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:
Project:
| Project ID: | PR001650 |
| Project DOI: | doi: 10.21228/M8DX4F |
| Project Title: | Extraction and Untargeted Analysis of Metabolome from Undemineralised Cortical Bone Matrix for Forensic Application |
| Project Summary: | Analysis of bone biomolecules for post mortem and age at death estimation in forensic contexts |
| Institute: | University of Central Lancashire |
| Last Name: | Bonicelli |
| First Name: | Andrea |
| Address: | 1 North Cliff street |
| Email: | abonicelli@uclan.ac.uk |
| Phone: | 07383974949 |
| Funding Source: | UKRI Future Leaders Fellowship under grant number MR/S032878/1 |
Subject:
| Subject ID: | SU002659 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 82 |
| Gender: | Female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | class | type |
|---|---|---|---|
| SA257238 | BLK B_RP_pos | Blank | Blank |
| SA257239 | BLK C_Hilic_pos | Blank | Blank |
| SA257240 | BLK B_Hilic_pos | Blank | Blank |
| SA257241 | BLK A_RP_pos | Blank | Blank |
| SA257242 | BLK C_Hilic_neg | Blank | Blank |
| SA257243 | BLK A_Hilic_neg | Blank | Blank |
| SA257244 | BLK B_Hilic_neg | Blank | Blank |
| SA257245 | BLK A_Hilic_pos | Blank | Blank |
| SA257246 | BLK C_RP_pos | Blank | Blank |
| SA257247 | BLK A_RP_neg | Blank | Blank |
| SA257248 | BLK C_RP_neg | Blank | Blank |
| SA257249 | BLK B_RP_neg | Blank | Blank |
| SA257250 | A1_Hilic_pos | Chlor_Meth | Sample |
| SA257251 | A5_Hilic_neg | Chlor_Meth | Sample |
| SA257252 | A3_Hilic_neg | Chlor_Meth | Sample |
| SA257253 | A4_Hilic_neg | Chlor_Meth | Sample |
| SA257254 | A2_RP_pos | Chlor_Meth | Sample |
| SA257255 | A3_RP_pos | Chlor_Meth | Sample |
| SA257256 | A2_Hilic_neg | Chlor_Meth | Sample |
| SA257257 | A3_RP_neg | Chlor_Meth | Sample |
| SA257258 | A2_RP_neg | Chlor_Meth | Sample |
| SA257259 | A4_RP_neg | Chlor_Meth | Sample |
| SA257260 | A5_RP_neg | Chlor_Meth | Sample |
| SA257261 | A4_RP_pos | Chlor_Meth | Sample |
| SA257262 | A5_RP_pos | Chlor_Meth | Sample |
| SA257263 | A1_RP_neg | Chlor_Meth | Sample |
| SA257264 | A1_RP_pos | Chlor_Meth | Sample |
| SA257265 | A4_Hilic_pos | Chlor_Meth | Sample |
| SA257266 | A1_Hilic_neg | Chlor_Meth | Sample |
| SA257267 | A3_Hilic_pos | Chlor_Meth | Sample |
| SA257268 | A5_Hilic_pos | Chlor_Meth | Sample |
| SA257269 | A2_Hilic_pos | Chlor_Meth | Sample |
| SA257270 | C1_RP_pos | Meth_ACN | Sample |
| SA257271 | C1_Hilic_pos | Meth_ACN | Sample |
| SA257272 | C2_Hilic_pos | Meth_ACN | Sample |
| SA257273 | C4_Hilic_pos | Meth_ACN | Sample |
| SA257274 | C3_Hilic_pos | Meth_ACN | Sample |
| SA257275 | C3_RP_pos | Meth_ACN | Sample |
