In reply to Felipe's point 3, I created a custom database for positive mode and negative mode with all common adducts.
Here is an example of the format I used for our positive database.. (first 5 entries only) ID m/z Retention Time Identity Formula na 145.169924 1.73 1,8-diaminooctane [M+H] C8H20N2 G00339 505.176316 1.81 kestose [M+H] C18H32O16 C02494 284.135331 5.51 1-methyladenosine [M+H] C11H17N5O4 na 219.112804 9.17 1-methyltryptophan [M+H] C12H14N2O2 na 165.069224 1.25 2-aminoethylscysteine [M+H] C5H12N2O2S na 167.152415 1.73 1,8-diaminooctane [M+Na] C8H20N2 G00339 527.158807 1.81 kestose [M+Na] C18H32O16 C02494 306.117822 5.51 1-methyladenosine [M+Na] C11H17N5O4 na 241.095295 9.17 1-methyltryptophan [M+Na] C12H14N2O2 na 187.051715 1.25 2-aminoethylscysteine [M+Na] C5H12N2O2S na 183.099355 1.73 1,8-diaminooctane [M+K] C8H20N2 G00339 543.105747 1.81 kestose [M+K] C18H32O16 C02494 322.064762 5.51 1-methyladenosine [M+K] C11H17N5O4 na 257.042235 9.17 1-methyltryptophan [M+K] C12H14N2O2 na 202.998655 1.25 2-aminoethylscysteine [M+K] C5H12N2O2S na 289.3326 1.73 1,8-diaminooctane [2M+H] C8H20N2 G00339 1009.345 1.81 kestose [2M+H] C18H32O16 C02494 567.2634 5.51 1-methyladenosine [2M+H] C11H17N5O4 na 437.2183 9.17 1-methyltryptophan [2M+H] C12H14N2O2 na 329.1312 1.25 2-aminoethylscysteine [2M+H] C5H12N2O2S C00881 455.1885 4.63 2'-deoxycytidine [2M+H] C9H13N3O4 I generated all possible common adducts using a Visual Basic program on top of an Access database of all our metabolite standards, but you could pretty easily do the same in Excel or an even smarter way is using the KNIME software which has cheminformatics tools built in. Also if you look on Oliver Fein's website he has a useful list of possible adducts for + and - modes which you can add to the adduct list. In reply to point 2 the adducts are pretty easy to spot as they have the same RT and peakshape and using accurate mass differences can be identified Cheers, Mark Earll Syngenta -----Original Message----- From: mzmine-devel-requ...@lists.sourceforge.net [mailto:mzmine-devel-requ...@lists.sourceforge.net] Sent: 14 August 2014 07:42 To: mzmine-devel@lists.sourceforge.net Subject: Mzmine-devel Digest, Vol 75, Issue 5 Send Mzmine-devel mailing list submissions to mzmine-devel@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/mzmine-devel or, via email, send a message with subject or body 'help' to mzmine-devel-requ...@lists.sourceforge.net You can reach the person managing the list at mzmine-devel-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Mzmine-devel digest..." Today's Topics: 1. Re: MZmine SVN and 2.11 pre-release (Tomas Pluskal) 2. Re: MZmine SVN and 2.11 pre-release (V?ctor Manuel Trevi?o Alvarado) 3. high quality auto wire leads and connector factory (steven) 4. Ministerio Publico federal 11 08 2014 07:35 (mzmine-devel@lists.sourceforge.net) 5. Persistent doubts in MZmine (Felipe Antunes dos Santos) 6. Re: Persistent doubts in MZmine (Tomas Pluskal) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Aug 2014 08:04:59 +0000 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] MZmine SVN and 2.11 pre-release To: Gauthier Boaglio <gauthier.boag...@gmail.com> Cc: Developer discussion <mzmine-devel@lists.sourceforge.net>, V?ctor Manuel Trevi?o Alvarado <vtrev...@itesm.mx> Message-ID: <d141d6cf-1ded-4b65-bb62-0295a5d17...@oist.jp> Content-Type: text/plain; charset="iso-8859-1" Hi Gauthier, Thank you for the report! Victor, can you take a look at this? It seems the error happens in the very beginning of the task: minMasa = mzV[0].getMZ(); Perhaps the data contains a scan with no data points, and that causes the exception. Cheers, Tomas On Aug 12, 2014, at 16:48, Gauthier Boaglio <gauthier.boag...@gmail.com> wrote: > Hi Tomas, > > To accomplish my duty, here is a bug I get with the GridMass - 2D module > (hope this is not a duplicate of any anterior report/fix). Usually, I would > have preferred to provide a fix, rather than just reporting, but I really > need to be far from keyboard for a moment... > > [9:26:25|INFO|GridMassTask]: Started GRIDMASS v1.0 [Apr-09-2014] on > T0_128_V3_221112.cdf > [9:26:25|SEVERE|WorkerThread]: Unhandled exception > java.lang.ArrayIndexOutOfBoundsException: 0 while processing task > Detecting chromatograms (RT) in > T0_128_V3_221112.cdf(java.lang.ArrayIndexOutOfBoundsException: > 0...@net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassTa > sk.run(GridMassTask.java:150)) > java.lang.ArrayIndexOutOfBoundsException: 0 > at > net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassTask.run(GridMassTask.java:150) > at > net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) > > Attachment: The ".mzmine" project file containing the raw dataset used for > testing, as well as the parameters used to get the error (even if I had the > same error for all the combinations of parameters I tried with the module). > > Note: The raw dataset I used, is one of those I systematically use, since I'm > working on/with MZmine2. So the input data ain't the cause... > > > Cheers > Gaut > > =============================================== 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 ------------------------------ Message: 2 Date: Tue, 12 Aug 2014 14:34:06 +0000 From: V?ctor Manuel Trevi?o Alvarado <vtrev...