I have uploaded an attachment. Please let me know if you are unable to download. 

don't see anything either, can you specify where the file is please?

Dear Charandeep

I do not see the file...

Anyway, below are the points that I would start to get an impression from a chromatogram:

1) Peak intensity (TIC and SIC)

2) Number of peaks

3) Noise intensity

4) Number/intensity of the peaks in the beginning/medium/end of the chromatogram

5) RT of the time standards

6) Peaks shape

7) Intensity and consistence of the internal standards

8) CV between replicates

Hope this will help You.

P.S. I think something wrong with this comments box, so I apologise if it will be published several times...

Dear Albert,

I can also email you the file.

Thanks Charan

Dear all,

I have uploaded the file on Cloud, as I was unable to do it on researchgate.

Link to the file:

http://ocnkuxpm.myknowhowcloud.com/item/b76ad912bc0b4414bba25af5b73e9304

Thanks in advance for your help.

Charan

Dear Pete,

Thanks a lot for the link. 

I tried XCMS earlier. But, thermo file is not directly compatible with this software, so I normally analyse data peak by peak. 

:)

Kind regards,

Charan

Dear CHaran,

Concerning data processing i can recommend you to check Mzmine 2.10 (http://mzmine.sourceforge.net/download.shtml) if you're looking for freeware software, if you're looking for a total solution software with statistics included i recommend you to check Progenesis QI for metabolomics from Nonlinear, a Waters company (http://www.nonlinear.com/progenesis/qi/). I use the software already for more than a year (after evaluating many other software packages), and i'm extremely enthousiastic about it, you can ask for a demo to process 100 samples. The software reads data automatically from all main MS vendors, including Thermo. I haven't had the time yet to look at your chromatogram, i downloaded it, but i will have a look as soon as i'm back from the UK.

Cheers, Geert.

Dear Geert,

Thanks for your reply. I downloaded mzMINE but still exploring the usage. I really appreciate if you can look at the data once you are back from the UK. 

We have also purchased SIEVE 2.1 and I am also trying SIEVE for differential analysis. 

Thanks

Charan

mzMINE is very useful and once R-dependancy issues are addressed it is far more easy than anything else. Please use Mass++ from MassBank to convert any format to any format for any mass-spec vendors, i.e., .cdf to mzXML, or .RAW to .cdf and so on. However, once to mzXML which is universally acceptable for MS-based metabolomics data, downstream would be easy too. XC-MS does brilliant job too, so does MeltDB.

Dear Biswapriya,

Thanks a lot for your answer. I have downloaded mzMine and Maven. I like Maven a lot. Its much more easy to use and free of any bugs.

Regards

Charan