Change Log

RIANA enables protein turnover data analysis from mass spectrometry-based proteomics experiments using metabolic heavy water (D2O) labeling, with DDA (quantms) and DIA (DIA-NN) identification intake.
Author

Edward Lau

Published

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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.
Keywords

Protein turnover, Proteomics, Mass spectrometry

Update v1.0.0

A major, breaking rewrite. See the repository CHANGELOG.md for the full enumerated list.

  • New package + typed streaming pipeline. mzML is read one fraction at a time; configuration is shared between the CLI and GUI so the two cannot drift.
  • Peak detection. Integration defaults to an apex-centred narrow window (--peak-rt apex, --integration-half-width 0.15) instead of a fixed retention-time rectangle. Reproduce the old behaviour with --peak-rt ms2 --integration-half-width 1.0.
  • Fractional synthesis via an IsoSpec forward model. riana fit solves θ against the full m0–m5 envelope with a per-peptide labeling-site (Spep) estimate, replacing the fixed-site analytic calculation; bootstrap confidence intervals and per-timepoint fraction-new (riana_fit_fractions.txt) are reported.
  • Identification intake. quantms mzTab (DDA) and DIA-NN report.parquet (DIA) are now first-class, keyed off an SDRF sample sheet; a stage-aware riana_manifest.tsv chains integrate → fit → rollup. Percolator remains as a single-mzML tier.
  • Protein roll-up. New riana rollup aggregates peptides to proteins (--parsimony unique|isoform, --method weighted|pooled). --model "linear simple" fits turnover in φ-space and reports a per-protein cross-condition Δk with Benjamini–Hochberg adjustment.
  • Match-between-runs returns for the DDA path as a gated, quality-controlled transfer (integrate --mbr).
  • Modifications. Variable-modification peptidoforms (phospho, acetyl, oxidation, …) are integrated at their correct m/z and envelope; phospho and side-chain acetyl roll up as distinct proteoforms.
  • New GUI. A PySide6 desktop app, riana gui, with Integrate / Model / Protein tabs (install the [gui] extra). The old Tkinter GUI was removed.
  • CLI rewrite (breaking). A Typer CLI replaces the argparse interface; riana fit requires --coefficients; thread flags were replaced by process workers (-W/--workers); the bundled Snakemake pipeline was retired in favour of an orchestration-agnostic design.

Update v0.9.0

  • Stabilization release ahead of the 1.0 rewrite: correctness fixes, modern packaging, and continuous integration.
  • Mass-tolerance semantics corrected — -m N now means ±N ppm (previously applied at half the requested value).

Update v.0.8.3

  • Minor bug fixes
  • The isotopomer columns are now named iso0, iso1, etc. instead of m0, m1. This may affect compatibility.

Update v.0.8.1

  • Minor bug fixes

Update v.0.8.0

  • Added support for automatic isotopomer selection. To use this feature, run riana/riana.py with --fs Auto.
  • Added experimental support for in vitro heavy water labeling. To use this feature, run riana/riana.py with --label hw_cell.

Update v.0.7.3

  • Added graphical user interface (GUI) for RIANA. To use the GUI, run riana/riana_ui.py in the command line.

Update v.0.7.2

  • Included additional Snakemake options in the config files
  • The argument for isotope now takes in multiple numerical values separated by space e.g., 2 4 6 8

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.