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 Search Results Explained
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MassMatrix Chemical Formula Syntax
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MassMatrix PC GUI Manual
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MassMatrix Search Form Help
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