TimsRust

A crate to read Bruker TimsTof data.

Stability

NOTE: TimsRust does not yet have a stable version! Use with caution.

Installation

Add this crate to your Cargo.toml:

[dependencies]
timsrust = "x.x.x"

Usage

TimsRust is intended to be used as a library and not as a stand-alone application. An example of how to use it is found in e.g. Sage.

Basics

Two primary data types are exposed through TimsRust:

• Spectra: A traditional representation that expresses intensitites in function of mz values for a given precursor.
• Frames: All recorded data from a single TIMS elution (i.e. at one specific retention_time).

File formats

Two file formats are supported:

• TDF - Bruker .d folder containing:

  • analysis.tdf
  • analysis.tdf_bin

• miniTDF - ProteoScape optimized Bruker file-format. Similar to TDF, miniTDF consists of multiple files: a binary '.bin' and an index '.parquet' file. The file-names are made up to the following convention: <producing-engine-name>.<domain-name>.<extension>. e.g. for MS2 spectrum information: <producing-engine-name>.ms2spectrum.<extension>. Therefore the following files are expected in the provided ms2 folder:

  • *.ms2spectrum.bin

  • *.ms2spectrum.parquet

Python bindings

The timsrust_pyo3 package is an example of how the performance of TimsRust can be utilized in Python

Planned changes for future versions

TODO

• Improve docs
• Improve tests
• Pase CompressionType1
• Tarred file reader
• Clean up src (FrameReader, ...)
• Cleaner try_from conversions/readers
• Make Path of TimsTOF data into special type
• Single access point for all readers?
• Few unchecked unwraps left
• Queryable data in all dimensions
• ...