[BiO BB] question on processing LC/MS data

Paulo Nuin nuin at genedrift.org
Sat Apr 8 08:11:44 EDT 2006

Hi James



I have a program that aligns GC/MS data and deals with txt files from 3
different machines (you can get it at www.genedrift.org/gasp.php). I can
take a look on your data and see if I can help you, as it might similar
structure. Currently my program converts Xcalibur, HP Chemstation and AMDIS
txt files.


Let me know if I can help







From: bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org
[mailto:bio_bulletin_board-bounces+pnuin=terra.com.br at bioinformatics.org] On
Behalf Of James Anderson
Sent: April 7, 2006 6:41 PM
To: The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] question on processing LC/MS data


Hi, llya
  Thanks for your email. Unfortunately, we don't have Waters Masslynx
software. I asked some people in this field, they said that Masslynx can
convert those raw files (binary file) to mzXML. However, the raw data we
have is not binary file, it is txt file. I don't know how to deal with this.



Ilya Venger <ivenger at wisemail.weizmann.ac.il> wrote:

If you have Waters QTOF you might also have the MassLynx software. You
can use the program "databridge" that comes with the Waters Masslynx
software (it can be found in the "start" menu in the same tab where the
MassLynx is). It is a converter between the different file formats. It
will produce more than one file, the biggest one contains the relevant

If you have any more question don't hesitate to ask.


>>> janderson_net at yahoo.com 04/07/06 6:10 AM >>>


I am now working on some LC/MS data (the machine is made by 

Waters). I have the raw data file, each sample has very large size (in
the order 

of several G bytes). Each file has 3 functions and each function has a

of scans with each scan corresponding to a retention time. I have 6 

control samples and 6 dosed samples, the purpose is to find those
proteins that 

are differentially expressed between the two groups (control and dose).
The data is the raw txt file produced by Water Q Tof. However, I don't
know how
to convert those txt files to NetCDF or mzXML format which could be
by some software. In addition, the format of each sample is 
as follows:
Each sample has 3 functions. 
Function 1. Full scan data
Function 2. Cell collision voltage data, this is developed by Waters to
identify peptides.
Function 3. Lock mass data, which is used to calibrate the spectrum.
Does anybody have similar experience processing this kind of data?

Many thanks.


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