Tips & Tricks
Add “ph” behind a phophorylated residue in your peptide sequence, e.g. “PEPTphIDE”. Same works for oxidation (“ox”) and carbamidomethylation (“cm”). You can define additional modifications and also amino acid labels, e.g. labelled Lys or Arg, in ‘Data setup’ -> ‘Formulae’. For experts, in the same location, N-terminal and C-terminal modifications can also be defined, using “[" and "]” respectively. These are added automatically to the peptide and do not need to be added to the peptide sequence. Note that numbers are not allowed in the modification code, i.e. dimethylation may be written as “dm” but not as “me2″.
Expert Tip: Losses are defined in ‘Data setup’ -> ‘Losses’. These need special symbols as they are shown in peak labels. Note: In case you wonder about dashes in the peak labels, these denote isotope peaks being labelled. We label the expected most intense peak of an isotope cluster (as this one has the highest likelyhood of being observed and of having the smallest m/z error). No dash means mono isotopic peak, one dash: first isotope peak, two dashes: second isotope peak and so on.
Tip on figure making: Export your spectrum as “.svg” and open this in your favourite drawing programme, e.g. Adobe Illustrator. You will then be able to change colours and sizes of all elements. Note that the actual view is being exported. This means you can also make zooms into regions of special interest.