Analysis of a three TMT labeling experiment of the developing mouse lens processed with MaxQuant 1.5.7.4.
Click on the Jupyter notebook file (multiple_TMT_MQ.ipynb) to see the notebook in your browser. It may take a minute for the page to render and load, so please be patient.
The data is SPS (multi-notch) MS3 of 10-plex TMT. There are 6 developmental time points in each of three TMT experiments. Despite the lack of any common reference channels, the balanced experiment design lends itself to an internal reference scaling like treatment using the TMT experiment averages as proxies for standards.
Khan, S.Y., Ali, M., Kabir, F., Renuse, S., Na, C.H., Talbot, C.C., Hackett, S.F. and Riazuddin, S.A., 2018. Proteome Profiling of Developing Murine Lens Through Mass Spectrometry. Investigative Ophthalmology & Visual Science, 59(1), pp.100-107.
There are data files, some spreadsheets, a Jupyter notebook file, and an HTML rendering. Some detailed data filtering was done in Excel before analysis in R. There is a file with the detailed step-by-step details.