OPBI: An open pipeline for biomarker identification

Biomarker discovery is one particular pipeline utilized in shotgun proteomics, which is made up of series of phases starting from a set of mass spectrum files and ending with some significantly expressed proteins that are related to a particular disease condition. Different techniques and tools have been introduced to perform protein identification and biomarker identification, and they still consume days/hours to carry out the processes. Further, they ignore MS1 information and consider only the information included in MS2 spectra. In this paper, we present an open-source, R-based, accurate biomarker identification pipeline, which provides solutions to time consumption problem in current biomarker discovery pipelines and utilizes the information of MS1 spectra. The developed pipeline was validated using three raw datasets of PRIDE database. We observed around 2–4 times speed-up and FDR ranges from 0.0003 to 0.0009. The biomarker identification system is accurate and operates in a considerable speed than commonly used, open-source MaxQuant tool.