Hi Chris and Tomas,
Thanks very much for your reply.
It does make sense to the peak lists generated by each sample. But I am
still wondering how NIST MS Search works on the peak list after alignment.
eg. I used two samples as test to do NIST search with alone and alignment
peak lists (3 peak lists). Then I checked a same identification from 3
lists, they all show slightly different spectra peaks.
On the other hand, I am still wondering whether the spectra peaks that have
been extracted will be took out or returned, whether they can used several
times.
Best regards,
Chi
2013/10/23 Pudney Chris (ext) GBJH <chris.pud...@syngenta.com>
> G'day,
>
> Yes, I wrote the NIST MS Search module.
>
> Regarding you questions:
>
>
> > Does it return all the mass peaks within the RT tolerance then take the
> top N Max.?
>
> From the manual and Help page:
> https://bit.ly/MZmineManual#h.**daszn7p4b0vi<https://bit.ly/MZmineManual#h.daszn7p4b0vi>
>
> "The number of peaks used to form a mass spectrum can be limited by
> setting the Max. peaks per spectrum parameter to a value greater than zero.
> If this parameter is set to N then the N rows whose RTs are closest to that
> of the row (and within the specified RT tolerance) are used to form the
> mass spectrum."
>
> So, it takes the N peaks closest in RT to the peak list row's RT and
> within the RT tolerance.
>
>
> > And is there any consideration on the deconvolution(there are two or
> more spectra within the RT tolerance) during this process?
>
> No, there isn't.
>
> Wouldn't deconvolution be performed separately before searching?
>
> Regards,
> Chris.
>
>
> On 23/10/13 10:12, Tomáš Pluskal wrote:
>
>> Hi Chi,
>>
>> The NIST search module was written by Chris (in cc), so he might comment
>> on this. But perhaps the best way to find your answers is to read the
>> source code of the module:
>>
>> http://sourceforge.net/p/**mzmine/code/HEAD/tree/trunk/**
>> src/main/java/net/sf/mzmine/**modules/peaklistmethods/**
>> identification/nist/**NistMsSearchTask.java<http://sourceforge.net/p/mzmine/code/HEAD/tree/trunk/src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/nist/NistMsSearchTask.java>
>>
>> Best regards,
>>
>> Tomas
>>
>>
>> On Oct 22, 2013, at 12:42 AM, chi zhang <zhangch...@gmail.com <mailto:
>> zhangch...@gmail.com>> wrote:
>>
>> Hi guys,
>>>
>>> I'm trying to process some GC-MS data with MZmine 2 and got some
>>> questions about the NIST MS search.
>>>
>>> Before doing the library search, a spectrum is extracted according to
>>> the Spectrum RT tolerance and Max. peaks per sepctrum I set. Anybody could
>>> give more details about MZmine how to generate this spectrum? Does it
>>> return all the mass peaks within the RT tolerance then take the top N Max.?
>>> And is there any consideration on the deconvolution(there are two or more
>>> spectra within the RT tolerance) during this process?
>>>
>>> Thanks to all.
>>>
>>> Chi
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>>
>> ==============================**=================
>> Tomas Pluskal
>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>> University
>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>> WWW: https://groups.oist.jp/g0
>> TEL: +81-98-966-8684
>> Fax: +81-98-966-2890
>>
>>
>
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