The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.

Area of Science:

• Proteomics
• Bioinformatics
• Data Standards

Background:

• The Proteomics Standards Initiative mzIdentML (version 1.1) was established in 2012 as an open data standard for peptide and protein identification software outputs.
• It has since gained widespread adoption in commercial and open-source software and is a common format for public data repositories.

Purpose of the Study:

• To release mzIdentML version 1.2, incorporating new features to align with advancements in proteome informatics practices.
• To ensure the standard remains relevant and supportive of emerging analytical techniques.

Main Methods:

• Introduction of new features to support peptide modification localization scores and peptide-level statistics.
• Enhanced support for the identification of cross-linked peptides and proteogenomics approaches.
• Improved encoding for *de novo* peptide sequencing, spectral library searches, and protein inference.

Main Results:

• mzIdentML version 1.2 includes support for modification localization, peptide statistics, cross-linked peptides, and proteogenomics.
• The underlying XML schema modifications are minimal, facilitating a smooth transition from version 1.1.
• The new version offers backward compatibility, with most mzIdentML 1.1 reading software functioning without adaptation.

Conclusions:

• mzIdentML 1.2 provides enhanced capabilities for complex proteomic data analysis.
• The standard's backward compatibility and minor schema changes simplify adoption for software developers.
• This release offers a stable foundation for ongoing development in proteome informatics software.