Support for negative mode data

[Steffen Lemke]

Dear Jimmy,

I was wondering whether it's possible to analyze negative mode proteomics data with Comet. From what I can tell, the documentation only references positively charged precursors.

Best regards,
Steffen

[Jimmy Eng]

(Updating the google group thread ... I replied to Steffen directly yesterday)

It might have come up over the years and I've just forgotten but yours is the only inquiry for negative mode data support that I can recall.  Which means unfortunately Comet only works for positive ion mode data.

I believe OMSSA (no longer supported but hopefully still functional) and Byonic are the two peptide ID tools that support negative mode data.  

Jimmy

EDIT:  I should add that I'm not opposed to adding such support into Comet but this would take some time to get to. If you have flexibility on time frame (months out) and are interested in helping to drive this development, let me know and I'll follow-up with you when I have free time to tackle this.