Summary of Study ST002558
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 PR001650. The data can be accessed directly via it's Project DOI: 10.21228/M8DX4F 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 | ST002558 |
Study Title | Extraction and Untargeted Analysis of Metabolome from Undemineralised Cortical Bone Matrix for Forensic Application |
Study Summary | Untargeted metabolomics has become the gold standard for the profiling of low-molecular-weight compounds. Recently, metabolomics has shown great potential in forensic science in the field of toxicology and postmortem interval estimation. The current study aims to evaluate three extraction protocol and four liquid chromatography coupled with mass spectrometry assays that could offer a valuable tool to identify biomarkers for PMI estimation. One fragment for anterior human skeletal tibia from a 82 years old male individual belonging to the Forensic Anthropology Center - Texas State University collection was powdered and extracted in five replicates to be extracted according to a the biphasic chloroform/methanol/water protocol and two single phase protocols based on methanol/water and methanol/acetonitrile/water. Formal analysis was carried out ThermoFisher Ultimate 3000 HPLC in hydrophilic interaction (HILIC) and reverse phase (RP) liquid chromatography coupled with SCIEX 6600 TripleTOF Q-TOF mass spectrometer. |
Institute | University of Central Lancashire |
Department | Natural Sciences |
Last Name | Bonicelli |
First Name | Andrea |
Address | 1 North Cliff street |
abonicelli@uclan.ac.uk | |
Phone | 07383974949 |
Submit Date | 2023-03-15 |
Num Groups | 3 |
Total Subjects | 1 |
Num Males | 1 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | LC-MS |
Release Date | 2024-03-17 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN004214 | AN004215 | AN004216 | AN004217 |
---|---|---|---|---|
Analysis type | MS | MS | MS | MS |
Chromatography type | HILIC | HILIC | Reversed phase | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
Column | Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um) | Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um) | Thermo Accucore C18 (150 x 2.1mm,2.6um) | Thermo Accucore C18 (150 x 2.1mm,2.6um) |
MS Type | ESI | ESI | ESI | ESI |
MS instrument type | Triple TOF | Triple TOF | Triple TOF | Triple TOF |
MS instrument name | ABI Sciex 6600 TripleTOF | ABI Sciex 6600 TripleTOF | ABI Sciex 6600 TripleTOF | ABI Sciex 6600 TripleTOF |
Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
Units | area integration | area integration | area integration | area integration |
MS:
MS ID: | MS003961 |
Analysis ID: | AN004214 |
Instrument Name: | ABI Sciex 6600 TripleTOF |
Instrument Type: | Triple TOF |
MS Type: | ESI |
MS Comments: | The mass spectrometer was ran under the following source conditions: curtain gas pressure, 50 psi; temperature, 400 °C; ESI nebulizer gas pressure, 50 psi; heater gas pressure, 70 psi; declustering potential, 80 V. Data was acquired in an information dependent manner across 10 high sensitivity product ion scans, each with an accumulation time of 100 ms and a TOF survey scan with accumulation time of 250 ms. Total cycle time was 1.3 s. Collision energy was determined using the formula CE (V) = 0.084 x m/z +12 up to a maximum of 55 V. Isotopes within 4 Da were excluded from the scan. Acquired data were checked in PeakView 2.2 and imported into Progenesis Qi 2.4 for metabolomics, where they were aligned, peaks were picked, normalised to all compounds and deconvoluted according to standard Progenesis workflows. Annotations were made by searching the accurate mass, MS/MS spectrum and isotope distribution ratios of acquired data against the NIST MS/MS metabolite library. Metabolites were identified by searching retention times and accurate masses against an in-house chemical standard library. |
Ion Mode: | POSITIVE |
MS ID: | MS003962 |
Analysis ID: | AN004215 |
Instrument Name: | ABI Sciex 6600 TripleTOF |
Instrument Type: | Triple TOF |
MS Type: | ESI |
MS Comments: | The mass spectrometer was ran under the following source conditions: curtain gas pressure, 50 psi; temperature, 400 °C; ESI nebulizer gas pressure, 50 psi; heater gas pressure, 70 psi; declustering potential, 80 V. Data was acquired in an information dependent manner across 10 high sensitivity product ion scans, each with an accumulation time of 100 ms and a TOF survey scan with accumulation time of 250 ms. Total cycle time was 1.3 s. Collision energy was determined using the formula CE (V) = 0.084 x m/z +12 up to a maximum of 55 V. Isotopes within 4 Da were excluded from the scan. Acquired data were checked in PeakView 2.2 and imported into Progenesis Qi 2.4 for metabolomics, where they were aligned, peaks were picked, normalised to all compounds and deconvoluted according to standard Progenesis workflows. Annotations were made by searching the accurate mass, MS/MS spectrum and isotope distribution ratios of acquired data against the NIST MS/MS metabolite library. Metabolites were identified by searching retention times and accurate masses against an in-house chemical standard library. |
Ion Mode: | NEGATIVE |
MS ID: | MS003963 |
Analysis ID: | AN004216 |
Instrument Name: | ABI Sciex 6600 TripleTOF |
Instrument Type: | Triple TOF |
MS Type: | ESI |
MS Comments: | The mass spectrometer was ran under the following source conditions: curtain gas pressure, 50 psi; temperature, 400 °C; ESI nebulizer gas pressure, 50 psi; heater gas pressure, 70 psi; declustering potential, 80 V. Data was acquired in an information dependent manner across 10 high sensitivity product ion scans, each with an accumulation time of 100 ms and a TOF survey scan with accumulation time of 250 ms. Total cycle time was 1.3 s. Collision energy was determined using the formula CE (V) = 0.084 x m/z +12 up to a maximum of 55 V. Isotopes within 4 Da were excluded from the scan. Acquired data were checked in PeakView 2.2 and imported into Progenesis Qi 2.4 for metabolomics, where they were aligned, peaks were picked, normalised to all compounds and deconvoluted according to standard Progenesis workflows. Annotations were made by searching the accurate mass, MS/MS spectrum and isotope distribution ratios of acquired data against the NIST MS/MS metabolite library. Metabolites were identified by searching retention times and accurate masses against an in-house chemical standard library. |
Ion Mode: | POSITIVE |
MS ID: | MS003964 |
Analysis ID: | AN004217 |
Instrument Name: | ABI Sciex 6600 TripleTOF |
Instrument Type: | Triple TOF |
MS Type: | ESI |
MS Comments: | The mass spectrometer was ran under the following source conditions: curtain gas pressure, 50 psi; temperature, 400 °C; ESI nebulizer gas pressure, 50 psi; heater gas pressure, 70 psi; declustering potential, 80 V. Data was acquired in an information dependent manner across 10 high sensitivity product ion scans, each with an accumulation time of 100 ms and a TOF survey scan with accumulation time of 250 ms. Total cycle time was 1.3 s. Collision energy was determined using the formula CE (V) = 0.084 x m/z +12 up to a maximum of 55 V. Isotopes within 4 Da were excluded from the scan. Acquired data were checked in PeakView 2.2 and imported into Progenesis Qi 2.4 for metabolomics, where they were aligned, peaks were picked, normalised to all compounds and deconvoluted according to standard Progenesis workflows. Annotations were made by searching the accurate mass, MS/MS spectrum and isotope distribution ratios of acquired data against the NIST MS/MS metabolite library. Metabolites were identified by searching retention times and accurate masses against an in-house chemical standard library. |
Ion Mode: | NEGATIVE |