Hi Jimmy,
Yes, you are right. SSM411 is how I named my sample, and F030382 is the .DAT
file name generated by MASCOT.
I have renamed them by SSM411.*.
I didn't convert the .mgf file using MzXML2Search ealier. I used the pkl
files generated by PLGS (Waters) from .raw data to do the Mascot
There's no surprise that generating mgf files using other tools can
cause Mascot to perform (much) better as those tools apply things like
peak picking which MzXML2Search doesn't do. MzXML2Search pretty much
just takes the input spectral data and writes it back out into the
chosen output format.
Hi Brian,
I ran the Mascot search again with trypsin as enzyme, instead of
tryspin/P. The .dat file was able to convert to .pep.xml file successfully
(cool!). Well, there is a warning at the end of the command lines, and I
don't know how important this is.
...
333. opening
Try renaming the mzXMl file to F030382.mzXML, maybe?
On Mon, Jun 28, 2010 at 4:37 PM, Jing Wang fayfay9...@gmail.com wrote:
Hi Brian,
I ran the Mascot search again with trypsin as enzyme, instead of
tryspin/P. The .dat file was able to convert to .pep.xml file successfully
(cool!). Well,
When charge states are not listed in the mzXML file you should run the command:
MzXML2Search -mgf -c1-3 *.mzXML
This will generate the mgf files to submit to Mascot.
Once you get the .dat files back you should rename that to the
original basename of the mzXML file with the .dat extension.
Now
Actually, after a discussion on the phone with Jimmy, I think that the
-c1-3 option is not needed in this case and will cause some extra
searches being run. Just use
MzXML2Search -mgf *.mzXML
And then rename the resulting .dat file to match the input basename.
-David
On Mon, Jun 28, 2010 at
Brian,
Thanks for looking into my search file.
Anything I can do now to fix the first problem?
Sorry for uploading the file to the wrong place. I did what the link, how
to upload files to the SPC team, describes at
http://groups.google.com/group/spctools-discuss?hl=en. Couldn't believe I
I don't see it there...
On Fri, Jun 18, 2010 at 5:57 PM, Jing Wang fayfay9...@gmail.com wrote:
Hi Brian,
Thanks!
I have uploaded my mascot search file (F030337.dat).
Fay
On Fri, Jun 18, 2010 at 2:52 PM, Brian Pratt brian.pr...@insilicos.comwrote:
Hard to say what's going on. Perhaps
Hi all,
I posted my questions yesterday, but they were a bit too long to read,
so I shortened it (still seems long).
I am trying to use TPP (4.3.1) to run some cICAT data I collected a
while ago. All these cICAT data have been searched by Mascot (I have
all the .dat files). So far I have not got
Hard to say what's going on. Perhaps you could upload your new mascot
result file to the files area at
http://groups.google.com/group/spctools-discuss?hl=en. and someone can have
a look.
Brian
On Fri, Jun 18, 2010 at 11:09 AM, Fay Wang fayfay9...@gmail.com wrote:
Hi all,
I posted my
Hi Brian,
Thanks!
I have uploaded my mascot search file (F030337.dat).
Fay
On Fri, Jun 18, 2010 at 2:52 PM, Brian Pratt brian.pr...@insilicos.comwrote:
Hard to say what's going on. Perhaps you could upload your new mascot
result file to the files area at
11 matches
Mail list logo
