MRMPilot™ Software
MRMPilot™ Software streamlines the building and optimization of targeted peptide quantitative assays on AB SCIEX QTRAP®, TripleTOF™, and Triple Quad™ systems for biomarker verification or other targeted quantitative proteomic applications.
The software allows protein discovery data to be used directly to build MRM methods (Multiple Reaction Monitoring on QTRAP or Triple Quad Systems), MIDAS™ Workflow acquisition methods (MRM Initiated Detection and Sequencing on QTRAP Systems), Scheduled MRM™ Algorithm acquisition methods (QTRAP or Triple Quad Systems), and MRMHR methods (High Resolution MRM-like acquisition on a TripleTOF 5600 System). In addition, the software enables iterative optimization of MRM transitions and stores and organizes all assay development results for easy viewing. Additionally, MRMPilot Software has powerful graphics and visualization tools to assist in selecting optimized MRM transitions based on iterative data collection and evaluation. The end result is an optimized quantitative MRM assay.
To download a trial version and obtain license keys, visit our MRMPilot™ Trial Software Download Registration Site
- Supports QTRAP, TripleTOF, and Triple Quad systems by creating MRM, Scheduled MRM Algorithm, MRMHR, or MIDAS Workflow acquisition methods using previously acquired discovery data, protein or peptide sequence information, or MRM transition information
- Supports input from ProteinPilot™ Software, Mascot, Sequest, Spectrum Mill, BioML, PeptideAtlas, and MRMAtlas
- Allows iterative optimization for the creation of robust peptide quantitation assays
- Provides tools for reviewing the quality of large numbers of quantitative MRM results and MS/MS identification results
- Easily supports stable isotope labeled internal standards strategies (synthetic peptides and isobaric and non-isobaric tagging reagents)
- Allows archiving results to a ProteinAssay Catalogue so future assays can be built from previously optimized protein MRM transitions
Status: Available 
Build Preliminary MRM Experiments for Optimization Initial MRM, MRMHR, or MIDAS™ Workflow acquisition methods can be built for peptides and proteins of interest by importing protein ID results from ProteinPilot™ Software, Mascot, Sequest, Spectrum Mill, BioML (XTandem), PeptideAtlas, or MRMAtlas or alternatively, entering protein sequences directly. MRMPilot™ Software intelligently creates a set of initial MRM transitions based on real or predicted fragment data. The software automatically recommends specific transitions for use based on intelligent chemical knowledge of anticipated peptide charge, mass range, and fragmentation pattern. The software also smartly considers post translational modifications and chemical labeling, using additional rules for fragmentation and collision energy to ensure the highest quality MRM transitions are created. When there are groups of related proteins to consider from ProteinPilot Software, MRMPilot Software will create transitions that are common to a family of proteins or unique to specific proteins based upon the user's choice. Once the transitions are created, MRMPilot Software then builds the Analyst® Software acquisition method. The data are then collected using this new method and re-imported back into MRMPilot for processing and evaluation. Figure 1:Steps to Create a Robust MRM Assay
Select the best transitions with confidence The key to developing optimized peptide MRM assays is to ensure the best MRM transitions are used without overlap from contaminating peaks. Unique to the QTRAP® System technology, the MIDASTM Workflow combines an MRM based survey scan with a high sensitivity product ion scan to allow examination of all fragment ions in the same spectrum for sequence confirmation and optimization. This capability allows easy selection of an alternate fragment ion for the MRM transition for those cases where the original transition may suffer from interference from other peaks. The TripleTOFTM 5600 System also benefits from a similar workflow because the full scan MS/MS data is acquired in a looped fashion which can be evaluated post-acquisition. Additionally, the sensitivity of both the QTRAP and TripleTOF systems in these full scan modes allows development of assays for even very low level peptides from complex real-world biological matrices - without the use of standards. Figure 2:The MRMPilot™ Software User Interface
Create optimized MRM transitions for robust and reliable assays MRMPilot™Software generates optimum MRM transitions by adjusting various MS parameters such as fragment ion and collision energy by using an iterative process (Figure 1). The intuitive user interface allows for assessment of the quality of each MRM transition for each peptide, enabling easy selection of high quality MRM transitions (Figure 2). The final step in producing a reliable MRM based method is to acquire replicate analyses and evaluate which MRM transitions are the most sensitive and reproducible. A Stats Graph allows easy visualization of which peptides have the highest intensity and reproducibility for quantitative purposes. These transitions can then be set as "Optimized" indicating that no further iterative optimization is required and they are ready to be used in a real biological quantitative MRM assay. MRMPilot™ Software allows a user to create robust quantitative MRM assays to quantitate peptides / proteins / PTMs in complex biological matrices. The selection of MRM transitions are based on either previously acquired MS/MS identifications, or predicted based on protein sequence. MRMPilot Software then helps to iteratively optimize MRM transitions by allowing the evaluation of quantitative and qualitative results by calculated metrics as well as intelligent and user friendly graphs and tables. The final result is a set of high quality MRM transitions that can be used in a true biological assay. For Research Use Only. Not for use in diagnostic procedures.
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.jpg "Steps to Create a Robust MRM Assay")
