Recent Publications

jmzTab-M: A Reference Parser, Writer, and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics Standard

Abstract

mzTab 2.0 for metabolomics (mzTab-M) is the most recent standard format developed in collaboration by the Proteomics and Metabolomics Standards Initiatives including contributions by the recently founded Lipidomics Standards Initiative. mzTab-M is a redesign of the original mzTab format which was geared toward reporting of proteomics results and, as such, provided only limited support for metabolites. As a tab-delimited, spreadsheet-like format, mzTab-M captures experimental metadata, summary information on small molecules across assays, MS features as a basis for quantitation, and evidence to support the reporting of individual or feature group identifications. Here, we present the Java reference implementation for reading, writing, and validating mzTab-M files. Furthermore, we provide a web application for conveniently validating mzTab-M files by a graphical user interface, and a command line validator that accompanies the library. The jmzTab-M library, version 1.0.4 (https://doi.org/10.5281/zenodo.3362151), is available at https://github.com/lifs-tools/jmzTab-m and from Maven Central at https://search.maven.org/search?q=jmztabm under the terms of the open source Apache License 2.0. The web application as well as the Python and R implementations are available at https://github.com/lifs-tools. The respective Web sites link to additional API documentation, as well as to usage examples.

 

Hoffmann, N. et al. jmzTab-M: A Reference Parser, Writer, and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics Standard. Analytical Chemistry (2019)
doi:10.1021/acs.analchem.9b01987

Quantitative Fragmentation Model for Bottom-up Shotgun Lipidomics

Abstract

Quantitative bottom-up shotgun lipidomics relies on molecular species-specific “signature” fragments consistently detectable in MS/MS spectra of analytes and standards. Molecular species of glycerophospholipids are typically quantified using carboxylate fragments of their fatty acid moieties produced by higher-energy collisional dissociation of their molecular anions. However, employing standards whose fatty acids moieties are similar, yet not identical to the target lipids could severely compromise their quantification. We developed a generic and portable fragmentation model implemented in the open-source LipidXte software that harmonizes the abundances of carboxylate anion fragments originating from fatty acid moieties having different sn-1/2 position at the glycerol backbone, length of the hydrocarbon chain, number and location of double bonds. The post-acquisition adjustment enables unbiased absolute (molar) quantification of glycerophospholipid species independent of instrument settings, collision energy, and employed internal standards.

 

Schuhmann, K. et al. Quantitative Fragmentation Model for Bottom-up Shotgun Lipidomics. Analytical Chemistry (2019)
doi:10.1021/acs.analchem.9b03270

Lipidomics needs more standardization

Abstract

Modern mass spectrometric technologies provide quantitative readouts for a wide variety of lipid specimens. However, many studies do not report absolute lipid concentrations and differ vastly in methodologies, workflows and data presentation. Therefore, we encourage researchers to engage with the Lipidomics Standards Initiative to develop common standards for minimum acceptable data quality and reporting for lipidomics data, to take lipidomics research to the next level.

Lipidomics Standards Initiative Consortium Lipidomics needs more standardization. Nature Metabolism (2019)
doi:10.1038/s42255-019-0094-z

mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics

Abstract

Mass spectrometry (MS) is one of the primary techniques used for large scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition and re-analysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative and the Metabolomics Society, we have created mzTab-M to act as common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but, importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g. LC-MS, GC-MS, DIMS, etc), as well as different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.

Hoffmann, N. et al. mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. Analytical Chemistry (2019)
doi:10.1021/acs.analchem.8b04310