title: MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.
abstract: BACKGROUND
  Selected and multiple reaction monitoring involves monitoring a multiplexed assay of proteotypic peptides and associated transitions in mass spectrometry runs. To describe peptide and associated transitions as stable, quantifiable, and reproducible representatives of proteins of interest, experimental and analytical validation is required. However, inadequate and disparate analytical tools and validation methods predispose assay performance measures to errors and inconsistencies.
  
  
  RESULTS
  Implemented as a freely available, open-source tool in the platform independent Java programing language, MRMPlus computes analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for "Tier 2" assays - that is, non-clinical assays sufficient enough to measure changes due to both biological and experimental perturbations. Computed measures include; limit of detection, lower limit of quantification, linearity, carry-over, partial validation of specificity, and upper limit of quantification.
  
  
  CONCLUSIONS
  MRMPlus streamlines assay development analytical workflow and therefore minimizes error predisposition. MRMPlus may also be used for performance estimation for targeted assays not described by the Assay Development Working Group. MRMPlus' source codes and compiled binaries can be freely downloaded from https://bitbucket.org/paiyetan/mrmplusgui and https://bitbucket.org/paiyetan/mrmplusgui/downloads respectively.
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Robert H and Clarice Smith Building, Room 4000C, 400 North Broadway, Baltimore, MD, 21287, USA. paul.aytton@gmail.com.
authors.forename: Paul
authors.initials: P
authors.lastname: Aiyetan
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Robert H and Clarice Smith Building, Room 4000C, 400 North Broadway, Baltimore, MD, 21287, USA. sthoma92@jhmi.edu.
authors.forename: Stefani N
authors.initials: SN
authors.lastname: Thomas
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Robert H and Clarice Smith Building, Room 4000C, 400 North Broadway, Baltimore, MD, 21287, USA. zzhang7@jhmi.edu.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Department of Pathology, The Johns Hopkins University School of Medicine, Robert H and Clarice Smith Building, Room 4000C, 400 North Broadway, Baltimore, MD, 21287, USA. huizhang@jhu.edu.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
mesh_terms: D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D010446:Peptide Fragments / Q000032:analysis*; D011506:Proteins / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012984:Software
chemical_list: D010446:Peptide Fragments; D011506:Proteins; D020543:Proteome