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 mzXML was
annotated to be in profile mode and profile mode DTAs and MGFs are senseless AFAIK.
Hope this helps,
-Matt
On 1/30/2013 2:41 PM, David Zhao wrote:
Hi Matt and Jimmy,
I'm processing a Thermo Q-exactive generated raw file, and I see some
discrenpencies in the mzXML ms/ms peak data and dta generated using
mzxml2search tool by using msconvert or ReAdW-4.6.0.exe.
mzXML was generated using standard parameters without any filter.
ReAdW.exe --mzXML -c
msconvert.exe --mzXML --32
and I used mzxml2search from TPP to convert mzXML to dta files, please
find attached dta files for scan 3, they are quite different.
Thanks,
David
On Mon, Jan 21, 2013 at 1:08 PM, Jimmy Eng <[email protected]> wrote:
David,
ReAdW requires the corresponding XRawfile2.dll from Thermo's Xcalibur
software; it currently won't work with the one from MSFileReader. If I get
time this week, I can see if I can get it working with MSFileReader.
On Mon, Jan 21, 2013 at 12:51 PM, David Zhao <[email protected]> wrote:
Thanks, Jimmy. Another question (sorry :-): does ReAdW expects
Xrawfile2.dll to reside in a particular directory? My PC is 64 bit Windows 7
machine, I downloaded Msfilereader from Thermo (I don't have Xcalibur
installed on my machine), and installed the 32 bit version. Msconvert works
fine. However, even after I run "regsvr32 C:\Program Files
(x86)\Thermo\MSFileReader\XRawfile2.dll", ReAdW still gives me an error:
Unable to initialize Xcalibur 2.0 interface; falling back to 1.4 interface
Unable to initialize XCalibur 1.4 interface; check installation
hint: try running the command "regsvr32
C:\<path_to_Xcalibur_dll>\XRawfile2.dll"
unable to interface with Thermo library
So first of all, can I use the dll from MSFileReader with ReAdW.exe, if I
can, how should I register it so it'll be found the program.
Thanks so much!
David
On Sun, Jan 20, 2013 at 11:22 AM, Jimmy Eng <[email protected]> wrote:
You can find the ReAdW binary I use here:
https://proteomicsresource.washington.edu/tools.php
There's no huge changes from previous releases. Mainly minor fixes to
support the Q Exactive instrument, remove 0 intensity peaks for file size,
etc.
On Sun, Jan 20, 2013 at 8:50 AM, David Zhao <[email protected]>
wrote:
Thanks Jimmy. I may need a updated version of ReAdW. Do you know if I
can let ReAdW or msconvet to output raw file header information, such as
method used, serial number, processing mode, etc.
David
On Wednesday, January 16, 2013 9:43:47 AM UTC-8, Jimmy Eng wrote:
Yes, that is the standalone project which is now also used in the TPP.
For converting Thermo raw files to mzXML, consider using msconvert
which is now the default converter in the TPP.
I happen to still use ReAdW though. That code actually does get update
as needed but it doesn't get built and distributed via the Sashimi
SourceForge project anymore. Feel free to email me offlist if you want an
updated binary.
There is no one who currently "owns" jrap. Consider taking ownership
of it yourself if you think you can update it.
On Wed, Jan 16, 2013 at 8:40 AM, David Zhao <[email protected]> wrote:
Thanks, Jimmy. Is this the project you are referring to:
https://code.google.com/p/mstoolkit/ ?
Is ReAdW still the de facto tool to use to convert Thermo's raw files
to mzXML? It hasn't been updated for years, but like you said, mzXML specs
hasn't changed either.
BTW, is jrap no longer supported? Could you point to the right person
if it still is.
Thanks,
David
On Wednesday, January 16, 2013 8:08:00 AM UTC-8, Jimmy Eng wrote:
I believe MzXML2Search currently uses the mzParser code which you can
find in MSToolkit.
On Tue, Jan 15, 2013 at 10:23 PM, David Zhao <[email protected]>
wrote:
Thanks Jimmy and Eric. I'll look into other alternatives as
suggested. My problems that we have a lot of codes still rely on jrap to
parse mzXML file, but jrap can't seem to parse mzXML generated by ReAdW from
the latest Thermo q exactive instrument ( some scans return negative mz and
intensities).
However, mzxml2search from TPP can parse the mzXML just fine, which
makes me think the jrap is out of date. What parser does mzXML2search use
in this case then?
Thanks,
David
On Tuesday, January 15, 2013 9:25:41 PM UTC-8, Eric Deutsch wrote:
And if you’re in the market for a Java implementation (like JRAP),
then I’d recommend jmzreader:
http://code.google.com/p/jmzreader/
Cheers,
Eric
From: [email protected]
[mailto:[email protected]] On Behalf Of Jimmy Eng
Sent: Tuesday, January 15, 2013 9:18 PM
To: [email protected]
Subject: Re: [spctools-discuss] Re: JRAP question
At this point, you can probably not worry about jrap not being
updated because the mzXML format isn't really in flux. But if you want to
look for alternatives ...
Quite a few folks here would tell you to look at ProteoWizard
http://proteowizard.sourceforge.net/
Possibly look into OpenMS (I honestly have no clue how pertinent
this is): http://open-ms.sourceforge.net/
Also MSToolkit: https://code.google.com/p/mstoolkit/
Other folks should chime in if there are other parsing libraries
out there (which I know there are).
On Tue, Jan 15, 2013 at 7:20 PM, David Zhao <[email protected]>
wrote:
Thanks Jimmy! So it sounds like jrap is not being updated anymore.
If i'd like to keep up to date with a mzXML parser, which library should I
follow?
Thanks,
David
On Tuesday, January 15, 2013 7:14:17 PM UTC-8, Jimmy Eng wrote:
I'm not a jrap user nor do I know what file are associated with
what versions. But if you are looking for jrap_3.0.jar and
jakarta-regexp-1.4.jar, you can find them here:
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/sax2/
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