Summary of Study ST003483
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002139. The data can be accessed directly via it's Project DOI: 10.21228/M84F91 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003483 |
| Study Title | Tissue niche influences immune and metabolic profiles to Staphylococcus aureus biofilm infection (Extracellular data) |
| Study Summary | Infection is a devastating post-surgical complication, often requiring additional procedures and prolonged antibiotic therapy. This is especially relevant for craniotomy and prosthetic joint infections (PJI), both of which are characterized by biofilm formation on the bone or implant surface, respectively, with S. aureus representing a primary cause. The local tissue microenvironment likely has profound effects on immune attributes that can influence treatment efficacy, which becomes critical to consider when developing therapeutics for biofilm infections. However, the extent to which distinct tissue niches influence immune function during biofilm development remains relatively unknown. To address this, we compare the metabolomic, transcriptomic, and functional attributes of leukocytes in mouse models of S. aureus craniotomy and PJI complemented with patient samples from both infection modalities, which reveals profound tissue niche-dependent differences in nucleic acid, amino acid, and lipid metabolism with links to immune modulation. These signatures are both spatially and temporally distinct, differing not only between infection sites but evolving over time within a single model. Collectively, this demonstrates that biofilms elicit unique immune and metabolic responses that are heavily influenced by the local tissue microenvironment, which will likely have important implications when designing therapeutic approaches targeting these infections. This submission contains the extracellular metabolomic data for the larger project. |
| Institute | University of Nebraska Medical Center |
| Department | Department of pathology, microbiology and immunology |
| Last Name | Shinde |
| First Name | Dhananjay |
| Address | DRC 2, 7066, UNMC, Emily st |
| dhananjay.shinde@unmc.edu | |
| Phone | 4025597623 |
| Submit Date | 2024-09-14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-09-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005719 | AN005720 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Relative intensities | Relative intensities |
MS:
| MS ID: | MS005442 |
| Analysis ID: | AN005719 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A HRMS Orbitrap (Exploris 480; Thermo Fisher Scientific) was operated in polarity switching mode and was used for untargeted metabolomics in a data-dependent MS/MS acquisition mode (DDA). Electrospray ionization (ESI) parameters were optimized as follows: electrospray ion voltage of -2700V and 3500V in negative and positive mode respectively, ion transfer tube temperature was maintained at 400°C, and m/z scan range was 70-1050 Da. Orbitrap resolution for precursor ion scans were maintained at 240,000 for intracellular and 120,000 for extracellular whereas fragment ion scans were maintained at 120,000 and 60,000, for intracellular and extracellular respectively. Normalized collision energies at 30, 50, and 150% were used for fragmentation and data was acquired in profile mode. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005443 |
| Analysis ID: | AN005720 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | A HRMS Orbitrap (Exploris 480; Thermo Fisher Scientific) was operated in polarity switching mode and was used for untargeted metabolomics in a data-dependent MS/MS acquisition mode (DDA). Electrospray ionization (ESI) parameters were optimized as follows: electrospray ion voltage of -2700V and 3500V in negative and positive mode respectively, ion transfer tube temperature was maintained at 400°C, and m/z scan range was 70-1050 Da. Orbitrap resolution for precursor ion scans were maintained at 240,000 for intracellular and 120,000 for extracellular whereas fragment ion scans were maintained at 120,000 and 60,000, for intracellular and extracellular respectively. Normalized collision energies at 30, 50, and 150% were used for fragmentation and data was acquired in profile mode. |
| Ion Mode: | POSITIVE |
