PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface

Protein
inference connects the peptide spectrum matches (PSMs)
obtained from database search engines back to proteins, which are
typically at the heart of most proteomics studies. Different search
engines yield different PSMs and thus different protein lists. Analysis
of results from one or multiple search engines is often hampered by
different data exchange formats and lack of convenient and intuitive
user interfaces. We present PIA, a flexible software suite for combining
PSMs from different search engine runs and turning these into consistent
results. PIA can be integrated into proteomics data analysis workflows
in several ways. A user-friendly graphical user interface can be run
either locally or (e.g., for larger core facilities) from a central
server. For automated data processing, stand-alone tools are available.
PIA implements several established protein inference algorithms and
can combine results from different search engines seamlessly. On several
benchmark data sets, we show that PIA can identify a larger number
of proteins at the same protein FDR when compared to that using inference
based on a single search engine. PIA supports the majority of established
search engines and data in the mzIdentML standard format. It is implemented
in Java and freely available at https://github.com/mpc-bioinformatics/pia.