan Stevanovic and Rammensee, {Hans Georg} and Pierre Thibault and Claude Perreault and Michal Bassani-Sternberg and Ruedi Aebersold and Etienne Caron",
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Shao, W, Pedrioli, PGA, Wolski, W, Scurtescu, C, Schmid, E, Vizcaíno, JA, Courcelles, M, Schuster, H, Kowalewski, D, Marino, F, Arlehamn, CSL, Vaughan, K, Peters, B, Sette, A, Ottenhoff, THM, Meijgaarden, KE, Nieuwenhuizen, N, Kaufmann, SHE, Schlapbach, R, Castle, JC, Nesvizhskii, AI, Nielsen, M, Deutsch, EW, Campbell, DS, Moritz, RL, Zubarev, RA, Ytterberg, AJ, Purcell, AW, Marcilla, M, Paradela, A, Wang, Q, Costello, CE, Ternette, N, Van Veelen, PA, Van Els, CACM, Heck, AJR, De Souza, GA, Sollid, LM, Admon, A, Stevanovic, S, Rammensee, HG, Thibault, P, Perreault, C, Bassani-Sternberg, M, Aebersold, R & Caron, E 2018, 'The SysteMHC Atlas project', Nucleic Acids Research, vol. 46, no. D1, pp. D1237-D1247. https://doi.org/10.1093/nar/gkx664

The SysteMHC Atlas project. / Shao, Wenguang; Pedrioli, Patrick G.A.; Wolski, Witold; Scurtescu, Cristian; Schmid, Emanuel; Vizcaíno, Juan A.; Courcelles, Mathieu; Schuster, Heiko; Kowalewski, Daniel; Marino, Fabio; Arlehamn, Cecilia S.L.; Vaughan, Kerrie; Peters, Bjoern; Sette, Alessandro; Ottenhoff, Tom H.M.; Meijgaarden, Krista E.; Nieuwenhuizen, Natalie; Kaufmann, Stefan H.E.; Schlapbach, Ralph; Castle, John C.; Nesvizhskii, Alexey I.; Nielsen, Morten; Deutsch, Eric W.; Campbell, David S.; Moritz, Robert L.; Zubarev, Roman A.; Ytterberg, Anders Jimmy; Purcell, Anthony W.; Marcilla, Miguel; Paradela, Alberto; Wang, Qi; Costello, Catherine E.; Ternette, Nicola; Van Veelen, Peter A.; Van Els, Cécile A.C.M.; Heck, Albert J.R.; De Souza, Gustavo A.; Sollid, Ludvig M.; Admon, Arie; Stevanovic, Stefan; Rammensee, Hans Georg; Thibault, Pierre; Perreault, Claude; Bassani-Sternberg, Michal; Aebersold, Ruedi; Caron, Etienne.

In: Nucleic Acids Research, Vol. 46, No. D1, 01.01.2018, p. D1237-D1247.

Research output: Contribution to journalArticleOtherpeer-review

TY - JOUR

T1 - The SysteMHC Atlas project

AU - Shao, Wenguang

AU - Pedrioli, Patrick G.A.

AU - Wolski, Witold

AU - Scurtescu, Cristian

AU - Schmid, Emanuel

AU - Vizcaíno, Juan A.

AU - Courcelles, Mathieu

AU - Schuster, Heiko

AU - Kowalewski, Daniel

AU - Marino, Fabio

AU - Arlehamn, Cecilia S.L.

AU - Vaughan, Kerrie

AU - Peters, Bjoern

AU - Sette, Alessandro

AU - Ottenhoff, Tom H.M.

AU - Meijgaarden, Krista E.

AU - Nieuwenhuizen, Natalie

AU - Kaufmann, Stefan H.E.

AU - Schlapbach, Ralph

AU - Castle, John C.

AU - Nesvizhskii, Alexey I.

AU - Nielsen, Morten

AU - Deutsch, Eric W.

AU - Campbell, David S.

AU - Moritz, Robert L.

AU - Zubarev, Roman A.

AU - Ytterberg, Anders Jimmy

AU - Purcell, Anthony W.

AU - Marcilla, Miguel

AU - Paradela, Alberto

AU - Wang, Qi

AU - Costello, Catherine E.

AU - Ternette, Nicola

AU - Van Veelen, Peter A.

AU - Van Els, Cécile A.C.M.

AU - Heck, Albert J.R.

AU - De Souza, Gustavo A.

AU - Sollid, Ludvig M.

AU - Admon, Arie

AU - Stevanovic, Stefan

AU - Rammensee, Hans Georg

AU - Thibault, Pierre

AU - Perreault, Claude

AU - Bassani-Sternberg, Michal

AU - Aebersold, Ruedi

AU - Caron, Etienne

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.

AB - Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.

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DO - 10.1093/nar/gkx664

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

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Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA et al. The SysteMHC Atlas project. Nucleic Acids Research. 2018 Jan 1;46(D1):D1237-D1247. https://doi.org/10.1093/nar/gkx664