Example 1: TMT based Quantitation of complex experimental setups

This example demonstrates the analysis of a complex quantitative experiment. A549 cells were treated with nano particles (CuO) or left untreated (Control). Both conditions were harvested at six different time points. The different time points were labeled with 6plex TMT (Tandem mass tags). Analysis was performed using OpenMS and isobar [1].

Please note that the name of the sample (A549_CuO) and the path were the report files should be stored are encoded as flow variables in the workflow.

The sample_data folder contains the mzML files of the individual MS runs, the used sequence database, and the experimental configuration (labeling schema).

References

[1] Breitwieser F. P., Müller A., Dayon L., Köcher T., Hainard A., Pichler P., Schmidt-Erfurth U., Superti-Furga G., Sanchez J.-C., Mechtler K., Bennett K. L., and Colinge J. General Statistical Modeling of Data from Protein Relative Expression Isobaric Tags Journal of Proteome Research 2011 10 (6), 2758-2766