Daniel Polasky

Hi Adam, We don't combine the HCD and EThcD scans - each is searched and quantified independently. But there's nothing that (should) prevent scans that are matched to a glycopeptide...

The numbers seem pretty reasonable as you say - I'm not sure why the MSFragger histogram looks so bad given how the smaller comparison looks. What is going into that...

Thanks, that helps a lot. I tested with some hybrid data here to see if I could get something similar. The dataset I used for testing is fractionated - if...

Support for pairing specific diagnostic ions, fragment remainder ions, and/or peptide remainder ions to specific mass offsets is now available in MSFragger 4.1 and FragPipe 22, using the new detailed...

Hi Hans, We have indeed now implemented O-Pair search in FragPipe, which supports searching for multiply O-glycosylated peptides if you have both collisional (HCD/CID) and electron-based (ETD/EThcD/etc) scans in your...

Hi Hans, I see - this actually sounds like a great case for our new labile search mode (https://www.sciencedirect.com/science/article/pii/S1535947623000488), which can use what we call "fragment remainder ions" (the 120...

Hi Rebecca, This is still on our to-do list, but I am optimistic it will be getting done in the relatively near future. Stay tuned! Best, Dan

Hi Antje, Yes, we are planning to implement modification (mass offset)-specific ions to allow this kind of search and filtering. It is not ready yet, but I will post here...

Support for pairing specific diagnostic ions, fragment remainder ions, and/or peptide remainder ions to specific modifications is now available in MSFragger 4.1 and FragPipe 22, using the detailed mass offset...

Hi Kevin, Reporting a list of specific ions matched for each PSM is not a feature in MSFragger at this time. You can see the total number of matched ions...