MRM Pilot™ Software by Thermo Fisher Scientific

MRMPilot™ Software streamlines the building and optimization of peptide MRM quantitative assays on QTRAP® systems and Triple Quadrupole based instruments.

The software allows protein discovery data to be used directly to build MRM and MIDAS™ Workflow acquisition methods in addition to enabling iterative optimization of MRM transitions and storing and reporting qualitative and quantitative results. Additionally, MRMPilot Software has powerful graphics and visualization tools to assist you in selecting optimized MRM transitions based on iterative data collection and evaluation. The end result is an optimized quantitative MRM assay.

* Creates MRM or MIDAS™ Workflow acquisition methods using previously acquired discovery or identification data or protein sequence information
* Allows iterative optimization for robust peptide MRM assays
* Works directly with MultiQuant™ Software for quantitation of MRM peaks
* Provides tools for reviewing the quality of large numbers of quantitative MRM and MS/MS identification results
* Supports all biomarker verification and targeted quantitative proteomics applications

Build Preliminary MRM Experiments for Optimization
Initial MRM or MIDAS™ Workflow acquisition methods can be built for peptides and proteins of interest by importing protein ID results from either ProteinPilot™ Software or Mascot searches or alternatively, entering protein sequences directly. MRMPilot™ Software is used to intelligently create a set of initial MRM transitions based on real or predicted fragment data. The software automatically recommends specific transitionsfor 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 (such as mTRAQ™ Reagents), using additional rules for fragmentation and collision energy to ensure the highest quality MRM transitions are created. Once the transitions are created, MRMPilot Software then builds the Analyst ® Software acquisition method. The data are then collected using this new method and processed with MultiQuant™ Software.

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 MIDAS™ Workflow combines an MRM based survey scan with a high sensitivity full 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. Additionally, this level of sensitivity allows development of assays for even very low level peptides from complex real-world biological matrices – without the use of standards.


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. 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. 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 Summary 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.