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Messages - Ratnasekhar Ch

1
Mass Spectrometry Interest Group / UNTARGETED METABOLOMICS: Polling or not pooling samples
Hi,

Here i have a query regarding GC-MS metabolomics data processing. Normally after deconvolution by AMDIS  each single peak consists different metabolites. These metabolites can be integrated by extracted ion approach by keeping specific m/z. Finally the data yields peak table consists of retention time, m/z in columns and samples in rows. Even though the procedure is specific and reproducible, but it is time taken. Especially for large samples like more than 100 samples, the procedure is too tedious. My query is that, is there any software tools available for retention time alignment and integration of extracted ions. I have used XC-MS for Rt alignment and integration by uploading GC-MS raw files (XCalibur) but it is giving numerous extracted ions for a single peak. By this procedure i have got 9474 specific extracted ions for a single sample. So other than XC-MS, is there any software tool available for making peak table from raw data after processing ( Rt alignment, noise removal etc) ????. If you know the information, kindly help me in solving the GC-MS data.
2
Mass Spectrometry Interest Group / Welcome
Here i have a query regarding GC-MS metabolomics data processing. Normally after deconvolution by AMDIS  each single peak consists different metabolites. These metabolites can be integrated by extracted ion approach by keeping specific m/z. Finally the data yields peak table consists of retention time, m/z in columns and samples in rows. Even though the procedure is specific and reproducible, but it is time taken. Especially for large samples like more than 100 samples, the procedure is too tedious. My query is that, is there any software tools available for retention time alignment and integration of extracted ions. I have used XC-MS for Rt alignment and integration by uploading GC-MS raw files (XCalibur) but it is giving numerous extracted ions for a single peak. By this procedure i have got 9474 specific extracted ions for a single sample. So other than XC-MS, is there any software tool available for making peak table from raw data after processing ( Rt alignment, noise removal etc) ????. If you know the information, kindly help me in solving the GC-MS data.


Thanks and Regards

Ratnasekhar Ch
3
Mass Spectrometry Interest Group / How can we share critical analytical information.
Dear all,
Can any one give suggestion to solve my problem
I have analyzed Drosophila melanogester  polar extract using GC-MS after methoxyamine hydrochloride derivatization and TMS protection. Due to high abundance of disaccharide peak intensities, i am unable to solve their mass spectra with the help of NIST and willy libraries. I have also analysed 4 standards of disaccharides. But the sample peak Rt were not matching with the standard Rt. I am using Thermo Quantum XLS triple quadrapole mass spectrometer. Can anay one suggest to identify disaccharides.
Ratnasekhar Ch
Rsearch srudent
CSIR-IITR
India
4
Metabolite Identification Interest Group / Welcome to the new interest group
Dear all,

Can any one give suggestion to solve my problem

I have analyzed Drosophila melanogester  polar extract using GC-MS after methoxyamine hydrochloride derivatization and TMS protection. Due to high abundance of disaccharide peak intensities, i am unable to solve their mass spectra with the help of NIST and willy libraries. I have also analysed 4 standards of disaccharides. But the sample peak Rt were not matching with the standard Rt. I am using Thermo Quantum XLS triple quadrapole mass spectrometer. Can anay one suggest to identify disaccharides.

Ratnasekhar Ch
Rsearch srudent
CSIR-IITR
India
5
Metabolite Identification Interest Group / Welcome to the new interest group
As i am working on Mass spectrometry based metabolomics i can suggest that in case of MS based metabolomics comibned with chromatographic approaches (like GC-MS and LC-MS ), targeted ion approach  is good as it is specific with respective metabolite and with good reproduciblity.

Ratnasekhar Ch 
India