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GPMAW™ General Protein Mass Analysis for Windows

Mass spectrometric analysis of proteins and peptides and more.

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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 these 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 may even run it on a netbook.

GPMAW™ General Protein Mass Analysis Program content


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.

 

GPMAW™ General Protein Mass Analysis Program Features


Sequence window

The sequence window is the default view of a sequence. From here you can call most of other sequence related functions (either through the menu, the toolbar, or the pop-up menu).

The display can be configured in various ways, 1- or 3-letter display, average mass/monoisotopic mass, fixed residue width, sidebar with sequence information, show disulfide bridges etc. By highlighting part of the sequence you can easily obtain the mass of the given section. For easy navigation you can color specific residues (three different colors and underlining are available).

Most of the settings can easily be pre-set.

The sequence window is the parent window from which a large number of derived daughter windows can be created:

  • Peptide window
  • Ms/ms window
  • Mass search, composition search
Available graphs
  • Hydrophobicity
  • Secondary structure
  • Charge vs. pH
  • Dot-plot
  • Alpha-helical wheel
Peptide window

The peptide window is normally called from the sequence window through the automatic digest commend. However, there are alternative methods like manual or semi-automatic cleavage.

The peptide window lists all the peptides that will be generated from the given protein along with a large number of physical-chemical parameters (charge single/multiple/negative, peptide number, location, HPLC index, theoretical pI, Bull & Breese index, sequence - 1/3-letter etc.).

Peptides can be generated with partial cleavages, modified termini, modified residues (even partial modifications are supported in a limited way). Specific residues may be colored for easier referencing.

The actual parameters presented can be configured by the user.

Sorting and reverse sorting can take place on any column by clicking on the header.

Through the toolbar and/or the pop-up menu (right mouse click) you can access a large number of additional functions related either to the digest (like the simulated HPLC reversed phase chromatogram) or to the currently selected peptide (ms/ms cleavage, peptide information, charge vs. pH graph).

User Defined pI Values

How are these pKa values then used by GPMAW? For the modifications, it is quite simple, as the pKa values are taken into the calculations of pI and charge whenever they are defined in a sequence (i.e. whenever a residue is modified with the relevant modification).

However, for the mass file GPMAW has a user-defined table, as GPMAW has four different tables.

The first and third are values taken from the literature (references in the on-line help and the manual). The second option is based on the values for free amino acid residues. The fourth and last option is based on the definitions in the currently selected mass file and has to be checked in order to use these values.

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