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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi James<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I have a program that aligns GC/MS data
and deals with txt files from 3 different machines (you can get it at <a
href="http://www.genedrift.org/gasp.php">www.genedrift.org/gasp.php</a>). 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Let me know if I can help<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Regards<o:p></o:p></span></font></p>
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10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Paulo<o:p></o:p></span></font></p>
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10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
bio_bulletin_board-bounces+pnuin=terra.com.br@bioinformatics.org
[mailto:bio_bulletin_board-bounces+pnuin=terra.com.br@bioinformatics.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>James Anderson<br>
<b><span style='font-weight:bold'>Sent:</span></b> <st1:date Year="2006" Day="7"
Month="4" ls="trans" w:st="on">April 7, 2006</st1:date> <st1:time Minute="41"
Hour="18" w:st="on">6:41 PM</st1:time><br>
<b><span style='font-weight:bold'>To:</span></b> The general forum at
Bioinformatics.Org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [BiO BB] question on
processing LC/MS data</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi, llya<br>
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. <br>
<br>
Thanks.<br>
<br>
James<br>
<br>
<b><i><span style='font-weight:bold;font-style:italic'>Ilya Venger
<ivenger@wisemail.weizmann.ac.il></span></i></b> wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi,<br>
If you have Waters QTOF you might also have the MassLynx software. You<br>
can use the program "databridge" that comes with the Waters Masslynx<br>
software (it can be found in the "start" menu in the same tab where
the<br>
MassLynx is). It is a converter between the different file formats. It<br>
will produce more than one file, the biggest one contains the relevant<br>
data.<br>
<br>
If you have any more question don't hesitate to ask.<br>
<br>
Ilya<br>
<br>
>>> janderson_net@yahoo.com <st1:date Year="06" Day="07" Month="04"
ls="trans" w:st="on">04/07/06</st1:date> <st1:time Minute="10" Hour="6" w:st="on">6:10
AM</st1:time> >>><br>
<br>
Hi,<br>
<br>
I am now working on some LC/MS data (the machine is made by <br>
<br>
Waters). I have the raw data file, each sample has very large size (in<br>
the order <br>
<br>
of several G bytes). Each file has 3 functions and each function has a<br>
lot <br>
<br>
of scans with each scan corresponding to a retention time. I have 6 <br>
<br>
control samples and 6 dosed samples, the purpose is to find those<br>
proteins that <br>
<br>
are differentially expressed between the two groups (control and dose).<br>
The data is the raw txt file produced by Water Q Tof. However, I don't<br>
know how<br>
to convert those txt files to NetCDF or mzXML format which could be<br>
processed<br>
by some software. In addition, the format of each sample is <br>
as follows:<br>
Each sample has 3 functions. <br>
Function 1. Full scan data<br>
Function 2. Cell collision voltage data, this is developed by Waters to<br>
identify peptides.<br>
Function 3. Lock mass data, which is used to calibrate the spectrum.<br>
Does anybody have similar experience processing this kind of data?<br>
<br>
<br>
<br>
Many thanks.<br>
<br>
<br>
<br>
James<br>
<br>
<br>
<br>
---------------------------------<br>
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Bioinformatics.Org general forum - BiO_Bulletin_Board@bioinformatics.org<br>
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board<o:p></o:p></span></font></p>
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