GPMAW - General Protein/Mass Analysis for Windows
The GPMAW program is primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis.
The program runs on all 32-bit versions of Windows since Windows 2000 (i.e. 2000, XP, Vista, Win7). It will also run on current 64-bit versions, but has not been thoroughly tested on this platforms. It can also run on Mac systems with a Windows emulator, but full compatibility is not guaranteed.
Except for the ms/ms search, the program does not need a strong processor or fast hard disk but can run on any system. Running the ms/ms search you need a screen with SVGA+ resolution, otherwise, you can even run it on a netbook.
Documentation for GPMAW is presented in the HELP section, the manual is available for download here.
An introduction is also available as a ‘Dummies guide’.
Sequence handling: Import of sequences from a number of different formats with direct database search in Entrez and in local databases (FastA format and Swiss-Prot). Sequences can be saved in local files (databases) for future reference.
From the sequence window a large number of actions can be performed. Sequences can be exported in FastA format (either singly or all sequences at once) for easy transfer to other programs.
Mass analysis: The protein can be cleaved by automatic methods (e.g. a flexible nomenclature for defining enzyme actions) or manually. The peptides are displayed with a number of parameters (various mass values - mono, ave, charges - Bull&Breese index, HPLC index, pI, charge) and can be further worked upon (e.g. cross-linked, new cleavage).
Peptide mass searches can be performed on any local database in FastA format.
Bioinformatics: A number of graphs can be displayed, hydrophobicity, dot-plot, secondary structure prediction. BLAST searches can be performed on local databases. Multiple alignment using ClustalW.
The CustalW executable is now part of the GPMAw package, but on previous versions you have to install yourself. Read here how.
For more details please see the following:
User defined pI values.
Working with labeled residues
If you have identified a protein using peptide mass fingerprinting - how can you use GPMAW to extend these findings?
Cross-linking with transglutaminase.
Databases. GPMAW is able to take advantage of the large databases that are available on the Internet. Read how to use and download them here.
Pricing and ordering information can be found in the Price info section.
Note on directory structure layout.