Hi Anas,
I don't know what a "lockmass function" is in the context of a Thermo instrument. Do you have it set
up as a separate scan event? I thought lockmass was calibrated based on finding the given masses
inside normal MS1 scans. Msconvert will certainly export ALL scan events by default, so if XCMS
isn't picking some of them up that's not an msconvert bug. :) If you WANT to export just certain
scan events, use the scanEvent filter:
# skip scan event 5
--filter "scanEvent 1-4 6-"
Hope this helps,
-Matt
On 11/1/2012 9:57 AM, Anas wrote:
Hi all,
How did this problem got solved eventually ? I have acquired Q-Exactive data
with lockmass on (for
metabolomics uses) and the lockmass functions seems the only one to be
recognized by xcms,
I appreciate your help,
Cheers,
Anas
On Friday, June 25, 2010 11:36:27 PM UTC+2, Matt Chambers wrote:
Hi Andris and Charlie,
Overdue support for filter lines found in Exactive files has finally been
added to ProteoWizard
(as of r2087). Also there was a problem with parsing the
instrument model and that should also be fixed.
Thanks for your reports and for uploading the files.
-Matt
On 6/24/2010 3:46 PM, Zhenyu Chang wrote:
However, I have encountered the following problem when using msconvert
tool. I was trying to
convert a .RAW data generated by Thermo Fisher Exactive instrument
to mzML 1.1 data format.
On 11/17/2009 3:19 AM, Andris Jankevics wrote:
> Hi Matt.
>
> Thank you for your work, these data will be mostly metabolomics data
> sets which will be analyzed by XCMS and several other software tools.
> It would be nice to have functionality in ReAdW to extract only mzXML
> file by based on scan event (for example only lock mass corrected
> positive slice), but this is not so essential.
>
> best regards,
> Andris
>
> On Mon, Nov 16, 2009 at 8:36 PM, Matthew Chambers
> <[email protected] <javascript:>> wrote:
>> That file requires Xcalibur 2.1, which doesn't run on Windows 7 x64...I
>> had to use a Windows VM to view it. It indeed appears they've put scan
>> segment and scan event in the filter line, and have added a new keyword
>> ("lock"). The lock keyword appears to only be applied if at least one of
>> the configured lock masses was found in the spectrum, in which case some
>> adjustment has been applied; otherwise, it won't have the lock keyword
>> and no adjustment is applied. It shouldn't be difficult to add support
>> for these changes, although I'm curious what you're planning to do with
>> this data once it's in mzXML format.
>>
>> -Matt
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