Ariadne’s Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data

Selected
reaction monitoring (SRM) MS is a highly selective and
sensitive technique to quantify protein abundances in complex biological
samples. To enhance the pace of SRM large studies, a validated, robust
method to fully automate absolute quantification and to substitute
for interactive evaluation would be valuable. To address this demand,
we present Ariadne, a Matlab software. To quantify monitored targets,
Ariadne exploits metadata imported from the transition lists, and
targets can be filtered according to mProphet output. Signal processing
and statistical learning approaches are combined to compute peptide
quantifications. To robustly estimate absolute abundances, the external
calibration curve method is applied, ensuring linearity over the measured
dynamic range. Ariadne was benchmarked against mProphet and Skyline
by comparing its quantification performance on three different dilution
series, featuring either noisy/smooth traces without background or
smooth traces with complex background. Results, evaluated as efficiency,
linearity, accuracy, and precision of quantification, showed that
Ariadne’s performance is independent of data smoothness and
complex background presence and that Ariadne outperforms mProphet
on the noisier data set and improved 2-fold Skyline’s accuracy
and precision for the lowest abundant dilution with complex background.
Remarkably, Ariadne could statistically distinguish from each other all different
abundances, discriminating dilutions as low as 0.1 and 0.2 fmol. These
results suggest that Ariadne offers reliable and automated analysis
of large-scale SRM differential expression studies.