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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
Which is most important for you? Measuring amounts of metabolties or exact mass of metabolites?