Proteomics Quality Control: Quality Control Software for MaxQuant Results

Mass spectrometry-based proteomics
coupled to liquid chromatography
has matured into an automatized, high-throughput technology, producing
data on the scale of multiple gigabytes per instrument per day. Consequently,
an automated quality control (QC) and quality analysis (QA) capable
of detecting measurement bias, verifying consistency, and avoiding
propagation of error is paramount for instrument operators and scientists
in charge of downstream analysis. We have developed an R-based QC
pipeline called Proteomics Quality Control (PTXQC) for bottom-up LC–MS
data generated by the MaxQuant software
pipeline. PTXQC creates a QC report containing a comprehensive and
powerful set of QC metrics, augmented with automated scoring functions.
The automated scores are collated to create an overview heatmap at
the beginning of the report, giving valuable guidance also to nonspecialists.
Our software supports a wide range of experimental designs, including
stable isotope labeling by amino acids in cell culture (SILAC), tandem
mass tags (TMT), and label-free data. Furthermore, we introduce new
metrics to score MaxQuant’s Match-between-runs (MBR) functionality
by which peptide identifications can be transferred across Raw files
based on accurate retention time and m/z. Last but not least, PTXQC is easy to install and use and represents
the first QC software capable of processing MaxQuant result tables.
PTXQC is freely available at https://github.com/cbielow/PTXQC.