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

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 integr...