XLMOD: Cross-linking and chromatography derivatization reagents ontology

TL;DR

This paper introduces xlmod, an ontology for standardizing the description of cross-linking reagents and modifications in mass spectrometry, facilitating reproducibility and data sharing in structural proteomics.

Contribution

The paper presents the development and integration of xlmod ontology within HUPO-PSI standards for consistent reporting of cross-linking reagents and modifications.

Findings

xlmod enables standardized annotation of cross-linking reagents.

Integration of xlmod improves reproducibility of mass spectrometry experiments.

xlmod supports reporting in multiple data formats.

Abstract

Mass spectrometry has experienced a rapid development since its first application for protein analysis in the 1980s. While the most common use of mass spectrometry for protein analysis is identification and quantification workflows on peptides (digested from their parent protein), there is also a rapidly growing use of mass spectrometry for structural proteomics. One example is the analysis of cross-linked proteins that can give valuable structural information, complementing the information gained by classical protein structure determination methods, useful for integrated methods of structure determination and modeling. For a broad and reproducible application of cross-linking mass spectrometry a standardized representation of cross-linking experimental results is necessary. This paper describes the developing and release of the xlmod ontology from the HUPO-PSI. xlmod contains terms for the description of reagents used in cross-linking experiments and of cross-linker related chemical modifications together with their main properties relevant for planning and performing cross-linking experiments. We also describe how xlmod is used within the new release of HUPO-PSI-s mzIdentML data standard, for reporting the used cross-linking reagents and results in a consistent manner. In addition xlmod contains terms for GC-MS and LC-MS derivatization reagents for specifying them in the upcoming mzTab-M and mzTab-L formats.