A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics

Abstract

Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography-mass spectrometry, ion mobility or MS imaging approaches on MS¹ and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.

Keywords: FAIR; bioinformatics; data format; database; lipidomics; mass spectrometry; standardization.

Figure 1

Data flow for different lipidomics software tools. From top to bottom, the supported ‘data format paths’ of selected lipidomics software tools that support at least one PSI standard data format are highlighted with a solid white outline. Those with planned or upcoming support are highlighted with a dashed white outline. The various software tools are represented by blue rectangles with the tool name in white. Data formats are represented by gray rectangles. On the right, the theoretically possible data flow between the PSI standard data formats, mzML and mzTab-M, is depicted (orange background) via supporting software and repositories/databases (white rectangle outline). In this figure, ‘Vendor Format’ stands for various proprietary, vendor-specific raw data formats (i.e., Thermo Fisher .raw, Agilent .d, ABSciex .wiff and Waters .raw), which can be converted to mzML (among other formats) using msConvert. (1) ‘csv/xlsx’ represents non-standardized output formats such as Microsoft XLSX, comma/tab separated text file formats and HTML. (2) ‘mgf/msp/ms2‘ are text-based formats that encode mass spectral data but generally do not have a strongly defined metadata schema. (3) ‘mzXML/mzData’ represent the legacy raw data and peak list formats mzXML and mzData. (4) ISA-Tab (used by MetaboLights) and mwTab (used by Metabolomics Workbench) are text-based, tabular data formats based on a defined metadata model, which simplifies validation and tooling. (5) Only some tools support quantification. See Table 1 for details.