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
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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