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

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

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Escherichia Coli Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Horvatovich Péter  

LAB HEAD: Peter Horvatovich

PROVIDER: PXD024584 | Pride | 2021-08-18

REPOSITORIES: Pride