Differential Abundance between samples

Question

[catfishtom]

I'm new to the field and I'm trying to solve this problem - I have two files

preprocessed.csv contains pre processed spectra for the samples. In particular, the spectra have been de noised (by using wavelets) and the baseline has been removed.

mz.csv contains a list of m/z coordinates with putative peaks, obtained based on a mean spectrum.

I need to quantify the intensity at each putative peak location, indicated in the mz.csv file, by using the maximum observed normalized intensity in the window around the putative peak location bounded to the left and right by local minima.

Does anyone have any idea how to do this ?

I also need to answer the question: Are there locations, at which normal samples are statistically significantly different from the cancer samples?

Answer 1

[i.sudbery]

For protein mass spec one would usually use software such as MaxQuant to convert your spectra to peptide counts. https://www.maxquant.org/

The MaxQuant authors also offer Perseus, which can do statistical analysis of the MaxQuant output, although I think that limma is also used.