Matlab MS preprocessing files

We include here the set of scripts used for preprocessing the original MS data. See the previous section for a more detailed explanation on each of these tasks.

Example of how the preprocessing code could look like (the user must set the value for the minLevel parameter, all the rest parameters are set to the suggested values):

% 1. Baseline removal
Y_bs = msbaseremove(Y,[0; ones(298,1); 0]);

% 2. Normalization
Y_bs_norm = msslidenorm(MZ, Y_bs, 200);

% 3. Smoothing
Y_bs_norm_sm = mssmooth(Y_bs_norm, 6, 10);

% 4. Peakbin construction
peaks = mspeakdetect(MZ, Y_bs_norm_sm, minLevel, 3);
[P_union, index, P_w]= mspeakunion(peaks);

% 5. Peakbin assembling and quantification
[peakBins, Y_peaks]= mspeakassemble(Y_bs_norm_sm,index,0.80);

Please, notice that this material is provided under no warranty and no responsibility for its use. You can download a zip file with the scripts source from