Hi Martin,

I too wanted to be able to add together scans, or even better subtract one from 
another. This would have been a good way to remove background peaks by 
subtracting blank runs for example.

However when you sit down and think about this it becomes very problematic for 
accurate mass data. We even attempted to do this but the resultant 
chromatograms were awful because the slight variation in mass meant there was 
effectively missing data in some parts of the scan. We thought long and hard 
about this, I think the only way to do this would be to re-sample the data onto 
a common grid and then align the peaks before subtraction. We realised that 
this would result in quite a radical re-engineering of MZmine so we abandoned 
the idea as it was taking too much of our resources and there were other more 
important areas to focus on like peak picking.

Cheers,

Mark

-- -----------------------------------------
Mark Earll
Research Leader - Metabolomics
Syngenta
Jealott's Hill International Research Centre
Bracknell
Berkshire
RG42 6EY
United Kingdom





-----Original Message-----
From: mzmine-devel-requ...@lists.sourceforge.net 
[mailto:mzmine-devel-requ...@lists.sourceforge.net]
Sent: 22 October 2012 11:54
To: mzmine-devel@lists.sourceforge.net
Subject: Mzmine-devel Digest, Vol 53, Issue 6

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Today's Topics:

   1. Re: Is there a way to export "raw" files? (Martin Lewitt)
   2. grouping of samples (gegoe)
   3. Re: is there a scan summing or stacking method? (Geert Goeminne)


----------------------------------------------------------------------

Message: 1
Date: Sun, 14 Oct 2012 22:35:32 -0600
From: Martin Lewitt <martin.lew...@veritomyx.com>
Subject: Re: [Mzmine-devel] Is there a way to export "raw" files?
To: Developer discussion <mzmine-devel@lists.sourceforge.net>
Message-ID:
        <CAHd=Pt3Rnj_tsQ0kNyNFN_wjqMAbrHUaWymnuUxhW=b8afv...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Thanx, I wasn't going to involve R, I just figured that baselining was an 
example of where you were exporting the same data I'll be dealing with.
Thanx for the pointer.  -- Martin

On Sun, Oct 14, 2012 at 9:37 PM, Tomas Pluskal <plus...@oist.jp> wrote:

>  Hi Martin,
>
>  I don't see the reason why R should be involved here. The easiest way
> is just to write a new java module that takes the raw data using the
> existing interface and writes a minimalistic mzML or mzXML file.
>
>  E.g. take a look at the Scan.getDataPoints() method:
> http://sourceforge.net/p/mzmine/code/3244/tree/trunk/src/main/java/net
> /sf/mzmine/data/Scan.java
>
>  Tomas
>
>
>
>   On Oct 15, 2012, at 12:18 PM, Martin Lewitt
> <martin.lew...@veritomyx.com>
> wrote:
>
> Where would you do it?  My inclination is to model it on where you
> pass the data to R.  Everything has to be there I would think.  Of
> course, I would put in in the proper place in the raw input/(export) menu.
>
>  thanx,
>     Martin
>
> On Sun, Oct 14, 2012 at 6:37 PM, Tomas Pluskal <plus...@oist.jp> wrote:
>
>> Hi Martin,
>>
>>  MZmine currently does not have a module to export RAW data.
>> Implementation of such module would not be difficult, though. If you
>> want to work on that, I can assist you.
>>
>>  Best regards,
>>
>>  Tomas
>>
>>
>>  On Oct 12, 2012, at 9:32 PM, Martin Lewitt
>> <martin.lew...@veritomyx.com>
>> wrote:
>>
>> mzmine-devel,
>>
>>  I don't see a way to export "raw" files under the raw files menu.
>> It would be helpful to be able to export intermediate results that
>> get stored as raw files for evaluation or processing by other
>> software.  If the facility doesn't exist would it be easy to
>> implement?  I envision retaining the scan structure in an XML or
>> mzXML format, and a possible stretch goal of being able to export just 
>> selected scans.
>>
>>  regards,
>>   Martin Lewitt
>>   martin.lew...@veritomyx.com
>>
>> ---------------------------------------------------------------------
>> --------- Don't let slow site performance ruin your business. Deploy
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>> http://p.sf.net/sfu/newrelic-dev2dev_________________________________
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>> Mzmine-devel mailing list
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>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>
>>
>>   ===============================================
>> Tom?? 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
>>
>>
> ----------------------------------------------------------------------
> -------- Don't let slow site performance ruin your business. Deploy
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> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>
>
>    ===============================================
> Tom?? 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
>
>
>
> ----------------------------------------------------------------------
> -------- Don't let slow site performance ruin your business. Deploy
> New Relic APM Deploy New Relic app performance management and know
> exactly what is happening inside your Ruby, Python, PHP, Java, and
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>
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Message: 2
Date: Mon, 22 Oct 2012 03:17:24 -0700 (PDT)
From: gegoe <ge...@psb.vib-ugent.be>
Subject: [Mzmine-devel] grouping of samples
To: mzmine-devel@lists.sourceforge.net
Message-ID: <1350901044071-4024102.p...@n3.nabble.com>
Content-Type: text/plain; charset=us-ascii

