Hi,
I am currently trying to compare a proteome dataset using only a small selection of protein abundances. Specifically, I want to use a selection of 21 proteins, sum the intensities of these proteins within each sample together, and compare the total intensity (log2 transformed) between several groups by T-testing.
I am however unsure if this is possible/allowed?
Any help is greatly appreciated.
Yes, but there are limitations in the methodology due to the fact that MS abundance is unidirectional. Look at the following:
Method Mass Spectral Data Processing
Method ISOTOPIC VECTOR ANALYSIS IN MASS SPECTROMETRY
Sure you can do that. But depending on what you want to conclude from this it might not be fair. For example, if one protein has much greater influence on the total than the others, you might innaccurately decide they are all higher. Why not just do the things tests on each protein and follow with q value correction? Also be sure to detail exactly what you did in the methods section.
If you're looking for specific tools, I've used Maxquant for label free quantification coupled with Inferno for results visualization and statistical analysis. (links attached).
https://omics.pnl.gov/software/infernordn
http://www.biochem.mpg.de/227318/MaxQuant
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