PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments

• Published in: Journal of proteomics Vol. 106; pp. 151 - 161
• Main Authors: Mohammed, Yassene, Domański, Dominik, Jackson, Angela M., Smith, Derek S., Deelder, André M., Palmblad, Magnus, Borchers, Christoph H.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 25.06.2014
• Subjects: Algorithms; Animals; Computational Biology - methods; computer software; Data integration; Databases, Protein; Humans; Internet; Mass Spectrometry; Mice; Models, Statistical; monitoring; MRM; Peptide selection; peptides; Peptides - chemistry; Programming Languages; protein isoforms; proteins; Proteome; proteomics; Proteomics - methods; Reproducibility of Results; Scientific workflow; Software; SRM; Targeted proteomics; Trypsin - chemistry; User-Computer Interface; Workflow; MRM; Targeted proteomics; Scientific workflow; Data integration; Peptide selection; SRM
• ISSN: 1874-3919; 1876-7737
• DOI: 10.1016/j.jprot.2014.04.018

One challenge in Multiple Reaction Monitoring (MRM)-based proteomics is to select the most appropriate surrogate peptides to represent a target protein. We present here a software package to automatically generate these most appropriate surrogate peptides for an LC/MRM–MS analysis. Our method integrates information about the proteins, their tryptic peptides, and the suitability of these peptides for MRM which is available online in UniProtKB, NCBI's dbSNP, ExPASy, PeptideAtlas, PRIDE, and GPMDB. The scoring algorithm reflects our knowledge in choosing the best candidate peptides for MRM, based on the uniqueness of the peptide in the targeted proteome, its physiochemical properties, and whether it previously has been observed. The modularity of the workflow allows further extension and additional selection criteria to be incorporated. We have developed a simple Web interface where the researcher provides the protein accession number, the subject organism, and peptide-specific options. Currently, the software is designed for human and mouse proteomes, but additional species can be easily be added. Our software improved the peptide selection by eliminating human error, considering multiple data sources and all of the isoforms of the protein, and resulted in faster peptide selection — approximately 50 proteins per hour compared to 8 per day. Compiling a list of optimal surrogate peptides for target proteins to be analyzed by LC/MRM–MS has been a cumbersome process, in which expert researchers retrieved information from different online repositories and used their own reasoning to find the most appropriate peptides. Our scientific workflow automates this process by integrating information from different data sources including UniProt, Global Proteome Machine, NCBI's dbSNP, and PeptideAtlas, simulating the researchers' reasoning, and incorporating their knowledge of how to select the best proteotypic peptides for an MRM analysis. The developed software can help to standardize the selection of peptides, eliminate human error, and increase productivity. [Display omitted] •A scientific workflow for automated peptide selection for MRM assays is presented.•The software integrates data from multiple online repositories with expert knowledge.•Our automatic workflow runs faster than manual selection.•Our software resulted in more possible peptides, and pointed out human errors.•The software is modular and extendable to meet the needs of different laboratories.