Writing up the pipeline for external FTMS users

original file from 2009; updated 12 August 2024 by Krista Longnecker

Department of Marine Chemistry and Geochemistry
Woods Hole Oceanographic Institution
klongnecker@whoi.edu

MATLAB changed their rules for name resolution, see details here. We have not edited the code to handle this change, so you must use MATLAB versions prior to R2019b for this to work.

The database required to run this code exceeds GitHub's limits on file sizes. The database is available upon request from Liz Kujawinski (ekujawinski@whoi.edu) or can be downloaded from here. The name of the file is: LongneckerKujawinski_fullCompoundList.2016.11.21.mat

Step 1.

Align the peaks within the desired margin of error. For the WHOI instrument, we have been using 1 ppm. In the line below, the first '1' indicates that the code should use a 1 ppm margin of error for the peaks. The second '1' instructs MATLAB to show you its progress - that can be changed to '0' if you don't want to have any information printed out in the command window.

Note that code expects 'data' to be a matrix with multiple cells. There will be one cell per sample. Within each cell, there is a two column matrix. The first column is the list of m/z values in that sample and the second column is the peak heights for each m/z value.
[Peaks Intensity] = multiple_spectra_KL4(data,1,1);

The original reference for the alignment code is: Mantini,Petrucci,Pieragostino, Del Boccio, Di Nicola, Di Ilio, Federici, Sacchetta, Comani and Urbani (2007). "LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise." BMC Bioinformatics 8: 101.

Step 2. Find the elemental formulas for your peaks.

We've provided our algorithm below (based on Kujawinski & Behn, Analytical Chemistry 2006) and modified in Kujawinski et al., GCA, 2009. The citation details are:

• Kujawinski, E. B. and M. D. Behn (2006). "Automated analysis of electrospray ionization Fourier-transform ion cyclotron resonance mass spectra of natural organic matter." Analytical Chemistry 78: 4363-4373.
• Kujawinski, E. B., K. Longnecker, N. V. Blough, R. Del Vecchio, L. Finlay, J. B. Kitner and S. J. Giovannoni (2009). "Identification of possible source markers in marine dissolved organic matter using ultrahigh resolution mass spectrometry." Geochimica et Cosmochimica Acta 73: 4384-4399.

Step 2a. Convert to neutral mass

You need to pick the right conversion to neutral masses based on your ionization mode. To convert to neutral mass you add or subtract as follows:
H = 1.007825032;
elec = 5.4858e-4;
IUPACpeak = Peaks + H - elec; %for negative ion mode
IUPACpeak = Peaks - H + elec; %for positive ion mode, Na-adducts are also likely

Step 2b. Call the MATLAB function

The database must be in the path before you run the MATLAB code. This means you will need to change this next line to the location of the database (LongneckerKujawinski_fullCompoundList.mat).
fDir = 'C:\Documents and Settings\Krista\My Documents\MSdataAnalysis';
path(path,fDir);
load LongneckerKujawinski_fullCompoundList.2016.11.21.mat

[formulas elementOrder] = findformula_useList_KL17(IUPACpeak, zeros(size(IUPACpeak)), 1, 20, 500,fullCompoundList,'HAcap',1);

Step 3 Now go through and find the C13-containing formulas

FormulasC13 = quick13C_KL_1(formulas,IUPACpeak,0);