Hi Javi,
How about when you convert your file to mzXML, does it produce the same result
as mzML, or does it look more like your original wiff file?
Tomas
On Feb 27, 2012, at 6:59 PM, Javi Ortiz wrote:
Sorry Tomas for the delay.
I attach the screenshot. The intensity is not the same in the original wiff,
and the '83.6609' does not exist. Seems a conversion problem ...
Javi.
De: Tomas Pluskal <plus...@oist.jp<mailto:plus...@oist.jp>>
Para: Developer discussion
<mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>>
CC: Javi Ortiz <corre...@yahoo.es<mailto:corre...@yahoo.es>>
Enviado: Viernes 10 de febrero de 2012 5:21
Asunto: Re: [Mzmine-devel] mzML -> Scan number not found in scan id
Hi Javi,
I do not have AB Sciex's MS Data Converter, but I tried opening the wiff file
with ProteoWizard.
By running ProteoWizard's mscat on your file, I get the following output:
# scanNumber msLevel m/z intensity
ms1 83.6609 412.00
ms1 83.9287 412.00
ms1 86.9248 412.00
ms1 86.9894 412.00
ms1 91.4040 412.00
ms1 91.5553 412.00
ms1 94.2769 412.00
ms1 97.9298 412.00
etc etc... (total 1.6GB text file)
Note that there are also no scan numbers recognized by ProteoWizard.
The data points seem exactly the same as shown in MZmine:
<mzmineshot.png>
The strange thing for me is that there are so many data points with intensity
equal to 412.
Also the isolated data points strongly suggest that the data is already
centroided.
Can you open the file in your instrument software and make a screenshot of the
scan #1 zoomed to the first few data points, such as the above screenshot from
MZmine?
Do you see the same data?
Thanks,
Tomas
On Feb 9, 2012, at 6:26 PM, Javi Ortiz wrote:
Hi Tomas,
The original data comes from a AB SCIEX TripleTOF™ 5600 System using Analyst TF
Instrument Workstation Software v1.5.1. The acquisition mode was the
instrument default and there are no settings for centroid or other mode. We
think that the data are continuous. When we convert to mzXML there are scan
numbers, but we d not know if these numbers come from the original data or are
added by the conversion software.
If it is usefull for you, you can find the .wiff file in
http://biolinux.uv.es/pub/ex_wiff.rar
Thanks again,
Javi.
De: Tomas Pluskal <plus...@oist.jp<mailto:plus...@oist.jp>>
Para: Developer discussion
<mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>>
CC: Javi Ortiz <corre...@yahoo.es<mailto:corre...@yahoo.es>>; Steve Robles
<steve_rob...@lecotc.com<mailto:steve_rob...@lecotc.com>>
Enviado: Miércoles 8 de febrero de 2012 8:09
Asunto: Re: [Mzmine-devel] mzML -> Scan number not found in scan id
Hi Javi,
I noticed that the ID of the spectra converted from WIFF files do not contain
scan numbers (scan=XXX). So I added a simple generator for sequential scan
numbers.
I also modified the mzML reader class to use the jmzml library, which added the
previously missing support for ReferenceableParamGroup in mzML.
Both these changes will be included in MZmine 2.6.
I have two questions regarding your data file:
1) Does your original WIFF file contain an identifier of each scan (scan
number)?
The converted mzML file only contains spectrum tags such as
<spectrum id="sample=1 period=1 cycle=1 experiment=1" defaultArrayLength="1477"
index="0">
<spectrum id="sample=1 period=1 cycle=1 experiment=2" defaultArrayLength="0"
index="1">
<spectrum id="sample=1 period=1 cycle=1 experiment=3" defaultArrayLength="0"
index="2">
<spectrum id="sample=1 period=1 cycle=2 experiment=1" defaultArrayLength="2642"
index="3">
etc.
There are no scan numbers.
2) Is your original data centroided or continuous? When I look at the spectrum,
I am a bit confused. Some data points are tightly packed together (such as
233.919 m/z in the attached screenshot), suggesting continuous data, but there
are no zero data points, which suggests centroid data.
Cheers,
Tomas
<Screen Shot 2012-02-08 at 4.02.58 PM.png>
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