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

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An open-source computational and data resource to analyze digital maps of immunopeptidomes is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.7554/ELIFE.07661
P932PMC publication ID4507788
P698PubMed publication ID26154972

P50authorHans-Georg RammenseeQ1577018
Ruedi AebersoldQ7377799
Alessandro SetteQ28324161
Anthony W. PurcellQ38523862
Ludovic C GilletQ39404642
Miguel MarcillaQ40011330
Cecilia S. Lindestam ArlehamnQ42893016
Eric W DeutschQ53584947
Nicola TernetteQ55762242
Robert L MoritzQ57025076
Sri Harsha RamarathinamQ57241689
Ralf B SchittenhelmQ61821990
Etienne CaronQ85556759
Stefan StevanovićQ86390097
Theo SturmQ101212895
P2093author name stringHenry Lam
Sangtae Kim
David S Campbell
Pedro Navarro
Daniel J Kowalewski
Heiko Schuster
Armin Rabsteyn
Lucia Espona
Adán Alpízar
Ching Chiek Koh
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Genetic basis for clinical response to CTLA-4 blockade in melanomaQ29620594
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Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictionsQ33953557
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimatesQ34005153
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysisQ34133645
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directionsQ34279143
Comet: an open-source MS/MS sequence database search toolQ34311405
Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subsetQ34566079
Kinetics of antigen expression and epitope presentation during virus infection.Q34574829
Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigensQ34788858
Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoiresQ34978613
HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL).Q34985471
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 systemQ35026886
A repository of assays to quantify 10,000 human proteins by SWATH-MS.Q35066504
Quantitative variability of 342 plasma proteins in a human twin populationQ35174121
The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation.Q35458694
Automated benchmarking of peptide-MHC class I binding predictionsQ35785418
The MHC class I peptide repertoire is molded by the transcriptome.Q36509857
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11Q36749382
Combining results of multiple search engines in proteomicsQ37160902
MS-GF+ makes progress towards a universal database search tool for proteomicsQ37283260
HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicityQ37414385
Increased diversity of the HLA-B40 ligandome by the presentation of peptides phosphorylated at their main anchor residueQ37563889
Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptidesQ37718264
Biochemical large-scale identification of MHC class I ligandsQ38074902
Accelerating next-generation vaccine development for global disease preventionQ38110775
The nature of self for T cells-a systems-level perspectiveQ38281500
Revisiting the arthritogenic peptide theory: quantitative not qualitative changes in the peptide repertoire of HLA-B27 allotypesQ38938313
A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides.Q39036828
The human leukocyte antigen-presented ligandome of B lymphocytesQ39182194
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome mapsQ39404529
Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosisQ40816049
Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometryQ41621455
Using iRT, a normalized retention time for more targeted measurement of peptidesQ41938071
Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapyQ44976497
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS dataQ48317444
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC moleculesQ55042699
Biomarkers in cancer immunotherapyQ86521792
Toward a human vaccines projectQ88103064
P407language of work or nameEnglishQ1860
P921main subjectopen-source softwareQ1130645
P577publication date2015-07-08
P1433published ineLifeQ2000008
P1476titleAn open-source computational and data resource to analyze digital maps of immunopeptidomes
P478volume4

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cites work (P2860)
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