Parsing Thermo Finnigan RAW files

In a rare move, I’m going to largely copy across a post from my work blog, because I hope it contains useful information. For background, I’m trying to write a simple python script that extracts particular metadata from a .RAW file, produced by a Thermo Finnigan mass spectrometer. Tools that exist for parsing these files require access to proprietary XCalibur libraries, which I do not have.

Thermo provided a link to MSFileReader, a ‘freeware’ COM object that should allow interaction with RAW files without an XCalibur installation. They also sent a PDF guide to the COM object. Although this will allow XCalibur to be avoided, the work is still Windows-bound.

Python and COM objects

Python can talk to COM objects, through the win32com.client package. As a test, I installed Python and MSFileReader and the pywin32 libs on my netbook (which is a Windows 7 machine). Can import the required Python module, but need to extent the PATH somewhat:

>>> sys.path.append('C:\Python26\Lib\site-packages\win32')
>>> sys.path.append('C:\Python26\Lib\site-packages\win32\lib')
>>> from win32com.client import Dispatch
>>> x = Dispatch("NAME")

The key thing here is “NAME”:

The provided PDF gives C snippets for each method available in the COM object. This only provides one clue as to the possible name of the COM object

// example for Open 
TCHAR* szPathName[] = _T(“c:\xcalibur\examples\data\steroids15.raw”); 
long nRet = XRawfileCtrl.Open( szPathName ); 
if( nRet != 0 ) {
    ::MessageBox( NULL, _T(“Error opening file”), _T(“Error”), MB_OK ); 
    ...
}

XRawfileCtrl is used to call the Open() method. However, this and MSFileReader as “NAME” both fail (Invalid class string).

Found ‘multiplierz‘ which seems to use MSFileReader to create mzAPI – which focusses on access to the actual data, rather than the metadata. The code gives some good clues as to how to use the COM object. [doi:10.1186/1471-2105-10-364]

MSFileReader.XRawfile is used as “NAME” in this code.

So:

>>> sys.path.append('C:\Python26\Lib\site-packages\win32')
>>> sys.path.append('C:\Python26\Lib\site-packages\win32\lib')
>>> from win32com.client import Dispatch
>>> x = Dispatch("MSFileReader.XRawfile")
>>> x.Open("C:\Users\path\to\file\msfile.RAW")
>>>

To be continued…

2 comments

  1. Hi,

    I’m trying too to parse the Thermo .raw files, did you continue this quest any further ? I would be very glad to hear from this ! Thanks and keep going

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s