Hi,
I know in Mzmine you can add extra parameters to the samples, like a group 
number, but how do you get this group number in the table after processing 
data? I want to be able to filter my results based on the groupnumber, or order 
them by groupnumber, but i can't find a way to get that groupnumber make appear 
in my table, anyone any idea how to do that? In the table properties you can 
not find that extra paramter, how come?

Thanks for the replies,

Cheers, Geert



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------------------------------

Message: 3
Date: Mon, 22 Oct 2012 12:29:18 +0200 (CEST)
From: "Geert Goeminne" <ge...@psb.vib-ugent.be>
Subject: Re: [Mzmine-devel] is there a scan summing or stacking
        method?
To: Developer discussion <mzmine-devel@lists.sourceforge.net>
Message-ID:
        <ba7a50e5-c8b0-4a0b-81be-a2fad9a8e...@psbzim01.psb.ugent.be>
Content-Type: text/plain; charset="utf-8"

Hi,
I know in Mzmine you can add extra parameters to the samples, like a group 
number, but how do you get this group number in the table after processing 
data? I want to be able to filter my results based on the groupnumber , or 
order them by groupnumber , but i can't find a way to get that groupnumber make 
appear in my table, anyone any idea how to do that? In the table properties you 
can not find that extra paramter, how come?

Thanks for the replies,

Cheers, Geert

----- Original Message -----

> From: "Tomas Pluskal" <plus...@oist.jp>
> To: "Developer discussion" <mzmine-devel@lists.sourceforge.net>
> Sent: Friday, August 31, 2012 9:00:19 AM
> Subject: Re: [Mzmine-devel] is there a scan summing or stacking
> method?

> Hi Martin,

> We currently don't have such method, although it would not be
> difficult to add it.
> If you send me a detailed description of how such algorithm should
> work, I can implement it.

> Best regards,

> Tomas

> On Aug 31, 2012, at 3:46 AM, Martin Lewitt <
> martin.lew...@veritomyx.com > wrote:

> > mzmine-devel,
>

> > I am a new user of MZmine 2. After selecting a set of raw scans
> > using the crop method, I would like to be able to sum them together
> > before further processing. I don't see a method to do this. I'm not
> > familiar with the UI organization. Have I missed such a method?
>

> > regards and thanx for any assistance,
>

> > Martin Lewitt
>
> > martin.lew...@veritomyx.com
> > --------------------------------------------------------------------
> > ----------
>
> > Live Security Virtual Conference
>
> > Exclusive live event will cover all the ways today's security and
>
> > threat landscape has changed and how IT managers can respond.
> > Discussions
>
> > will include endpoint security, mobile security and the latest in
> > malware
>
> > threats.
> > http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___________
> > ____________________________________
>
> > Mzmine-devel mailing list
>
> > Mzmine-devel@lists.sourceforge.net
>
> > https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>

> ===============================================
> Tom?? 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

> ----------------------------------------------------------------------
> --------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond.
> Discussions
> will include endpoint security, mobile security and the latest in
> malware threats.
> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Mzmine-devel mailing list
> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel

--

==================================================================
Geert Goeminne, Ing.

Tel:+32 (0)9 331 38 37 or (0)9 331 38 79
fax:+32 (0)9 331 38 09
VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 
9052 Gent, BELGIUM ge...@psb.vib-ugent.be http://www.psb.vib-ugent.be 
==================================================================
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