I suspect it's a SIM/SRM data file so by default the SIM/SRM data is represented as chromatograms
instead of spectra. The --simAsSpectra/--srmAsSpectra flags should work to address that.
-Matt
On 7/26/2013 11:00 AM, Jimmy Eng wrote:
I would suggest that you follow-up with a post at the Skylin
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 mzX
22k spectra to a 5gb file? Definitely profile mode, uncompressed! Run with
peakPicking filter and -z flag.
On Jan 28, 2013 6:28 PM, "Eric Deutsch" wrote:
> Hi SKV, thank you for your note. I don’t really know what the problem
> might be based on your description. As you surmise, there can be prob
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:
Instrument:
Filter line: "ITMS + c
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" wrote:
> Hey everybody:
>
> I have a bunch of LTQ-FT data with alternating MS1 scans in the IT or
> FT cells. I would like to
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" wrote:
> Thanks Kristian.
>
> I think you have summed up the situation well. I did use Tandem ETD in
> previo
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
conve
ProteinPilot 3 doesn't support the 5200 or 5600 afaik so neither can
msconvert. We're helping to test a new api that will add that support but it
won't be available until the testing is over (probably another month or so).
In the meantime, try to get a copy of the AB's new beta standalone converter
HARGE=" - 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
wrote:
Is there a way to make X! Tandem respect charge state(s) specified in an MGF
file?
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
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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 unders
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
U
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 n
Regarding pwiz for extracting extra metadata:
Our rawfile wrapper is a better bet if you're tied to c++, but if you just
want to experiment with what's available in the com interface, your best bet
is to access from managed code ala c#. Just add a reference to the xrawfile
dll and you're set.
-Mat
Watch out for the...
On Aug 1, 2010 12:32 PM, "Nikhil Garge" wrote:
Hi
Please click on the link below and enter your birthday into my calendar.
It's quick, easy, and you'll be helping me out.
http://www.birthdayalarm.com/bd2/87033002a678683483b1517742147c647119420d1386
Nikhil
--
You received
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 msconver
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.win32>omssacl
USAGE
omssacl.exe [-h] [-help] [-xmlhelp] [-pm param] [-d blastdb] [-umm]
[-f infile] [-fx xmlinfile] [-fb dtainfile] [-fp pklinfile]
[-fm pklinfile] [-foms om
spectra using an index 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 contacte
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 t
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
What file are you talking about? I was referring to
DP-dp_2strun_newpupi_22.mzML
in
http://www.peptideatlas.org/repository/tmp/DP_Opti_Newpupi_filter_mzML.tar.gz
which is a 331k file with only chromatograms in it. The other file is
DP-dp_2strun_newpupi_15.mzML
which is 23mb with both spectra and c
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 experiment
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]"
Th
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 the
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 3
Hi Jerry,
You'll want to use msconvert and mzML for this purpose, not
Readw->mzXML. The latter method wouldn't provide a way to know what kind
of spectrum you're looking at. Unfortunately, neither converter
currently supports non-MS RAW data, primarily because none of the
developers have had
for mzML?
>
> -Natalie
>
>
> On Mon, Feb 23, 2009 at 1:38 PM, Matt Chambers
> <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
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
My guess is no, mzWiff probably can't do this.
http://www.chm.bris.ac.uk/ms/theory/tandem-ms.html
-Matt
Natalie Tasman wrote:
> Hello Ronny,
>
> What is PIS data?
>
> Natalie
>
>
> On Thu, Feb 19, 2009 at 1:58 AM, Ronny wrote:
>
>> Dear mzWiff developers,
>>
>> I'm sorry, I recognized by n
Do you mean mzXML2Search instead of Mascot2XML? I agree that spectrum
averaging should be a more universal feature; it's something I plan to
put in msconvert but haven't gotten around to yet. What range of
settings did you try for spectrum averaging in mzWiff?
-Matt
Bill Nelson wrote:
> We w
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, bu
Hi Robert,
IMO, the most robust way to compare signal processing techniques is to
run the searches on each technique and use the one that maximizes your
results after simple target-decoy validation. I would not run any
parsimony on the searches. As Bill Nelson has discovered, it's possible
th
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