RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool

J Proteome Res. 2021 Apr 2;20(4):2098-2104. doi: 10.1021/acs.jproteome.0c00956. Epub 2021 Mar 3.


Every laboratory performing mass-spectrometry-based proteomics strives to generate high-quality data. Among the many factors that impact the outcome of any experiment in proteomics is the LC-MS system performance, which should be monitored within each specific experiment and also long term. This process is termed quality control (QC). We present an easy-to-use tool that rapidly produces a visual, HTML-based report that includes the key parameters needed to monitor the LC-MS system performance, with a focus on monitoring the performance within an experiment. The tool, named RawBeans, generates a report for individual files or for a set of samples from a whole experiment. We anticipate that it will help proteomics users and experts evaluate raw data quality independent of data processing. The tool is available at https://bitbucket.org/incpm/prot-qc/downloads. The mass-spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD022816.

Keywords: QC; Raw Data; nanoLC-MS/MS; quality control.

MeSH terms

  • Chromatography, Liquid
  • Data Accuracy*
  • Proteomics
  • Quality Control
  • Software*