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

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.