how to calculate mass with UniMod:188

[manto...@gmail.com]

Hi~

If the modification is formatted like: UniMod:188, how to calculate the mass of peptides? 

Thanks.

[Lev Levitsky]

Hi!

You can use one of the two Unimod interfaces to extract the modification mass.

With mass.Unimod (update to the latest commit for this to work):

In [1]: from pyteomics import mass
In [2]: db = mass.Unimod()

In [3]: db[188]['mono_mass']                                          
Out[3]: 6.020129

or with mass.unimod.Unimod:

In [1]: from pyteomics import mass

In [2]: db = mass.unimod.Unimod()

In [3]: db.get(188).monoisotopic_mass

Out[3]: 6.020129

You can then add the modification mass to the unmodified peptide mass.

Where are you getting the data from? Is it an MzIdentML file? Perhaps we should look into ways of integrating Unimod classes with mzid parser.