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质量分析:蛋白质可以通过自动方法(如定义酶作用的灵活命名法)或手动方法进行裂解。多肽显示与许多参数(各种质量值- mono, ave，电荷- Bull&Breese指数，HPLC指数，pI，电荷)，并可以进一步工作(如交联，新的分裂)。
生物信息学:可显示多种图形、疏水性、点图、二级结构预测。可以在本地数据库上执行BLAST搜索。使用ClustalW的多重对齐。CustalW可执行文件现在是GPMAw包的一部分，但是在以前的版本中，您必须自己安装。
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.
Every 10th residue is labeled with the residue number as a subscript when showing 3-letter residue code (divided by 10, i.e. residue 120 is labeled with 12) or as a small tick mark when showing 1-letter code. The feature can be turned off Setup. Use the 1/3 button in the toolbar to switch between 1- and 3- letter code.
By highlighting part of the sequence you can easily obtain the mass of the given peptide(s). For easy navigation you can color specific residues (three different colors and underlining are available).
Most of the settings can easily be pre-set in the System setup box.
The toolbar of the sequence window contains the following:
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