@itesm.mx> Subject: Re: [Mzmine-devel] MZmine SVN and 2.11 pre-release To: Tomas Pluskal <plus...@oist.jp> Cc: Developer discussion <mzmine-devel@lists.sourceforge.net> Message-ID: <5a8f93f2-d4d2-4f00-9ee5-1eb2500c8...@itesm.mx> Content-Type: text/plain; charset="iso-8859-1" Dear Tomas, Could you send me the attachment file or the raw data. This error is seems to be associated with the first scan, which may contain no data. Of course I can solve this, but I would like to confirm or know precisely the data to provide a general solution. Regards, vt ______________________________________ Dr. Victor Manuel Trevi?o Alvarado Profesor-Investigador, SNI - 1 C?tedra de Bioinform?tica Tecnol?gico de Monterrey, Campus Monterrey CITES, 304, Tel. 8888 2045 Aulas 7-421, Tel. 52-(81) 8358 2000 ext. 4536-103 http://homepages.mty.itesm.mx/vtrevino http://www.itesm.mx El contenido de este mensaje de datos no se considera oferta, propuesta o acuerdo, sino hasta que sea confirmado en documento por escrito que contenga la firma aut?grafa del apoderado legal del ITESM. El contenido de este mensaje de datos es confidencial y se entiende dirigido y para uso exclusivo del destinatario, por lo que no podr? distribuirse y/o difundirse por ning?n medio sin la previa autorizaci?n del emisor original. Si usted no es el destinatario, se le proh?be su utilizaci?n total o parcial para cualquier fin. The content of this data transmission must not be considered an offer, proposal, understanding or agreement unless it is confirmed in a document signed by a legal representative of ITESM. The content of this data transmission is confidential and is intended to be delivered only to the addressees. Therefore, it shall not be distributed and/or disclosed through any means without the authorization of the original sender. If you are not the addressee, you are forbidden from using it, either totally or partially, for any purpose. On Tue Aug 12, 2014, at 3:04 AM, Tomas Pluskal <plus...@oist.jp> wrote: > Hi Gauthier, > > Thank you for the report! > > Victor, can you take a look at this? It seems the error happens in the very > beginning of the task: > minMasa = mzV[0].getMZ(); > Perhaps the data contains a scan with no data points, and that causes the > exception. > > Cheers, > > Tomas > > > > On Aug 12, 2014, at 16:48, Gauthier Boaglio <gauthier.boag...@gmail.com> > wrote: > >> Hi Tomas, >> >> To accomplish my duty, here is a bug I get with the GridMass - 2D module >> (hope this is not a duplicate of any anterior report/fix). Usually, I would >> have preferred to provide a fix, rather than just reporting, but I really >> need to be far from keyboard for a moment... >> >> [9:26:25|INFO|GridMassTask]: Started GRIDMASS v1.0 [Apr-09-2014] on >> T0_128_V3_221112.cdf >> [9:26:25|SEVERE|WorkerThread]: Unhandled exception >> java.lang.ArrayIndexOutOfBoundsException: 0 while processing task >> Detecting chromatograms (RT) in >> T0_128_V3_221112.cdf(java.lang.ArrayIndexOutOfBoundsException: >> 0...@net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassT >> ask.run(GridMassTask.java:150)) >> java.lang.ArrayIndexOutOfBoundsException: 0 >> at >> net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassTask.run(GridMassTask.java:150) >> at >> net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) >> >> Attachment: The ".mzmine" project file containing the raw dataset used for >> testing, as well as the parameters used to get the error (even if I had the >> same error for all the combinations of parameters I tried with the module). >> >> Note: The raw dataset I used, is one of those I systematically use, since >> I'm working on/with MZmine2. So the input data ain't the cause... >> >> >> Cheers >> Gaut >> >> > > =============================================== > 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 > ------------------------------ Message: 3 Date: Wed, 13 Aug 2014 01:55:35 +0800 From: "steven" <ste...@cr-natural.com> Subject: [Mzmine-devel] high quality auto wire leads and connector factory To: "mzmine-devel" <mzmine-devel@lists.sourceforge.net> Message-ID: <201408130155357187...@cnwotofo.pw> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... ------------------------------ Message: 4 Date: Tue, 12 Aug 2014 17:08:29 -0300 From: <mzmine-devel@lists.sourceforge.net> Subject: [Mzmine-devel] Ministerio Publico federal 11 08 2014 07:35 To: <mzmine-devel@lists.sourceforge.net> Message-ID: <webwin03xsnqptgfryi0005b...@webwin03.tecla.com.br> Content-Type: text/plain; charset="iso-8859-1" VISUALIZAR-PROCESSO-MPF <http://bit.ly/1oUXDf2?pm=#ID#> Scan Security Avast, NOD 100% Seguro. -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 5 Date: Wed, 13 Aug 2014 20:56:06 -0300 From: Felipe Antunes dos Santos <fellipe-antu...