Change Log

RIANA enables protein turnover data analysis from mass spectrometry-based proteomics experiments. Supports multiple labeling strategies, including labeled amino acid and heavy water.
Author

Edward Lau

Published

April 25, 2023

Abstract
This page provides the documentation for the RIANA package, which is a tool for the analysis of stable isotope labeling experiments for protein turnover measurements.

Update v.0.7.1

  • Added parameter for mass defect -D to command line argument for riana integrate. See documentation for detail
  • Added the flag -p to the command line argument for riana fit, which toggles plotting fitted curves
  • Added the fag -w to the command line argument for riana integrate, for writing out pre-integration intensities

Update v.0.7.0

  • RIANA now supports a Snakemake pipeline that performs protein database search, filtering, integration and fitting
  • Added native support to perform curve-fitting and output best-fit curve plots
  • Added support for one-pool, two-compartment (Guan et al.) and three-exponent (Fornasiero et al.) models
  • Match between runs is temporarily disabled to support the Snakemake workflow and will return in a later version.

Update v.0.6.4

  • Added support for standalone Percolator results for v.3.0.5.
  • Organize the project in identical manner, include one psms.txt for target psms (output of Percolator -m tag) in each percolator folder.
  • When using standalone Percolator dist, peptide masses are calculated de novo
  • Toggle match between runs using –mbr or -b
  • No longer writes results of individual fractions separately.

Update v.0.6.3

  • Fixed an issue where mbr all-NaN slice causes an error
  • Changed project directory structure so that mzml files have to be within an mzml subfolder and percolator files are in the percolator folder

Update v.0.6.0

  • Started implementation of match between runs and restructured project for distribution via pip

Update v.0.5.0

  • Updated to use pymzml 2.2.
  • Multi-threading is now supported with the –thread argument.
  • RIANA now loads all the spectra needed for integration into memory.
  • Compared to v.0.4.0 there should now be a substantial speed gain and can finish a sizeable fraction (~1 Gb raw file) in 10 min.
  • User-definable mass tolerance for MS1 integration is now supported via the –masstolerance argument [default 100 ppm].

Update v.0.4.0

  • Updated to use python 3.5+, up-to-date scipy and numpy, pymzml.

  • Multi-fraction runs are now supported - the mzml files in the directory need to be the same as the order they appear in the Percolator indices (check the Percolator output log file if unsure). For the most cases this shouldn’t present a problem if the mzml directory contains exactly the same mzml files used for the database search, unless there is a difference in how the operating system order files on the search computer (e.g., file_10.mzml vs. file_2. mzml) or if one of the fractions contained no protein ID and Crux/Percolator decided to skip the file in its indexing.

  • To support multi-fraction analysis, RIANA now takes in Percolator tab delimited files for protein ID rather than mzid. Mzid support will be added back in in a future version.