HXMS: a standardized file format for HX-MS data

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Hydrogen/deuterium exchange-mass spectrometry (HX-MS) is crucial for studying protein conformational ensembles.
• Current HX-MS data analysis is inconsistent due to diverse software and non-standardized formats.
• Existing formats often use mean deuteration, losing valuable isotopic information.

Purpose of the Study:

• To introduce a unified, scalable, and human-readable file format (HXMS) for HX-MS data.
• To develop a Python package (PFLink) for converting existing HX-MS data to the new format.
• To enhance quantitative analysis, data sharing, and future applications like machine learning in HX-MS.

Main Methods:

• Developed the HXMS file format, inspired by protein structure and genomics standards.
• Created PFLink, a Python package to convert data from common HX-MS software to HXMS.
• Ensured HXMS preserves isotopic mass envelopes, time-course data, and experimental details.

Main Results:

• The HXMS format supports full isotopic envelopes, time-course data, PTMs, and replicates.
• PFLink facilitates seamless conversion of data from various HX-MS software.
• The combined tools enable higher-resolution quantitative analysis and improved data management.

Conclusions:

• The HXMS format and PFLink package address critical standardization needs in HX-MS.
• These tools will advance quantitative analysis, data sharing, and computational approaches in the field.
• Promotes broader adoption and further development of HX-MS techniques.