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| Status |
Public on Jul 07, 2011 |
| Title |
In vivo uninfected 1 |
| Sample type |
other |
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| Source name |
Bile
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: Salmonella enterica serovar Typhimurium SL1344 in vivo
sample type: bile
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| Treatment protocol |
For in vivo studies, C57BL/6 mice were infected with approximately 10^8 cells of Salmonella enterica serovar Typhimurium SL1344 by oral gavage.
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| Growth protocol |
For in vitro growth studies, an overnight culture of Salmonella enterica serovar Typhimurium SL1344 was used to inoculate 10 μL of bile at an approximate density of 5x10^6 cells/mL. Samples were incubated for 24 hours at 37 oC with shaking, and were then extracted as described.
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| Extracted molecule |
other |
| Extraction protocol |
After appropriate incubation, bile samples were centrifuged for 5-10 minutes at 13,000 g and 7 μL of the supernatant was removed and dried at room temperature in a centrifuge equipped with a vacuum pump. Dried extracts were then suspended in a mixture of acetonitrile and water (200 μL, 50% acetonitrile for in vitro samples; 400 μL, 75% acetonitrile for in vivo samples), vortexed and cleared by centrifugation. All extracts were kept at -80˚C until further use.
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| Label |
Not applicable
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| Label protocol |
Not applicable
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| Hybridization protocol |
Not applicable
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| Scan protocol |
Not applicable
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| Description |
Measured on both negative and positive ionization modes, with duplicate acquisition, resulting in 4 files.
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| Data processing |
Raw mass spectrometry data were processed using a custom-developed software package, as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). Mass spectra were batch-processed using a custom VBA script, within the instrument vendor’s data processing software package, DataAnalysis®. First, all the raw mass spectra acquired in positive and negative ion modes were internally calibrated with the reference masses of the spiked standard compounds and a ubiquitous known contaminant, N-butylbenzensulfonamide. Monoisotopic peaks corresponding to the isotopic distribution patterns were then automatically determined and those with signal-to-noise ratios above 3 were picked. The m/z values were subsequently converted to neutral masses by subtracting 1.007276 for positive ion mode or adding 1.007276 for negative ion mode. Next, the resulting mass lists from the individual mass spectra within each paired sample group were further processed with another custom software program developed with LabVIEW® (National Instruments, Austin, USA). The first step of this program is to remove the adduct ions, e.g., (M+Na)+ and/or (M+K)+ in positive ion mode and (M+Cl)- in negative ion mode, from the mass lists based on the expected mass differences for these ions within 2 ppm. Next, the peak intensity of each unique monoisotopic neutral mass was normalized to the intra-spectrum total ion intensity. Masses observed in at least 50% of the spectra from each paired sample group were aligned into unique masses (metabolite features) from the masses that matched within 2 ppm. Finally, a two-dimensional data matrix (neutral mass vs. peak intensity) was generated for each group and saved in a tab-delimited text format. To detect metabolite differences between the different sample groups, the masses were filtered in each list for metabolites that were present on one set of samples, but not the other. Additionally, the intensities were averaged of each unique mass in each set of biological replicates and calculated the ratio between the sample groups. To assign possible metabolite identities to the masses present only in one set or showing at least 2-fold changes, the monoisotopic neutral masses of interest were queried against the Human Metabolome Database (HMDB, http://www.hmdb.ca), with a tolerance of 0.001 Da.
Masses (daltons) with relative intensity
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| Submission date |
Jul 05, 2011 |
| Last update date |
Jul 07, 2011 |
| Contact name |
L. Caetano M. Antunes |
| E-mail(s) |
antunes@mail.ubc.ca
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| Phone |
604-827-3921
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| Organization name |
The University of British Columbia
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| Department |
Michael Smith Laboratories
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| Lab |
Finlay Lab
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| Street address |
#367 - 2185 East Mall
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z4 |
| Country |
Canada |
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| Platform ID |
GPL10454 |
| Series (1) |
| GSE30404 |
Metabolomics reveals phospholipids as important nutrient sources during Salmonella growth in bile in vitro and in vivo |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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