Integrating Peaks in AMDIS

[somestorm]

I've been running tissue sample extracts through a GC/MS and analyzing the metabolites through AMDIS, which I'm sure is not uncommon.

My problem now is that I need an integrated area under the curve 1) for each chromatographic peak and 2) for each target identified.

When I generate a text report after analysis, I see that there's a column for area, but that column isn't populated. It does give me the base peak height, which is loosely correlated to area sort of, but I really need the actual area to get concentration of compounds I already have a standard curve for. I can't find anything about integration or areas in the manual, but I -know- it has to calculate area because it defines peak tailing as the area on the right side of the base peak compared to the area on the left side of the base peak.

Any help would be much appreciated. Thanks!

[chemstation]

Hi Emma,
I have posted a reply similar to yours for

"AMDIS quantification of unknown peaks" @
viewtopic.php?t=13156&highlight=

by opening the *.txt that gets created in excel, it stops transcription errors too


Alex

[somestorm]

Hi Alex,

Thank you for the reply. I did read this section, however when I try to use this method the text file, whether I open it as text or open it using excel, has the column labels but is otherwise empty. What I did (please point out any errors):

- File --> Batch Job --> Create and Run Job ...
- Add --> added two data files
- Selected the bullet for "Simple" analysis
- Checked "Generate Report"
- Unchecked "Report All Hits"
- Hits to be reported is still at 1. I tried to change it to zero but it didn't like that.
- Save as 9B2A.job on desktop.
- Open 9B2A.job in excel, using tab delimited values.

What am I doing wrong?

Thanks.

[somestorm]

I've spoken to Gary Mallard, one of the creators of AMDIS. Apparently, the new version of AMDIS (2.69) may have a bug that is preventing it from displaying areas in either AMDIS proper or the report generated. I'm going to try using the older version of AMDIS to see if I can't sort it out.

Fun with software!

[chemstation]

Hi Emma,
What you wrote reads correctly ( i'm sure you writing that you opened 9B2A.job and not 9B2A.txt is just a typo)

the output below is from Version 2.69. and had the value 13399 in the Area & Intgr.Signal columns

Strange that it is not working for you, are you doing this with Administrator rights, as changing libraries is an issue if you don't have Admin rights. it may be related?

Sorry


Alex




FileName CAS Name RT RI Width Purity Model Min. Abund. Amount Scan Peak Tailing S/N (total) Base Peak Max. Amount Area Intgr.Signal Max. Area Extra Width Models Expec. RT RI-RI(lib) Net Weighted Simple Reverse Corrections (m/z) S/N (m/z) Area % (m/z) Conc. RT-RT(lib)
C:\NIST08\AMDIS32.266\DATA\HP\Eai002.FIN 111-65-9 Octane 7.029 3.5 scans 48% 57 m/z 15% 0.20% 266 1.2 18 1263 13399 13399 0-0 84 89 85 88
C:\NIST08\AMDIS32.266\DATA\HP\Eai002.FIN 124-18-5 ? Decane 7.029 3.5 scans 48% 57 m/z 15% 0.20% 266 1.2 18 1263 13399 13399 0-0 78 82 81 81
C:\NIST08\AMDIS32.266\DATA\HP\Eai002.FIN 112-40-3 ? Dodecane 7.029 3.5 scans 48% 57 m/z 15% 0.20% 266 1.2 18 1263 13399 13399 0-0 72 75 77 74
C:\NIST08\AMDIS32.266\DATA\HP\Eai002.FIN 629-59-4 ?? Tetradecane 7.029 3.5 scans 48% 57 m/z 15% 0.20% 266 1.2 18 1263 13399 13399 0-0 68 71 75 70