Hi David,
-c is not a standard parameter. It is a filter that specifies centroiding instead of profile mode...
thus your ReAdW DTA has peaks and your msconvert DTA has profile data points. But I also suggest
that mzxml2search should have printed a warning (or did you ignore it?) because the
Moving to proteowizard-support.
Yes this bug is still there. I didn't know about NCD. What is NCD a percent of? I.e. how can real
electronvolts be calculated?
Thanks for reporting,
-Matt
On 12/14/2012 5:43 PM, Dmitrii Tchekhovskoi wrote:
Software:
software id=pwiz version=3.0.3495
cvParam
Hi Chris, did you try the analyzer filter? Filtering one file on IT and the
other on FT should do what you want with no hassle.
-Matt
On Feb 5, 2012 8:35 PM, Chris Rath chrisr...@gmail.com wrote:
Hey everybody:
I have a bunch of LTQ-FT data with alternating MS1 scans in the IT or
FT cells. I
The latest ProteinProspector performs as well as pfind if used properly. See
the 2011 abrf iprg study on etd analysis. Does pfind write pepxml?
-Matt
On Jul 26, 2011 2:00 AM, Amit Yadav amit007thech...@gmail.com wrote:
Thanks Kristian.
I think you have summed up the situation well. I did use
The compatability problems are usually between the version the file was
acquired with and the version of Analyst you have installed. Older versions
of mzwiff aren't likely to fix the problem afaik. However you can use
msconvert or, if you need peak picking (better than analyst), use absciex's
Is there a way to make X! Tandem respect charge state(s) specified in an MGF
file? I haven't tried mzXML/mzML (this is the TPP version) yet, would it work
for those formats?
-Matt
--
You received this message because you are subscribed to the Google Groups
spctools-discuss group.
To post to
= - but that gets lost along the way? Or does your MGF
possibly describe charge in another fashion? I have the impression
there are variants.
Brian
On Mon, Dec 13, 2010 at 9:09 AM, Matt Chambers
matt.chamber...@gmail.com wrote:
Is there a way to make X! Tandem respect charge state(s) specified
I'm pretty sure it indicates m/z error of the matched peak with the theoretical
m/z. I'm not sure what the ^3 means though.
-Matt
On 11/25/2010 9:32 PM, GATTACA wrote:
Hello.
Can someone explain to me the syntax in of the peaklists as they are
reported in the SpectraST *.sptxt file?
I
For an orbi/ltq run, myrimatch.cfg might look like:
PrecursorMzTolerance = 10
PrecursorMzToleranceUnits = ppm
FragmentMzTolerance = 0.5
FragmentMzToleranceUnits = daltons
ProteinDatabase = c:\foo\bar.fasta
NumMinTerminiCleavages = 1
CleavageRules = trypsin/p
DynamicMods = M * 15.9949 C * 57.0215
Did you extract ALL the files from the pwiz-bin package to the same directory?
-Matt
On 11/5/2010 8:40 PM, tgreco wrote:
I was having same problem with msconvert as described above (on
windows 7 64-bit). I installed MSfilereader and newest Proteowizard
package (to tpp-bin) as suggested. But
What is the purpose of the msRun startTime attribute? It's an
xsd:duration type so using it to store a point in time seems odd. But
the documentation The time at which the run was started. clearly seems
to refer to a point in time.
Andrew, a straightforward compromise here is to use msconvert
As Natalie suggested, Analysis.yep indicates the Bruker/Agilent YEP
format which ProteoWizard reads with CompassXtract. Msconvert will
automatically detect the format of the .d directory and use the
appropriate reader. Keep in mind the CompassXtract interface (which
supports Bruker FID/BAF and
It's not in the online command-line manual, but it's in the usage
statement for omssacl:
G:\work\omssa\omssa-2.1.7.win32omssacl
USAGE
omssacl.exe [-h] [-help] [-xmlhelp] [-pm param] [-d blastdb] [-umm]
[-f infile] [-fx xmlinfile] [-fb dtainfile] [-fp pklinfile]
[-fm pklinfile] [-foms
starting at 1, whilst msconvert
uses the Agilent scan ID (can be a very large number). MzXML2Search
conversion of the resulting file into mgf then fails once it reaches a
scan ID 99,999.
Have seen similar problems with other programs and contacted Matt
Chambers who said that the numbering
Hi Andris,
ReAdW gets the ms level and polarity from the filter line, but in this
case it doesn't know how to deal with the filter line so it seems to be
silently aborting the filter parser. The extra coding and hassle
should happen to the parser code instead of your own code (IMO). But in
Try a later release of pwiz. I know that's the one that the web page
points to as the default, we're working on a way to improve that.
Silvia Rocchiccioli wrote:
Hi Matt,
thank you.
I have tried to use ProteoWizard..., I can create the mzXML file
starting from mzML but when I try to
Probably you didn't pass it a valid Agilent path. The source file is
actually a directory (ends in .d). But the data is stored inside files
of course as MSPeak.bin or MSProfile.bin. IIRC you can pass it any of
those three (the .d directory, or the .bin files). Also, a MassHunter
installation
Msconvert should enumerate all the non-SRM and non-SIM spectra. Due to
performance issues of the API, it enumerates cycles first, then
experiments, then periods. For example:
sample=1 period=0 cycle=123 experiment=1
sample=1 period=0 cycle=124 experiment=1
sample=1 period=0 cycle=125
Hi Ben,
50gb for one file? That's impressive. That could be much improved with
compression (which the Agilent MH format also does), but since you need
to peak pick the MSn to identify them in most search engines, try this
command:
msconvert source.d --mzXML --filter peakPicking true [2,2]
It usually comes down to spectrum processing - specifically scan
combination, deisotoping, and centroiding. MassWolf and msconvert are
unlikely to be able to do as well as the vendor's own processing without
significant effort devoted toward optimizing on that platform. I'll take
a look at
Were all the wiff files acquired with the same version of Analyst? If
not, that's probably the issue.
I recommend trying msconvert which reads WIFFs with a different API from
mzWiff: instead of depending on the myriad of different Analyst
versions, it uses the unified DLLs from Protein Pilot
Natalie, the link I sent explains what a precursor ion scan is. A
data-dependent scan is a kind of product ion scan. A precursor ion scan
is quite different and can't even be represented in mzXML as far as I know.
-Matt
Natalie Tasman wrote:
Hi Ronny,
I now see that you meant precursor
, 2009 at 1:38 PM, Matt Chambers
matthew.chamb...@vanderbilt.edu
mailto:matthew.chamb...@vanderbilt.edu wrote:
Natalie, the link I sent explains what a precursor ion scan is. A
data-dependent scan is a kind of product ion scan. A precursor ion
scan
is quite different
I haven't followed the rest of this thread, but msconvert can convert
MGF to mzML or mzXML. It's pretty much impossible to match up the scan
numbers though without knowing exactly how to parse the TITLE attribute
(if it's even available!).
-Matt
marpello wrote:
Hi,
I tried to use -p0, but
24 matches
Mail list logo
