Skip to main content

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - rahulkapoore

1
Other metabolomics resources / Help in GOLM metabolome database
Hello there,

I am a final year PhD student at The University of Sheffield, England. I am working on improving the metabolome coverage of Chlamydomonas reinhardtii by hyphanated MS based techniques like GC-MS & LC-MS.

I am using AMDIS & NIST 11 database for my GC-MS analysis. I have GC-EI-Quardrupole-MS (Thermo-finnigan).

I have used GOLM database before, but I need to format my laptop for some reason so today I went to download GOLM database to again, but I see there were too many libraries available to download.

Could you please suggest me which one I should download based on above information I have given. I want to cover as many metabolites as possible to improve the metabolome coverage through GC-MS technique.

I will really appreciate if you could guide me on which library is best suitable in my case which I can integrate with NIST & AMDIS. or else do i have to use more than one library to meet my research requirements.

Currently I am in my final phases of my PhD, so I will really appreciate if you could help me on this issue.

Thanking you in advance.
2
Compound identification / AMDIS & NIST 2011
I will really appreciate if you could answer some of my queries regarding AMDIS. They are as follows,

1) Does AMDIS uses retention time to report name of the compounds or it just uses the MS fragmentation pattern to compare against NIST library. I am asking this question because I need to normalise my data with internal standard for any drift in the chromatographic retention time (Only if it uses RT for reporting)

2) I am using the internal standard in all my biological & technical replicated. How I can use AMDIS to do data analysis which will account for the RT of my internal standard before processing my data. I have a rough idea about it, that I need to create cal file with internal standard. But it didn't worked for some reason. (I might be wrong). Could you please advise me on this.

3) How we do the data normalisation with AMDIS?

4) Lastly, I have metabolomic flux analysis experiment where I am using isotopes to monitor the fluxes. Now before I should proceed for my data analysis I need to account for the shift in the masses in order to report true hit. How I can do this with AMDIS? I cannot process any of my data through AMDIS for this experiment as I am not sure how to account for this mass shift?
3
XCMS / Re: GC-MS settings for XCMS
Hi kelly,

Did you managed to workout what parameters you are selecting for processing GC-MS data??

I do have the same problem. Could you please help!!!!!
4
XCMS / GCMS data.. Problems in processing? Please help!!!
Hello there,

I have a GC-MS data from Thermo finnigaan quardrupole instrument in Xcalibur format. I have managed to convert the data to MZXML format. However I am confused which files to upload in Dataset 1 & 2. I have 3 Biological replicates. Within each Biological replicate I have 4 different conditions & for each condition I have 3 technical replicates. Could you please assist me in how to divide this data,  when it comes to uploading the data in 2 data sets in XCMS. Other query is, what parameters should I select for above instrument. I want to do Peak alignment, normalisation of my data with internal standard. So finally I want to compare the differences between 4 conditions that I have kept in my experiment. I want to see how metabolites concentration have changed across all 4 conditions. Is it possible to easily trace those metabolites which are showing drastic changes across 4 conditions. Can you suggest any better way to analyse data of this type using XCMS.

Many thanks in advance