#69 Tide theoretical spectra are limited to charge 2+ fragments

[Jeff Howbert]

Tide theoretical spectra are limited to charge 2+ fragments - see function AddIons in peptide.cc. This will lead to different theoretical spectra than those produced by Crux when precursor charge > 3+.

This points up the need for test sets that include spectra with precursor charge > 3+.

[William S Noble]

Jimmy Eng says:

For Comet, this is controlled by a user parameter "maximum_fragment_charge":

http://comet-ms.sourceforge.net/parameters/parameters_201302/max_fragment_charge.php

Historically, Sequest would consider fragment charges up to 1 less than the precursor charge irrespective of how large the precursor might be. But I decided to modify that given we started to analyze a lot of higher charged (5+, 6+, 7+) peptides; it just didn't make sense to consider 6+ fragment ions for a 7+ precursor. Comet now will behave the same way (1 less than precursor charge) up to the specified "maximum_fragment_charge" parameter value. So if this parameter is set to "3" here's the fragment charges that would be analyzed:

precursor charge maxmimum fragment charge
1+ 1+
2+ 1+
3+ 2+
>= 4+ 3+

I think we should implement this option after Crux v2.0.