bit basic but if you have both normal and stressed mass spec data (shotgun) try using mMass to subtract one from the other you should normalize your data sets first within the programt. I.e if i have a treated and untreated samples, once spectrums are normalized, can subtract the normal from the treated spectrums to highlight changes in both mass shifts and relative abundances. use your matrix fingerprints to double check the normalization as your data sets The same can be done to get rid of your peaks from the matrix.