I have 140 samples from (50 plant species) analysed by LC-MS.
Is there a way in which I could use TargetLynx (MassLynx 4.1) to automatically quantify all the compounds in all 140 samples that are above the noise level? Or, does the software force me to manually input all the compound masses and retention times manually? If I was working with one species, this would be feasible because the profiles would be mostly similar. but I have 50 species, so there will be many more compounds. I also only want to input compounds that are above a certain threshold only, and manually doing this with profiles that vary a lot, wont be possible?
Thanks
Chris
How are you quantifying the compounds? If you are doing it based on the mass then, yes, you have to input the compounds you are looking for. If what you are doing is comparing the peak areas to the area of an internal standard then you can get the software to integrate and output the areas in a table format without creating a calibration table. Take that table to Excel and work with the data there.
Hi Thanks for the answer.
I would basically like to quantify all the compounds in all 140 samples and then just remove the ones that are less than trace amounts. I'm not working with standards. I want a list of all compounds in each sample with their respective areas. Then afterwards cluster analysis of 140 samples. Surely TargetLynx can perform this automatically without me having to manually input each compound mass into it. Markerlynx and PCA does not require me to input compound masses manually.
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