Frequently Asked Questions
Protein turnover, Proteomics, Mass spectrometry
FAQs
Integrate
Q: What does the -D --mass_difference argument do for the integrate function?
A: The --mass_difference argument sets the accurate mass spacing between successive isotopomer channels. It defaults to 1.003355, the 13C − 12C mass difference, which is the correct unit spacing for heavy-water labeling (the labeled peptide’s envelope advances in ~1 Da neutron-mass steps). RIANA uses it to compute the accurate m/z of each successive isotopomer for extraction. (The earlier D/C13/SILAC token options were removed; supply a float directly.)
Fit
Q: What are the kinetic models being specified by the different fit options?
A: The simple, guan, and fornasiero options for the --model argument refer to a simple exponential (one-pool) model, a two-compartment model, and a two-compartment model that includes label reutilization. For protein-level analysis, riana rollup additionally offers "linear simple", a linearized φ-space fit that supports a cross-condition Δk test. See the Documentation page for details.
Q: What does the -l --label argument do, and how do I set the labeling sites?
A: --label selects the labeling chemistry — hw (heavy water / D2O, the default and only validated path; o18 is in progress). Cell-type or tissue specificity is not set through the label; it comes from the per-amino-acid labeling-site (Spep) table supplied with --coefficients. Pass a bundled preset — commerford (literature mammalian values) or the ac16 / ipsc / cm cell-line calibration tables — or a path to your own (amino_acid, coefficient) CSV. (The earlier amino-acid / SILAC fitting path and the hw_cell / params.py mechanism were removed in 1.0.0.)
Q: Does RIANA perform protein-level curve fitting?
A: Yes — riana rollup aggregates the peptide-level fits to proteins. Shared peptides are resolved by parsimony (--parsimony unique|isoform) and protein rate constants are estimated by an inverse-variance-weighted per-timepoint collapse (--method weighted) or a pooled fit (--method pooled). The earlier practice of taking a median or harmonic mean of peptide-level rate constants (as in our 2022 publication) is still available as a column on the output, but the weighted refit is the default.
Q: How do I retrieve half-life information on the peptide and protein?
A: The half-life of a peptide or protein can be calculated from the output k parameter using the equation:
\[ t_{1/2} = ln(2)/k \]
Q: How is fractional synthesis calculated, and can I restrict the isotopomers used?
A: In 1.0.0 fractional synthesis (θ) is solved against the full m0–m5 isotopomer envelope using an IsoSpec forward model — RIANA fits θ as the mixture of the natural-abundance and fully-labeled envelopes that best matches the observed pattern, given a per-peptide labeling-site estimate (see Documentation). This supersedes the earlier fine-structure ratio selection (m0_mA, Auto; Currie et al. J Proteome Res 2025). The --fs flag is reserved for a future channel-subset option (restricting the envelope to chosen isotopomers to dodge co-eluting interference) and is currently inactive.
General
Q: How can I contribute to RIANA?
A: Contact us at [edward.lau@cuanschutz.edu]