MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets
Autor: | Eric Bonneil, Qing Ma, Lukas Reiter, Isabelle Sirois, Joel Lanoix, Etienne Caron, Roland Bruderer, Pierre Thibault, Laura Wessling, David Hamelin, Pouya Faridi, Jerome Despault, Frederic Saab, Eustache Paramithiotis, Chen Li, Mathieu Courcelles, Anthony W. Purcell, Anne Jang, Peter Kubiniok, Kevin A. Kovalchik, Marco Tognetti |
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Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
Proteomics
Quality Control Downstream (software development) MVP MhcVizPipe Computer science Process (engineering) media_common.quotation_subject NB nonbinder CLI command line interface WSL Windows Subsystem for Linux Sample (statistics) BF binding fraction computer.software_genre Biochemistry Analytical Chemistry SB strong binder Special Issue: Immunopeptidomics BA binding affinity MHC major histocompatibility complex Quality (business) GUI graphical user interface Molecular Biology Graphical user interface media_common EL eluted ligand business.industry software HLA human leukocyte antigen Scale (chemistry) Histocompatibility Antigens Class I Technological Innovation and Resources immunopeptidomics MS KLD Kullback-Leibler Distance peptide Core Facility QC quality control WB weak binder LF length fraction Data mining MHC business Peptides computer Quality assurance |
Zdroj: | Molecular & Cellular Proteomics : MCP |
ISSN: | 1535-9484 1535-9476 |
Popis: | MS-based immunopeptidomics is maturing into an automatized and high-throughput technology, producing small- to large-scale datasets of clinically relevant major histocompatibility complex (MHC) class I-associated and class II-associated peptides. Consequently, the development of quality control (QC) and quality assurance systems capable of detecting sample and/or measurement issues is important for instrument operators and scientists in charge of downstream data interpretation. Here, we created MhcVizPipe (MVP), a semiautomated QC software tool that enables rapid and simultaneous assessment of multiple MHC class I and II immunopeptidomic datasets generated by MS, including datasets generated from large sample cohorts. In essence, MVP provides a rapid and consolidated view of sample quality, composition, and MHC specificity to greatly accelerate the “pass–fail” QC decision-making process toward data interpretation. MVP parallelizes the use of well-established immunopeptidomic algorithms (NetMHCpan, NetMHCIIpan, and GibbsCluster) and rapidly generates organized and easy-to-understand reports in HTML format. The reports are fully portable and can be viewed on any computer with a modern web browser. MVP is intuitive to use and will find utility in any specialized immunopeptidomic laboratory and proteomics core facility that provides immunopeptidomic services to the community. Graphical Abstract Highlights • MhcVizPipe is a software tool for QC in immunopeptidomics. • It provides numerical scores for QC analysis of tumor biopsies. • It performs rapid QC analysis of large clinical immunopeptidomic sample cohorts. • It generates organized and easy-to-understand reports in HTML format. In Brief Automated QC software tools capable of detecting sample and/or measurement issues are important for downstream data interpretation. We created MhcVizPipe, the first semiautomated GUI-based QC software tool that enables rapid and simultaneous assessment of multiple MHC class I and II immunopeptidomic datasets generated by MS. MVP is intuitive to use, generate QC reports in HTML formats, and will find utility in any immunopeptidomic laboratory. |
Databáze: | OpenAIRE |
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