Skip to main content ↑ ↓
Topic: UNTARGETED METABOLOMICS: Polling or not pooling samples (Read 18781 times) previous topic - next topic

UNTARGETED METABOLOMICS: Polling or not pooling samples

Hi to everyone.
I would like to have some feed-back on an issue that has been largely discussed in the field of genomics-proteomics (I coming from that)
UNTARGETED METABOLOMICS: Pooling  or not pooling plasma samples when using animal models ? (not when using patients)
In important issue in all omics is the need to reduced technical  (MS-MS) and biological variation gaining increased power to detect treatment differences.
In my opinion, when following an untargeted metabolomics approach using animal models, pooling biological samples might be a valid procedure to overcome these limitations.
Because pools represent averages, the dominant differences and similarities between treatment groups might be easier to find (Kendzionski et al., PNAS 2005; Diz et al., Electrophoresios 2009; Karp et al., Proteomics, 2009). The assumption of biological averaging is usually met in animal models where the sources of bias (subject-to-subject variation) are small and can be neglected (Karp et al., Proteomics 2009).
When the  initial interest is not on the individual (e.g. making a diagnosis) but rather on the characteristics of the population (e.g. changes in expression patterns in different groups) I usually perform a sample pooling strategy.

Any comment??
thanks so much

UNTARGETED METABOLOMICS: Polling or not pooling samples

Reply #1 –
We only pool samples to provide a common QC reference that is periodically injected among the individual samples, to check instrument performance during long runs for large sample sets.  This means we take an equal aliquot from each sample.  Pooling all the samples themselves for analyses is only done for sample sizes too small to analyze individually, since you lose all information about variance introduced by the analytical method, vs. the biological variance.  \"Precision\" is limited, in most all cases, by biological variance-and outliers can be significant. Outliers will contaminate your study, if you pool too aggressively.

UNTARGETED METABOLOMICS: Polling or not pooling samples

Reply #2 –
forces with Cessna Aviation and PrivatAir, signing a three-year settlement with the two companions. best replica watches  Through the approaching several a long time rolex prices    , Alpina Geneve, Cessna Aviation and PrivatAir will function collectively carefully to market their similarly substantial good quality merchandise and companies, via cross-marketing routines in Europe and North The usa. On top of that, breitling replica  watch sell  the creation of the Alpina Startimer Pilot timepieces might be confined at 8\'888 items they usually will likely be introduced inside a committed, high-class packaging, together with a Cessna Quotation Mustang scale product in

UNTARGETED METABOLOMICS: Polling or not pooling samples

Reply #3 –
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.

UNTARGETED METABOLOMICS: Polling or not pooling samples

Reply #4 –
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.
miraal