TB Biomarkers Analysis (Lipidomics)

# Wiki

#Blackburn lipid biomarkers of active TB analysis overview

## Brief description of the data from Suereta

We analyzed extracted lipids form intact aluminum foil disks using chloroform methanol. Samples were collected by different filter sizes; i.e. 01, 2.5 and 10 micrometer in size. You will notice in the excel sheet 'labeled separated_filters' there are samples with more than one entries (_10, _2.5, _01) which refer to the different filter sizes and for some filters there are more than one file. There is also another sheet labeled combined_filters which combined all the separate filters for a single sample. 

The extracts mixed with 2,5-Dihydroxybenzoic acid and were analyzed using the MALDI Mass spectrometer.

The raw data were analyzed using an in-house developed pipeline, in combination with mycobacterial database, to identify M. tuberculosis lipids. In a separate search we used Metabosearch to identify human lipids.

Further Zandi, used the R package Mass Spectrometry Wavelet on both the separate and combined datasets. I will be attaching the data set from this analysis to the email.

In the sample list you will notice batch 1 (controls: E_127 to E_168; cases: TDRS_006 to TDRS_024) and batch 2 (TDRS_027 to TDRS_083). These were analyzed on two separate occasions on the MALDI-MS. We can see a batch effect when we look at the data after our analysis.

## Important observations (Katie)

Strong technical artifacts in the dataset that are apparently also present within batch 1 between cases and controls, based on heavy autocorrelation detected in the dataset that currently precludes detection of robust biomarkers.

See plots under the files section for more.