Re: [Mzmine-devel] mzML -> Scan number not found in scan id

Tomas Pluskal Thu, 09 Feb 2012 20:21:20 -0800

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:

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>
Para: Developer discussion <mzmine-devel@lists.sourceforge.net>
CC: Javi Ortiz <corre...@yahoo.es>; Steve Robles <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>

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel

===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing 
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/

_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel

Re: [Mzmine-devel] mzML -> Scan number not found in scan id

Reply via email to