JRAP question

[Ning Zhang]

Please go to the following link http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/jrap/

And download two jar files (1)jrap_3.0.jar (2) Jakarta-regexp-1.4.jar

 

Put the two jar file in your classpath, and import org.systemsbiology.jrap.* in your program to instantiate a MSXMLParser object.

 

Hope this helps!

 

 

Ning Zhang, Ph.D.

Computational Proteomics

Ruedi Aebersold lab

nzh...@systemsbiology.org

Tel: (206)732-1244

 

[Jimmy Eng]

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/

On Tue, Jan 15, 2013 at 7:00 PM, David Zhao <weizh...@gmail.com> wrote:

Is there a maven repository hosting jrap? and the latest version is 3.0? We're still using 0.1 :-)

--

You received this message because you are subscribed to the Google Groups "spctools-discuss" group.

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/1NE7HndJpIYJ.
To post to this group, send email to spctools...@googlegroups.com.
To unsubscribe from this group, send email to spctools-discu...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.

[Jimmy Eng]

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 <weizh...@gmail.com> 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

[Eric Deutsch]

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

 

 

--

You received this message because you are subscribed to the Google Groups "spctools-discuss" group.

[David Zhao]

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

[Jimmy Eng]

I believe MzXML2Search currently uses the mzParser code which you can find in MSToolkit.

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/fGumFv11IeEJ.

[David Zhao]

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

[Jimmy Eng]

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.

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/XUSCMDHbbCUJ.

[David Zhao]

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

[Jimmy Eng]

Hopefully the msconvert developers will chime in on whether this info is already or can be exported; this certainly won't happen for ReAdW.

To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/ZqoIYJSivR0J.

[David Zhao]

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 <jke...@gmail.com> 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 <weizh...@gmail.com> 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 <jke...@gmail.com> 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 <weizh...@gmail.com>

>>>> https://groups.google.com/d/msg/spctools-discuss/-/ZqoIYJSivR0J.

[Jimmy Eng]

David,

You are centroiding "-c" with ReAdW and not with msconvert.  Remove centroiding in ReAdW or add it to msconvert and then compare results.

[Matt Chambers]

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

>>>>>>>>>> And if you�re in the market for a Java implementation (like JRAP),
>>>>>>>>>> then I�d recommend jmzreader:

[David Zhao]

Aha, thanks Matt! Does msconvert have a centroid mode then?
Thanks,

David

>>>>>>>>>>> And if you’re in the market for a Java implementation (like
>>>>>>>>>>> JRAP),
>>>>>>>>>>> then I’d recommend jmzreader: