title: Ariadne's Thread: A Robust Software Solution Leading to Automated Absolute and Relative Quantification of SRM Data.
abstract: 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.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH , Auguste-Piccard-Hof 1, ETH Hönggerberg, CH-8093 Zürich, Switzerland.|Institute of Molecular Life Sciences, University of Zurich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
authors.forename: Sara
authors.initials: S
authors.lastname: Nasso
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH , Auguste-Piccard-Hof 1, ETH Hönggerberg, CH-8093 Zürich, Switzerland.|Institute of Molecular Life Sciences, University of Zurich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
authors.forename: Sandra
authors.initials: S
authors.lastname: Goetze
authors.affiliation: Department of Medical Protein Research, VIB , Albert Baertsoenkaai 3, Ghent 9000, Belgium.|Department of Biochemistry, Ghent University , Albert Baertsoenkaai 3, Ghent 9000, Belgium.
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D000465:Algorithms; D001331:Automation; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D011506:Proteins
keywords: AQUA; Matlab software; PRM; SRM data analysis; absolute quantification; calibration; quantitative proteomics; relative quantification; targeted proteomics