TY - JOUR
T1 - MRMPlus
T2 - An open source quality control and assessment tool for SRM/MRM assay development
AU - Aiyetan, Paul
AU - Thomas, Stefani N.
AU - Zhang, Zhen
AU - Zhang, Hui
N1 - Publisher Copyright:
© 2015 Aiyetan et al.
PY - 2015/12/12
Y1 - 2015/12/12
N2 - 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/mrmplusguiand https://bitbucket.org/paiyetan/mrmplusgui/downloadsrespectively.
AB - 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/mrmplusguiand https://bitbucket.org/paiyetan/mrmplusgui/downloadsrespectively.
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U2 - 10.1186/s12859-015-0838-z
DO - 10.1186/s12859-015-0838-z
M3 - Article
C2 - 26652794
AN - SCOPUS:84960329565
SN - 1471-2105
VL - 16
JO - BMC Bioinformatics
JF - BMC Bioinformatics
IS - 1
M1 - 411
ER -