Please, I need a help with the use of the mascot on LabKey server.
When I sent a search on mascot server, I had the message:
Mascot search status: error=26
I verified that the mgf file that was generated by MzXML2search contain many peaks and not was performed the processing of the spectrum. In this case was not obtained one peaklist (not was obtained monoisotopic peaks) compatible with the mascot requirements.
When I use the same file generated to performe a search in mascot web, I receive a message that I have many peaks. I realize that the mzXML2search was not configured to processing the spectrum, but only made a conversion from mzXML to mgf. I need process my raw data using a good algorithm to obtain a best peaklist.
How can I configure the MzXML2search.exe? Is there some parameter file to the MzXML2Search? Or Will I need to complile a new executable file MzXML2search?
Someone can help me?
Thanks
Humberto Ramos |
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| jeckels responded: |
2009-11-19 18:49 |
Hello,
Can you attach the full log file that contains the error message?
Thanks,
Josh |
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| humramos responded: |
2009-11-23 08:54 |
Hi Josh
Thanks for attention
Please, see the log file.
Thanks
Humberto |
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| jeckels responded: |
2009-12-01 11:01 |
Hi Humberto,
This page describes the settings that CPAS currently supports for configuring MzXML2Search:
https://www.labkey.org/wiki/home/Documentation/page.view?name=pipelineMascot
There are other options available for MzXML2Search, but unfortunately CPAS doesn't handle them right now. Do you know if they would be enough for your usage?
When you successfully submitted your file manually to Mascot, what file format did you use? Did you do spectra preprocessing before handing it off to Mascot?
Thanks,
Josh |
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| humramos responded: |
2009-12-02 13:48 |
Hi Josh
Thanks for attention
My problem was the noise threshold, that is 0.01 in default mode of mzxml2search. So, I ran the mzxml2search from Trans proteomic pipeline (TPP), using the options to modify "the minimum threshold noise peak intensity".
Then, I searched the generated mgf file using my mascot local server. The identification was sucessful in this moment. I don't know how put the argument in mascot parameters file to change the options of the mzxml2search. I know how change the parameters but i don't know write them. Some thing like this.....
"
<note type="input" label="spectrum, minimum parent m+h">MIN_VALUE</note>
<note type="input" label="spectrum, maximum parent m+h">MAX_VALUE</note>
"
Do you know the argument for this case?
Thanks
Humberto Ramos |
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| jeckels responded: |
2009-12-08 09:58 |
Hi Humberto,
Since this was a very small change, I'm attaching an updated ms2.module that adds support for this parameter. You can use this patch with version 9.3 of LabKey Server/CPAS. Version 10.1 will include this change.
It adds support for a new parameter:
<note type="input" label="spectrum, minimum peak intensity">MIN_VALUE</note>
which will be passed to MzXML2Search as the -I argument.
To install this patch:
Shut down LabKey Server.
Back up the ms2.module file that is currently in <LABKEY_ROOT>/modules.
Copy the attached ms2.module file over the existing one in <LABKEY_ROOT>/modules.
Restart the server.
Try running your search again, adding the new parameter to your search configuration.
Thanks,
Josh |
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erro26 log html mascot.mht