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New features in GPMAW version 9.10
Version 9 of GPMAW was coded with a new version of the compiler, which converted all string handling to unicode. This broke quite a lot of code in GPMAW, with the result that a couple of minor version were released before all the bugs were weeded out. A few more errors have been corrected (most likely gone unnoticed) and as the Internet always develops, adaption to changes here have been made.
A number of improvements have been made to the ms/ms searching using the X!Tandem search engine.
Found sequences can now be saved to a FastA formatted file.
Click on mass/deviation graph will scroll peptide list to clicked entry.
Filter mgf files: saving of filtered files did not take changes in save dialog into account.
The related coverage maps has now been extended to 12 levels, and the code has been improved. You also now have a 'one missed cleavage' option. You can call the coverage map from the peptide list (right-click, pop-up menu), and you have the option of a 'heat map':
The 'About' box now has 'include info' and system info.
The theoretical ms/ms cleavage prediction now has a tab showing ms/ms of disulfide linked peptides (or other kind of cross-links).
Traditionally the sequence files, mass files etc has been located in sub-directories to the main gpmaw-directory. However, in recent versions of Windows (Vista, Win 7), this is not possible when the slightest restrictions has been imposed on the system (Windows User Access Control). This is the case for most companies and for this reason, the directory layout has been changed. In order for compatibility, the old structure is still supported, but if you get the slightest problem in saving files, you should change to the new directory layout.
A number of minor errors and fixes:
Various aspects of the cleavage analysis changed.
Protein Explorer drive selection fixed.
ClustalW calling fixed.
User-defined pI fixed
'Digest all' menu item fixed.
Number of N- and C-terminals increased to 13
Conversion of FastA files for better fit to Excel
Inclusion list can now be defined with 2-4 decimals.
Direct loading of modification files through dropdown menu (Insert Modif)
This list is by no means exhaustive, as many more minor changes have been made.
The manual has been updated (312 pages). Note that the manual has been designed in format A5, which means that is presents itself best when printed in 'booklet' format (2 printed pages / page). Download here.
The 'Dummies guide to GPMAW' is an introductory manual to GPMAW has been rewritten to be more of an introduction, and is updated to version 5.10. Format is the same as for the manual. Download here.
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