When proteins are expressed in real biological systems, the masses of target proteins may not be known exactly due to post-translational modifications (PTMs). Conveniently, ProMass can be configured to automatically search for user-defined PTMs for each target mass that is defined. PTM targets are different than normal ProMass target masses in that they are only displayed in the ProMass reports if they are found. PTM mass changes are defined in the znova_masses.ini configuration file. Putative PTMs are automatically listed in the Target Mass summary of the ProMass report as well as the Excel summary sheet if it is in use. In order for ProMass to automatically search for PTMs, the following conditions must be met:
ProMass will look for PTM target masses for each target mass that is specified by searching the appropriate list in the znova_masses.ini file. Each PTM is identified by a descriptive string and a mass difference from the target mass. For example, consider the list of configured PTMs below.
[PTMs]
Minus Met = -131
Plus Acetyl = 42
Phosphorylation = 80
In the example listed above, loss of methionine results in a decrease of the expected mass by -131 Da. Acetylation results in a 42 Da increase in the target mass, and a single phosphorylation results in an 80 Da increase. These modifications will be considered when searching for PTM target masses. Please note that ProMass will NOT consider all possible combinations of defined PTMs. For example, if you expect your protein to contain 2 or more phosphorylations, you need to enter separate entries for each possible phosphorylation state, e.g.:
[PTMs]
2X Phosphorylation = 160
3X Phosphorylation = 240
4X Phosphorylation = 320
Finally, the example below shows how to disable PTM searching by commenting out all of the PTM masses. To comment out an entry, put one or more # characters before the PTM definition.
[PTMs]
#Minus Met = -131
#Plus Acetyl = 42
#Phosphorylation = 80