Hi Xumin,
I checked the details you sent. You are correct, the HMDB search really does
not distinguish between average and monoisotopic mass. Other database modules
do not have this problem, only HMDB. The problem is actually caused by the HMDB
website itself, as you can check here:
http://www.hmdb.ca/search/chemquery/run?search=molecular_weight&query_from=129.113&query_to=129.115
http://www.hmdb.ca/search/chemquery/run?search=molecular_weight&query_from=129.042&query_to=129.043
These two links give the same results.
Unfortunately, I could not find a way how to search HMDB for only monoisotopic
mass. If you find a way, let me know.
I will try to contact the HMDB people about this. At this moment there is
nothing I can do in MZmine to fix this problem.
Best regards,
Tomas
On Mar 17, 2011, at 10:51 PM, Xumin Zhang wrote:
> Hi Tomas,
> Thank you for your prompt reply.
> The example is enclosed. Identifications with mass error of 0072 Da are
> accepted since the difference to the average mass is only 0.001 Da.
> I admit that it doesn’t trouble too much when searching the data manually,
> but it is a little annoying when employing the batch search of the whole list.
> Another small thing is about the isotopic pattern. In most cases, the second
> isotopic peak is not as precise as the monoisotopic, the error could be 10
> mDa instead of 2 mDa. Once the error exceed the mass tolerance, the
> corresponding isotopic pattern score would be 0. Is it possible to extent the
> mass tolerance for second and third isotopic peaks? And also, it would be
> very helpful to use the combined spectrum rather than single spectrum for
> high confident isotopic pattern.
> Thanks a lot .
> Best regards
> Xumin
>
>
>
>
> From: [email protected] [mailto:[email protected]] On Behalf Of Tomas Pluskal
> Sent: Thursday, March 17, 2011 1:47 PM
> To: Developer discussion
> Cc: Xumin Zhang
> Subject: Re: [Mzmine-devel] monoisotopic Mr or average Mr
>
> Hi Xumin,
>
> Can you please send more specific details?
> Please send a screenshot of the search dialog before you click "OK" and then
> a screenshot of the results window.
>
> Best regards,
>
> Tomas
>
> On Thu, Mar 17, 2011 at 8:53 PM, Xumin Zhang <[email protected]> wrote:
> Dear developers,
> Recently I jumped into the metabolomics study, and found the MZmine is really
> a delightful software for data analysis. Thank you all for your excellent
> work.
> I also find a minor thing unsatisfactory in the on-line database search. When
> I searched my data against the HMDB, surprisingly I found two different m/z
> peaks match the same compound in the database although the mass difference
> between is far higher than the mass tolerance. Finally I realized that the
> software did not distinguish the monoisotopic Mr and average Mr, both
> existing in the HMDB, then the compound was identified by two different m/z
> although both are acquired as monoisotopic mass.
> It would be very nice if you can correct it, or maybe I have some wrong
> settings?
> Kind regards
> Xumin Zhang
>
>
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> <Wrong assignment.ppt>
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology
1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
TEL: +81-98-966-8684
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