Reduced Cys

When you are working with the standard mass file, aa_mass.mss, Cys is defined as the composition C3H4N1O1S1 and thus having a monoisotopic mass of 102.00 Da. When this is the case, the oxidation status of Cys (i.e. whether it is oxidized as part of a disulfide bridge, SS, or in the reduced state, SH) is controlled by the ‘SS’ button next to the mass file selection box in the main toolbar.

You can now by clicking the ‘SS’ button change all Cys residues in a sequence from oxidized to reduced in a single click - the button will change its legend to ‘SH’. You will also notice that the mass of any protein on the desktop will increase by one for every Cys residue in the sequence.

How do I modify all my Cys residues?

A typical reaction to perform when analyzing proteins, is to reduce and alkylate all Cys residues in order to break disulfide bonds and to make cysteine resistant to spurious modifications. In GPMAW the easiest way to do this is to change the mass file. This will result in recalculation of all sequence windows containing mass values.
The default files delivered with GPMAW are these:

File	Derivatization	Comment/derivatizing agent
aa_mass.mss	None	Standard mass file. Cys is defined as reduced/non-reduced cys initially depending on the Setup (display defaults) then on the SS/SH button
acetamid.mss	Acetamide	Iodoacetamide
ae_cys.mss	Aminoethyl
cmcys.mss	Carboxymethyl	Iodoacetic acid
cysacid.mss	Oxidized	Cysteic acid
pe_cys.mss	Pyridylethyl	Vinylpyridine

By editing a mass file and saving under a new name, you can create additional modifications.

How do I modify a single Cys residue?

If you need a single residue to be modified, you can either double-click on the residue and in the Modify residue dialog box, enter the modification, or you may right-click on the residue and select the second option in the pop-up menu, Modify Cys-xx, where you can directly select a number of modifications. If you select the option Reduced Cys, a hydrogen will be added to the specified Cys residue, and the residue will stay reduced, you can thus mix oxidized and reduced Cys residues!.

When modified by either method, the Cys residue will stay modified without regard of the status of the ‘SS’ button.

Site last updated: April 14, 2024