I am trying to use Smiter to generate synthetic mzml data, using the PeptideFragmentorPyteomics to fragment a list of peptides. I tried following the basic example scripts (https://github.com/LeidelLab/SMITER/blob/dev/example_scripts/write_peptides.py), didn't even add noise. I'm giving as input about 100 peptides, but for some reason I keep getting a very small amount of MS2 scans (the logs says Write 1908 MS1 and 92 MS2 scans). In reality the data I'm trying to imitate would have a lot more MS2 scans than MS1 (since for every MS1 peptide there would be multiple MS2 fragments).
What am I doing wrong?
I am trying to use Smiter to generate synthetic mzml data, using the PeptideFragmentorPyteomics to fragment a list of peptides. I tried following the basic example scripts (https://github.com/LeidelLab/SMITER/blob/dev/example_scripts/write_peptides.py), didn't even add noise. I'm giving as input about 100 peptides, but for some reason I keep getting a very small amount of MS2 scans (the logs says
Write 1908 MS1 and 92 MS2 scans). In reality the data I'm trying to imitate would have a lot more MS2 scans than MS1 (since for every MS1 peptide there would be multiple MS2 fragments).What am I doing wrong?