Daniel Polasky

Hi Martin, Lots of great questions - our glyco tutorials are still a work in progress, so thanks for pointing out some areas where we need more information. I'll be...

Hi Martin, I actually do make my .glyc files in Excel, but transfer it to a text editor to save - you're right that skipping that step would make it...

Hi Martin, We can probably add glycan modifications to the composition assignment process in PTM-Shepherd without too much trouble (especially if you know of good datasets for testing that would...

@ndtivendale the [filename].tsv files are generated by MSFragger before any FDR filtering is done, so they will contain more (typically many more) entries than the Philosopher outputs since they have...

@ndtivendale there's almost no filtering - MSFragger will only report spectra with at least `minimum_peaks` ions in the spectrum and `min_matched_fragments` ions matched to a peptide, but nothing other than...

@ndtivendale Without going too much into the details, the 'raw' output from MSFragger gets modeled in PeptideProphet (and has protein inference done in ProteinProphet) before the actual FDR filtering done...

Hi Andy, As you surmised, at the moment we can't associate specific diagnostic ions with specific mass offsets (modifications) unfortunately, everything is treated together. I can definitely see how it...

Are you looking for multiple glyco sites in a single peptide, or on a whole protein? As Fengchao said, we currently can only identify a single mass shift per peptide...

Hi Wouter, We are planning to implement specific diagnostic ion modification pairs soon but have not done so yet, so currently all modifications are considered when diagnostic ions are found,...

Hi Adam, I'm also not sure why you're not seeing intensities, but have a couple of thoughts from the log. First, to clarify, PTM-Shepherd will actually write identified glycans to...