Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods

Tandem
mass spectrometry is one of the most popular techniques
for quantitation of proteomes. There exists a large variety of options
in each stage of data preprocessing that impact the bias and variance
of the summarized protein-level values. Using a newly released data
set satisfying a replicated Latin squares design, a diverse set of
performance metrics has been developed and implemented in a web-based
application, Quantitative Performance Evaluator for Proteomics (QPEP).
QPEP has the flexibility to allow users to apply their own method
to preprocess this data set and share the results, allowing direct
and straightforward comparison of new methodologies. Application of
these new metrics to three case studies highlights that (i) the summarization
of peptides to proteins is robust to the choice of peptide summary
used, (ii) the differences between iTRAQ labels are stronger than
the differences between experimental runs, and (iii) the commercial
software ProteinPilot performs equivalently well at between-sample
normalization to more complicated methods developed by academics.
Importantly, finding (ii) underscores the benefits of using the principles
of randomization and blocking to avoid the experimental measurements
being confounded by technical factors. Data are available via ProteomeXchange
with identifier PXD003608.