MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets

Kevin Kovalchik ,Mathieu Courcelles,Isabelle Sirois,Pierre Thibault,Lukas Reiter,Qing Ma,Éric Bonneil,Pouya Faridi,Anne Jang,Joël Lanoix,Frederic Saab,Chen Li,Peter Kubiniok,Marco Tognetti,Eustache Paramithiotis,Laura Wessling,Roland Bruderer,Anthony W Purcell,Jérôme Despault ,Étienne Caron ,David Hamelin

doi:10.1016/j.mcpro.2021.100178

Abstract

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.

Highlights

MhcVizPipe is a software tool for quality control (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
MVP, a graphical user interface (GUI)-based QC approach, to rapidly and simultaneously assess the quality and major histocompatibility complex (MHC) specificity of small to large immunopeptidomic datasets generated by MS
MVP can be perceived as a relatively basic software solution by experts in the field, this is, to the best of our knowledge, one of the first reports focusing on the development of QC software in MS-based immunopeptidomics

Summary

Graphical Abstract

In Brief Automated QC software tools capable of detecting sample and/or measurement issues are important for downstream data interpretation. Current software tools used to assess such QC measures to determine the MHC specificity of immunopeptidomic datasets include MHC peptide-binding prediction algorithms and clustering tools, such as NetMHCpan [40, 41], MHCFlurry [42, 43], GibbCluster [44], and MoDec [45] Widely used, these algorithms were not purposely built for QC in MSbased immunopeptidomics, and as a result, can process only one sample at a time and generally require further humanbased data manipulations (e.g., in Excel)—a relatively timeintensive and error-prone procedure that is not sustainable for QC in large-scale MS-based immunopeptidomics studies, as recently reported [46, 47]. We discuss the current limitations of MVP and how the software could be further developed to support QC in large-scale clinical immunopeptidomic studies

EXPERIMENTAL PROCEDURES

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DISCUSSION