PAWS is a program provided by Genomic Solutions Inc. as part of the Knexus package. It's acronym stands for Protein Analysis Work Sheet. The program was originally designed to manipulate protein sequences and perform calculations that aid in the interpretation of mass spectra. It has the capability of mapping mass spectrum information onto sequences as well as saving complex modifications to proteins.

PAWS can read a variety of different protein sequence file formats, including most of the common "flat file" formats. It has been designed to work with the mass spectrum viewing program m/z, but it is not necessary to use the two programs together.

PAWS is a program for manipulating protein sequences. Proteins can be modified by general modifications to all amino residues in the sequence of a selected type or by individual modifications to one specific residue. Proteins can be digested with enzymes from a pre-defined set of enzymes or a userdefined enzyme. Displayed peptide and protein masses can be selected as mono-isotopic or average molecular weight. Either masses or m/z values are displayed.

Highlighting of charged residues, hydrophilic residues and potential N-linked glycosylation sites or any combination of residues is possible. The font size and formatting of the displayed sequence can be controlled for report generation. Apart from the one-letter coding a special font is available that displays the amino acid residue with an icon representing the side-chain of the backbone.

Peptides from digested proteins can be matched against lists of m/z values. The matching peptides can be displayed by markings in the sequence or in a Coverage Map:

Peptides from a non-specific digest (cleavage at any point) can be matched against a m/z value. Labels describing the matched peptides can be copied to MoverZ to label peaks. All cleavage products can be copied to MoverZ to mark the place in the spectrum where a peptide could be expected. The cleavage product include all possible combinations of missed cleavages.