Vitek-Lab/MSstatsConvert: MSstats+
Year: 2026
Type: software
Abstract: This release corresponds to the version of MSstatsConvert used in the MSstats+ manuscript (Nature Communications, 2026). MSstatsConvert handles the extraction of peak quality metrics required by the MSstats+ workflow. Converters retain precursor-level quality metrics (e.g., delta retention time, MS1 and MS2 shape quality scores, peak correlations, acquisition time stamps) alongside fragment intensities, in addition to the standard MSstats pre-filtering and normalization steps. Included in this release: Isolation forest anomaly scoring, implemented in C++ via Rcpp, with multi-core parallelization across precursors CUSUM-based engineered quality metrics capturing longitudinal drift in precursor quality across acquisition time Quality metric extraction in the Spectronaut and DIA-NN converters CheckDataHealth(), which summarizes precursor-level anomaly scores using Pearson's moment coefficient of skewness to assess the prevalence of anomalous measurements in a dataset Licensed under Artistic-2.0. Available through Bioconductor release 3.22.
Authors: tonywu1999, Devon Kohler, Dogu, Eralp
Institutions: Northeastern University, Muğla University
Language: English
Subfield: Spectroscopy
Field: Chemistry
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7203878613