Minimal Information About an Immuno‐Peptidomics Experiment (MIAIPE)

Minimal information about an immuno‐peptidomics experiment (MIAIPE) is an initiative of the members of the Human Immuno‐Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement, and associated mass spectrometry (MS)‐related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (minimal information about a proteomics experiment) guidelines.

[1]  Dave Speijer,et al.  Major Histocompatibility Complex Class I Peptide Presentation after Salmonella enterica Serovar Typhimurium Infection Assessed via Stable Isotope Tagging of the B27-Presented Peptide Repertoire , 2004, Infection and Immunity.

[2]  S. Stevanović,et al.  Insights into MHC class I antigen processing gained from large-scale analysis of class I ligands , 2011, Cellular and Molecular Life Sciences.

[3]  J. Leunissen,et al.  The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes* , 2013, Molecular & Cellular Proteomics.

[4]  Martin Eisenacher,et al.  Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. , 2013, Journal of proteomics.

[5]  Mathieu Courcelles,et al.  Comparison of the MHC I Immunopeptidome Repertoire of B‐Cell Lymphoblasts Using Two Isolation Methods , 2018, Proteomics.

[6]  M. Mann,et al.  Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry , 2016, Nature Communications.

[7]  Arie Admon,et al.  The nature and extent of contributions by defective ribosome products to the HLA peptidome , 2014, Proceedings of the National Academy of Sciences.

[8]  M. Lotze,et al.  Identification of T-cell epitopes: rapid isolation of class I-presented peptides from viable cells by mild acid elution. , 1993, Journal of immunotherapy with emphasis on tumor immunology : official journal of the Society for Biological Therapy.

[9]  J. Yewdell,et al.  Defective ribosomal products (DRiPs): a major source of antigenic peptides for MHC class I molecules? , 1996, Journal of immunology.

[10]  Anthony W. Purcell,et al.  Kinetics of Antigen Expression and Epitope Presentation during Virus Infection , 2013, PLoS pathogens.

[11]  Albert J R Heck,et al.  Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD) , 2014, Proceedings of the National Academy of Sciences.

[12]  Sylvia Janetzki,et al.  "MIATA"-minimal information about T cell assays. , 2009, Immunity.

[13]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[14]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[15]  L. Jensen,et al.  Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation* , 2015, Molecular & Cellular Proteomics.

[16]  H. Grey,et al.  Characterization of a naturally processed MHC class II-restricted T-cell determinant of hen egg lysozyme , 1989, Nature.

[17]  Albert J R Heck,et al.  Stable Isotope Tagging of Epitopes , 2006, Molecular & Cellular Proteomics.

[18]  William Stafford Noble,et al.  Posterior error probabilities and false discovery rates: two sides of the same coin. , 2008, Journal of proteome research.

[19]  Shannon McWeeney,et al.  MIFlowCyt: The minimum information about a flow cytometry experiment , 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[20]  Alessandro Sette,et al.  An open-source computational and data resource to analyze digital maps of immunopeptidomes , 2015, eLife.

[21]  H. Rammensee,et al.  Characterization of naturally occurring minor histocompatibility peptides including H-4 and H-Y. , 1990, Science.

[22]  Mark Cobbold,et al.  Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry , 2015, Nature Protocols.

[23]  Elisa Pappalardo,et al.  Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells , 2015, Journal of Virology.

[24]  Albert J R Heck,et al.  Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07. , 2017, Journal of proteome research.

[25]  S. Stevanović,et al.  Biochemical large-scale identification of MHC class I ligands. , 2013, Methods in molecular biology.

[26]  Ilan Beer,et al.  Analysis of endogenous peptides bound by soluble MHC class I molecules: a novel approach for identifying tumor‐specific antigens , 2002, European journal of immunology.

[27]  Naoki Asakawa,et al.  Highly robust stainless steel tips as microelectrospray emitters. , 2002, Rapid communications in mass spectrometry : RCM.

[28]  Hans-Georg Rammensee,et al.  Isolation and analysis of naturally processed viral peptides as recognized by cytotoxic T cells , 1990, Nature.

[29]  R. Henderson,et al.  Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. , 1992, Science.

[30]  Hans-Georg Rammensee,et al.  Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices , 2017, The Journal of Immunology.

[31]  Chris F. Taylor,et al.  Guidelines for reporting the use of mass spectrometry in proteomics , 2008, Nature Biotechnology.

[32]  H. Rammensee,et al.  Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules , 1991, Nature.

[33]  K Kumagai,et al.  A simple method to eliminate the antigenicity of surface class I MHC molecules from the membrane of viable cells by acid treatment at pH 3. , 1987, Journal of immunological methods.

[34]  Ilan Beer,et al.  The Turnover Kinetics of Major Histocompatibility Complex Peptides of Human Cancer Cells* , 2006, Molecular & Cellular Proteomics.

[35]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[36]  Alexandre M J J Bonvin,et al.  Extended O-GlcNAc on HLA Class-I-Bound Peptides. , 2015, Journal of the American Chemical Society.

[37]  Hans-Georg Rammensee,et al.  Integrated functional genomics approach for the design of patient-individual antitumor vaccines. , 2002, Cancer research.

[38]  Hans-Georg Rammensee,et al.  Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy , 2016, PloS one.

[39]  Arie Admon,et al.  The Human Immunopeptidome Project, a Suggestion for yet another Postgenome Next Big Thing , 2011, Molecular & Cellular Proteomics.

[40]  J. Neefjes,et al.  Towards a systems understanding of MHC class I and MHC class II antigen presentation , 2011, Nature Reviews Immunology.

[41]  Etienne Caron,et al.  Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry* , 2015, Molecular & Cellular Proteomics.

[42]  Peter A van Veelen,et al.  Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. , 2014, Journal of proteomics.

[43]  Oliver Kohlbacher,et al.  The immunopeptidomic landscape of ovarian carcinomas , 2017, Proceedings of the National Academy of Sciences.

[44]  Hans-Georg Rammensee,et al.  Cellular peptide composition governed by major histocompatibility complex class I molecules , 1990, Nature.

[45]  Chris F. Taylor,et al.  Guidelines for reporting the use of mass spectrometry informatics in proteomics , 2008, Nature Biotechnology.

[46]  Ilan Beer,et al.  The Effect of Proteasome Inhibition on the Generation of the Human Leukocyte Antigen (HLA) Peptidome* , 2013, Molecular & Cellular Proteomics.

[47]  Ruedi Aebersold,et al.  A Case for a Human Immuno‐Peptidome Project Consortium , 2017, Immunity.