AMDIS quantification of unknown peaks

[micktrose]

Dear everyone,

I have a couple of questions re: metabolomic data processing using AMDIS that I hope someone might be able to help with:

1. I would like to export .csv data (RI plus TIC or even indidual m/z areas or intensities) on all deconvoluted peaks (including unknowns), prior to annotating/matching each peak via a library? Does anyone know if this is possible? Does this make sense?

2. Apparently I should be able to change the processing method for individual chromatograms in a batch job, however, although I can select different processing methods, it does not seem to save, resulting in all chromatograms being processed by the 'simple' analysis type. Does anyone have any tips for me on how to overcome this?

Thank you very much for your help,

[chemstation]

Hi Mick,
in terms of .csv data, when you do a batch job
select analysis type as simple,
tick the check box marked generate report,
Untick report all hits,
and save it as e.g. "micksdata.job", ( remember this directory!)
and run the batch,

in the exact same directory as you saved "micksdata.job", there will be a data file also created called "micksdata.txt".

open this file in excel, and you will have the information.

the latest version of AMDIS (version 2.68 ) is reported to have better Peak Integration Algorithms

N.B. this latest version of AMDIS (version 2.68 ) has a bug!

after installing AMDIS, the Nist library search will not work.

so edit the c:\windows\win.ini file so it has the following.

[NISTMS]
Amdis32Path=C:\NIST08\AMDIS32\
AmdisMSPath=C:\NIST08\AMDIS32\
Path32=C:\NIST08\MSSEARCH\
WorkDir32=C:\NIST08\MSSEARCH\

also it doesn't install the NISTEPA etc lib files, so copy from 2.65 version.


there is also in the AMDIS directory, in the ONSITE.ini file

[NISTMS]

PATHTOMAINLIB=C:\NIST08\AMDIS32

but it doesn't seem to worry the programme.


I don't know about changing processing methods for individual files in a batch ,

the only tip I can suggest is to save the batch Job with a different name and retrieve the .csv data from the different name .txt file.

Alex

[micktrose]

Great, thanks Alex. I'll give it a go

[fattuoni]

I'm sorry to reopen an old topic, but I have the same problem as Mick (and the suggested "batch job" procedure doesn't work for me): how can I export the whole components list from AMDIS? In every report I open with EXCELL I see only the targets list (with all relative parameters, amount, etc). It is possible to do this job?
Thanks to all
Claudia

[pgoodman]

I've never been able to get "Generate Report" to report out "Area" or "Intgr. Signal", and it only reports targets, not components. You have to type up component reports by hand, manually clicking from component to component in the Results window to get at the data. AMDIS' buggy reporting remains (as of v2.69) its greatest shortcoming.

Is the source code available? Lets get this thing fixed.

[carlo.annaratone]

There's a workaround to report all components: you must create a new library from scratch, then use the function to add all components to this otherwise empty library, then use it for quantification in a batch job!

[apappas]

carlo.annaratone: Can you provide a "step-by-step" of this workaround?