Ben,
Have you done anything special to handle the scan numbers (which
presumably are not consecutive anymore starting from scan 1) and the
scan index? If not, address those and re-test or find out if those
are important for MSGF-db.
On Thu, Jun 14, 2012 at 10:02 AM, Ben Temperton
Hi Jimmy,
I have updated the scan numbers using a new method (attached), but I am
stuck at changing the offset values for each of the scans in the
/index/offset elements. I think this is what is causing the 'premature end
of file' error - by not changing the offsets, MSGF-db can't find the
The index is technically optional, you should be able to just skip it
in your output.
(technically and should, as some parsers are brittle and will fail
without it - good luck!)
On Thu, Jun 14, 2012 at 12:38 PM, Ben Temperton btemper...@gmail.com wrote:
Hi Jimmy,
I have updated the scan
