Abstract
mzML and mzIdentML are commonly used, powerful tools for representing mass spectrometry data and derived identification information. These formats are complex, requiring non-trivial logic to translate data into the appropriate representation. Most published implementations are tightly coupled to data structures. The most complete implementations are written in compiled languages that cannot expose the complete flexibility of the implementation to external programs or bindings. To our knowledge, there are no complete implementations for mzML or mzIdentML available to scripting languages like Python or R. We present psims, a library written in Python for writing mzML and mzIdentML. The library allows writing either XML format using built-in Python data structures. It includes a controlled vocabulary resolution system to simplify the encoding process and an identity tracking system to manage entity relationships. The source code is available at https://github.com/mobiusklein/psims, and through the Python Package Index as psims, licensed under the Apache 2 common license.
Highlights
The proliferation of data processing and identification methods in mass spectrometry has led to ever increasing complexity for tools that need to describe their results
The most complete implementations are written in compiled languages that cannot expose the complete flexibility of the implementation to external programs or bindings
The source code is available at https:// github.com/mobiusklein/psims, and through the Python Package Index as psims, licensed under the Apache 2 common license
Summary
The proliferation of data processing and identification methods in mass spectrometry has led to ever increasing complexity for tools that need to describe their results. Over the last decade and a half, the community-driven XML standards for representing spectral data, mzML [1], and peptide/protein identification, mzIdentML [2], have become core to computational methods development [3]. These formats combine a complex XML schema for defining the structure of the information contained with a flexible vocabulary of terms for describing the contents [4]
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