@hotmail.com> Subject: [Mzmine-devel] Persistent doubts in MZmine To: "plus...@oist.jp" <plus...@oist.jp>, MZmine.devel <mzmine-devel@lists.sourceforge.net> Message-ID: <blu174-w3ab4ffb625dfd8c87adc5eb...@phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Hi! I am Master's Degree Student at University of S?o Paulo (Brazil) I am using MZmine 2.9.1 for metabolomics and I am having serious doubts regarding the method of how it operates in the following steps: 1 - Complex Search; 2 - Search Adduct; 3 - Custom Database Search. 1 - Firstly, in the "Ionization Method" section (Complex Search), when we select the positive method (M + H), does MZmine add the proton mass to the peaks detected, or withdraws, or does nothing? 2 - How the "Search Adduct" tool knows who are the adduct peaks? If I inform to the sofware that the molecules are complexed with sodium (selecting M+Na), how MZmine knows that particular one peak is the sodium adduct M+ion or any other molecule? 3 - Finally, and most important: Since I select the ionization method (positive, eg), and the possible adducts (M + Na, eg) that form in the mass spectrometry, should we create database file with the m/z proton added to the m/z molecule and only then make the identification through the "Custom Database Search"? Should we also create a specific database file with m/z adducts? If yes, why then we should previously inform to the software that the peaks are from the positive method (1) and select the possible adducts (2)? Sincerely, Thank you very much! Felipe Antunes dos Santos------------------------------------------MSc Student - University of S?o Paulo - BrasilSchool of Pharmaceutical Sciences of Ribeir?o Preto/ Laboratory of Pharmacognosy Web address: http://www.asterbiochem.org/ http://tematicoasteraceae2011.blogspot.com.br/ -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 6 Date: Thu, 14 Aug 2014 06:41:35 +0000 From: Tomas Pluskal <plus...@oist.jp> Subject: Re: [Mzmine-devel] Persistent doubts in MZmine To: "mzmine-devel@lists.sourceforge.net" <mzmine-devel@lists.sourceforge.net> Cc: Felipe Antunes dos Santos <fellipe-antu...@hotmail.com> Message-ID: <c0e2ed26-0d5a-4e75-8a96-26481da18...@oist.jp> Content-Type: text/plain; charset="iso-8859-1" Hi Felipe, Please find the answers to your questions below. 1 - Firstly, in the "Ionization Method" section (Complex Search), when we select the positive method (M + H), does MZmine add the proton mass to the peaks detected, or withdraws, or does nothing? In electrospray ionization (ESI), you can often see that when one ion [M1+H]+ coelutes with another ion [M2+H]+, you will also observe the peak of a complex ion [M1+M2+H]+. This is what MZmine is searching for. Therefore, if you select M+H as ionization type, it will substract proton mass from all peaks, then add the mass of 2 individual peaks together, and add the proton mass to this complex, and look for a peak of that mass. This process is fairly basic and not at all comperehensive - for example, it does not take into account situations where the two ions have different type of ionization (e.g. M+H and M+NH4). 2 - How the "Search Adduct" tool knows who are the adduct peaks? If I inform to the sofware that the molecules are complexed with sodium (selecting M+Na), how MZmine knows that particular one peak is the sodium adduct ion or any other molecule? The adduct search finds pairs of peaks that have very similar retention time and specified mass difference (relative to each other). Of course MZmine cannot know for sure that the peaks are truly M+Na adducts, but as long as your mass accuracy is high enough (e.g. +-0.001 m/z) and retention time is almost same, you can have very good confidence in the results. 3 - Finally, and most important: Since I select the ionization method (positive, eg), and the possible adducts (M + Na, eg) that form in the mass spectrometry, should we create database file with the m/z proton added to the m/z molecule and only then make the identification through the "Custom Database Search"? Should we also create a specific database file with m/z adducts? If yes, why then we should previously inform to the software that the peaks are from the positive method (1) and select the possible adducts (2)? The "Custom database search" is one of the methods to assign identity to some peaks. The "Adduct search" and "Complex search" are other methods for the same purpose. You can find your adducts using the "Adduct search", or you can add them to your custom database and find them using the "Custom database search" - either way is fine. Best regards, Tomas =============================================== 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 -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ ------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel End of Mzmine-devel Digest, Vol 75, Issue 5 ******************************************* ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
