Problem with ReAdW

[oosula]

I'm having difficulty converting my .RAW file to mzXML using the ReAdW
program. After downloading the program along with all the necessary
files ( zlib.dll, .RAW file, etc), I then went to the command prompt,
found my directory which contained the ReAdW and the file of interest,
and from there tried to do the conversion. I basically typed "ReAdW
filename.RAW c after the path name based on some online directions I
found, and it just keeps taking me back to instructions that can be
found in the README text that comes with the program. In other words,
it won't convert the file at all. Can anyone help me??

[Jimmy Eng]

You're calling it wrong (old style). Type 'ReAdW' without any other
arguments to find the current usage statement. Assuming you want to
centroid, compress (which you should), invoke it as

ReAdW --centroid --compress --mzXML filename.RAW

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[Omoruyi Osula]

It worked. Thank you.

[Eileen Yue]

I try to use TPP to analyze the SILAC results, which is from Velo (Xcalibar : 2.1). The result files (total 30 fraction files) are really big (14G after zipped). I tested one fraction with TPP and it can transfer to mzxml and pepxml after I install Xcalibar 2.1. When I tried to load more such as 5 fraction or more, it does not work. Can anyone have some advice or experience for this?

Thanks for your help

Eileen

[Amit Yadav]

Is there no way to convert RAW files without using XCalibur SDK ?
Regards,

Amit Kumar Yadav
Senior Research Fellow (SRF-CSIR)
IGIB, New Delhi (India)

http://masswiz.igib.res.in

[Jimmy Eng]

Correct for ReAdW right now. You can use ProteoWizard's msconvert
tool in combination with Thermo's free version of their MSFileReader
though.

[Amit Yadav]

HI Jimmy

Thanks. I figured it out as i kept searching. 

For others facing similar problem, I am elaborating on how i solved it -

1. Downloaded and unzipped proteowizard from sourceforge

2. Download Thermo's MSFilereader setup from http://sjsupport.thermofinnigan.com/public/detail.asp?id=624 (i hope it doesnt change)

3. Install MSFilereader using either the exe or the msi provided.

4. Goto "C:\Program Files\Thermo\MSFileReader\" (or the installation directory)and copy "XRawfile2.dll" to the pwiz folder

5. Now you can easily run msconvert.exe (it did for me).

Regards,

Amit Kumar Yadav
Senior Research Fellow (SRF-CSIR)
IGIB, New Delhi (India)

http://masswiz.igib.res.in

[Matthew Chambers]

Hi Amit,

Recent pwiz snapshots come bundled with the necessary MSFileReader DLLs. No other installation is required.
http://teamcity.labkey.org:8080/repository/download/bt36/10408:id/pwiz-bin-windows-x86-vc90-release-shared-2_0_1881.tar.bz2

-Matt

[Amit Yadav]

Hi Matt,

Thanks for the great info. It will surely save a lot of trouble for people trying this out.

Regards,

Amit Kumar Yadav
Senior Research Fellow (SRF-CSIR)
IGIB, New Delhi (India)

http://masswiz.igib.res.in