Support for mmSearch

(LC-MS/MS database search software)


Question  –  What do the color coded amino acids mean in your results?

Answer  –  Please refer to the online manual (pages 8-14).

Question  –  Any suggestions on how I can reduce the time it takes to do a crosslink analysis on my PC?

Answer  – You can reduce “max # of xlinks/peptide” from 2 to 1.  This reduction will decrease the number of theoretical peptides by ~10.  Reduction of the search space will make the search run much faster.

Question  –  Will reduction in the “max # of xlinks/peptide” from 2 to 1 compromise my search results?

Answer  –  For chemical crosslink searching, it is rare to have a high quality peptide match with two chemical crosslinks. The data can be searched again with a higher value to rule out any possible missed crosslinks.

MassMatrix Manuals

MassMatrix Search Results Explained

Download MassMatrix Search Results Explained (PDF)

MassMatrix Chemical Formula Syntax

Download MassMatrix Chemical Formula Syntax (PDF)

MassMatrix PC GUI Manual

Download MassMatrix_PC_GUI_Manual (PDF)

MassMatrix Search Form Help

Open MassMatrix Search Form Help (html)

Ask a Support Question

If you have any questions or comments about MassMatrix, please complete the Ask a Support Question form.

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