MSQC1 and MRM/SRM: The ProteoRed Multicentric Experiment 8 Study (Poster)

By: Francesc Canals1, Joan‐Josep Bech‐Serra1, Núria Colomé‐Calls1, Salvador Martínez‐Bartolomé2, Jim J. Walters3, Kevin B. Ray3, Juan‐Pablo Albar2, ProteoRed‐ISCIII Consortium4,

1 Proteomics Laboratory, Vall d’Hebron Institute of Oncology (VHIO) Vall d’Hebron University Hospital, 08035 Barcelona, Spain
2 Centro Nacional de Biotecnologia‐CSIC, Madrid, Spain
3 Sigma‐Aldrich, St. Louis, MO
4 ProteoRed‐ISCIII Consortium. Spanish Networked Proteomics Platform

 

The mass spectrometry (MS) methodology known as multiple reaction monitoring (MRM), or selected reaction monitoring (SRM), has increased in prominence in protein biology, systems biology and clinical biomarker studies.1,2 Sigma-Aldrich has developed the MS performance standard MSQC1 (MS Qual/Quant QC Mix) with MRM methodology particularly in mind. Given the sensitivity of MS, robust MS standards are vital to insure not only the reliability and performance of a given instrument, but also to insure that MRM methodology is reproducible across different laboratories, and on different instruments within the same laboratory.3

In this poster presentation at the European Proteomics Association (EuPA) 2013 Scientific Meeting in October 2013, the ProteoRed consortium of proteomics facilities in Spain reported a study where MS labs were invited to test the robustness of their quantitative proteomics methods. The test material consisted of yeast lysate digest to which different amounts of Sigma-Aldrich MSQC1 were added, to give a set of 5 test samples. 27 different MS laboratories across Europe, as well as the US and Canada, tested these 5 yeast lysate digest/MSQC1 samples using MRM or pseudo-MRM methodology according to their own chromatographic and MS protocols.

Analysis of the data from the 27 laboratories was under the overall direction of Dr. Francesc Canals of Vall d’Hebron University Hospital (Barcelona, Spain) and Dr. Juan-Pablo Albar of the Centro Nacional de Biotecnologia – CSIC (Madrid, Spain). The ProteoRed team found a good degree of reproducibility in the MRM analyses, and consistency in the targeted quantitation results by the different laboratories, across different analytical methods and instruments. Further analysis (PDF) by Dr. Kevin Ray and Dr. Jim Walters of the Sigma-Aldrich Analytical R&D group compared the ProteoRed results directly with the QC data for the specific lot of MSQC1 used in the study. The data from the 27 laboratories showed a strong consistency with the Sigma QC results of the ratio of the stable isotope-labeled (“heavy”) peptides to the corresponding tryptic peptides.

Overall, this study indicates the value of MSQC1 as a highly reliable MS performance standard across different laboratories, in different countries, on different instruments.

Materials

     

 References

  1. Shi, T., et al., Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomicsProteomics, 12(8), 1074-1092 (2012).
  2. Liebler, D.C., and Zimmerman, L.J., Targeted quantitation of proteins by mass spectrometryBiochemistry, 52(22), 3797-3806 (2013).
  3. Martínez-Bartolomé, S., et al., Guidelines for reporting quantitative mass spectrometry based experiments in proteomicsJ. Proteomics, 95, 84-88 (2013).