dear list,
i modified some of my mzXML files by removing ms2 spectra which did not
fulfill certain criteria.
afterwards i tried to analyze them via xtandem but got error messages like
might be a corrupted file.
to overcome this problem i used indexmzXML which corrected the index by
generating a
Hi Andreas,
You may need to re-number the indices so that the scans start at 1
have no gaps between subsequent ones, as well as adjust the total scan
count in the header of the file. Then apply the re-indexing.
Hope this helps,
--Luis
On Tue, Mar 23, 2010 at 9:46 AM, Andreas Quandt
hey luis,
nice to hear from you and many thanks for your fast answer!
unfortunately this does not do the trick :-(
i renumbered the scans starting from 1 (for ms1 and ms2 in ascending order),
ran indexmzXML on the file (successfully) and
tried 'MzXML2Search -mgf' afterwards.
and then
Does the file pass general XML validation? That is, did you possibly damage
it structurally?
It's hard to discuss these things without looking at the actual file, can
you upload to the group's files area?
Brian
On Tue, Mar 23, 2010 at 1:20 PM, Andreas Quandt quandt.andr...@gmail.comwrote:
hey brian,
nice to hear from you too and also thanks for picking up on this :-)
according to xmlwf the modified.mzXML is valid.
i uploaded both, original.mzXML and modified.mzXML to
ftp.systemsbiology.net/incoming.
it would be great if you guys could spare some time to help me with this as
i am
Andreas,
I don't believe Brian or any other helpful external person can access
the files when you place it in ISB's ftp site.
Anyways, the ramp parser is frail and finicky and expects an mzXML to
be formatted just the way it expects. Your modified mzXML has a lot
of formatting changes. The
Andreas,
When I modified your file get rid of all whitespace between the
peaks tags, the MzXML2Search program subsequently ran fine.
change:
peaks precision=32 byteOrder=network pairOrder=m/z-int
Q0BLmUBez4BDSRBhQQDRN0NN...w==
/peaks
to:
peaks precision=32
