- General Usage
Should you prefer to manually provide your experiment settings or tweak those suggested by auto-detect then you can toggle manual mode by checking the "manual entry" checkbox. Once checked the input fields will become enabled and you can alter any settings of your choosing.
The labels are limited to those modifications which are found in the data, if your label is missing this is due to it not being present in the data. The most likely cause is due to it either not being searched, or the search not finding the specified modification. You should repeat your identification search with Progenesis again, and then re-export the data to Proteolabels.
Further, the list of residues suggested for each modification is limited to those residues which the modification is found on. If a residue is missing then, as previous, the modification has not occured on that residue in the data. If you believe this is incorrect, the identification search will need to be recompleted.
The mass tolerance value is dependent upon the resolution of your MS instrument. If you are unsure as to the correct value it is suggested you perform a search on a wide value and then reduce the value after inspecting the mass delta plot.
The retention time tolerance value should correspond to your data type, for example in SILAC experiments we would expect an RT shift of near-zero. However, in other experiment types a retention shift may occur (i.e. dimethyl). If you are unsure on the most appropriate value, try a search with a wide tolerance and then reduce accordingly after viewing the retention time delta plot.