Pipelines and Systems for Threshold-Avoiding Quantification of LC–MS/MS Data

The accurate processing of complex liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) data from biological samples is a major challenge for metabolomics, proteomics, and related approaches. Here, we present the pipelines systems threshold-avoiding quantification (PASTAQ) LC–MS/MS preprocessing toolset, which allows highly data-dependent acquisition datasets. PASTAQ performs compound using single-stage (MS1) implements novel algorithms high-performance quantification, retention time alignment, feature detection, linking annotations multiple identification engines. offers straightforward parameterization automatic generation quality control plots assessment. This design results in smaller variance when analyzing replicates proteomes mixed with known ratios detection peptides over larger dynamic concentration range compared widely used proteomics tools. performance pipeline also demonstrated human serum dataset gender-related proteins.