| SA257276 | C4_RP_pos | Meth_ACN | Sample |
| SA257277 | C1_RP_neg | Meth_ACN | Sample |
| SA257278 | C2_RP_neg | Meth_ACN | Sample |
| SA257279 | C4_RP_neg | Meth_ACN | Sample |
| SA257280 | C5_RP_neg | Meth_ACN | Sample |
| SA257281 | C5_RP_pos | Meth_ACN | Sample |
| SA257282 | C5_Hilic_pos | Meth_ACN | Sample |
| SA257283 | C3_RP_neg | Meth_ACN | Sample |
| SA257284 | C2_RP_pos | Meth_ACN | Sample |
| SA257285 | C4_Hilic_neg | Meth_ACN | Sample |
| SA257286 | C2_Hilic_neg | Meth_ACN | Sample |
| SA257287 | C1_Hilic_neg | Meth_ACN | Sample |
| SA257288 | C5_Hilic_neg | Meth_ACN | Sample |
| SA257289 | C3_Hilic_neg | Meth_ACN | Sample |
| SA257290 | B5_RP_neg | Meth_Water | Sample |
| SA257291 | B4_RP_neg | Meth_Water | Sample |
| SA257292 | B3_RP_neg | Meth_Water | Sample |
| SA257293 | B5_Hilic_pos | Meth_Water | Sample |
| SA257294 | B1_Hilic_neg | Meth_Water | Sample |
| SA257295 | B2_Hilic_neg | Meth_Water | Sample |
| SA257296 | B5_Hilic_neg | Meth_Water | Sample |
| SA257297 | B4_Hilic_neg | Meth_Water | Sample |
| SA257298 | B3_Hilic_neg | Meth_Water | Sample |
| SA257299 | B4_Hilic_pos | Meth_Water | Sample |
| SA257300 | B3_Hilic_pos | Meth_Water | Sample |
| SA257301 | B1_RP_pos | Meth_Water | Sample |
| SA257302 | B1_Hilic_pos | Meth_Water | Sample |
| SA257303 | B1_RP_neg | Meth_Water | Sample |
| SA257304 | B2_RP_neg | Meth_Water | Sample |
| SA257305 | B2_RP_pos | Meth_Water | Sample |
| SA257306 | B3_RP_pos | Meth_Water | Sample |
| SA257307 | B2_Hilic_pos | Meth_Water | Sample |
| SA257308 | B5_RP_pos | Meth_Water | Sample |
| SA257309 | B4_RP_pos | Meth_Water | Sample |
| SA257310 | QC05_Hilic_pos | QC | QC |
| SA257311 | QC08_Hilic_pos | QC | QC |
| SA257312 | QC01_RP_neg | QC | QC |
| SA257313 | QC02_RP_neg | QC | QC |
| SA257314 | QC03_RP_neg | QC | QC |
| SA257315 | QC04_RP_neg | QC | QC |
| SA257316 | QC07_Hilic_pos | QC | QC |
| SA257317 | QC06_RP_neg | QC | QC |
| SA257318 | QC05_RP_neg | QC | QC |
| SA257319 | QC08_RP_neg | QC | QC |
| SA257320 | QC07_RP_neg | QC | QC |
| SA257321 | QC06_Hilic_pos | QC | QC |
| SA257322 | QC07_RP_pos | QC | QC |
| SA257323 | QC01_Hilic_pos | QC | QC |
| SA257324 | QC04_Hilic_neg | QC | QC |
| SA257325 | QC03_Hilic_neg | QC | QC |
| SA257326 | QC02_Hilic_pos | QC | QC |
| SA257327 | QC03_Hilic_pos | QC | QC |
| SA257328 | QC06_Hilic_neg | QC | QC |
| SA257329 | QC07_Hilic_neg | QC | QC |
| SA257330 | QC08_Hilic_neg | QC | QC |
| SA257331 | QC02_Hilic_neg | QC | QC |
| SA257332 | QC01_Hilic_neg | QC | QC |
| SA257333 | QC05_RP_pos | QC | QC |
| SA257334 | QC06_RP_pos | QC | QC |
| SA257335 | QC05_Hilic_neg | QC | QC |
| SA257336 | QC04_RP_pos | QC | QC |
| SA257337 | QC03_RP_pos | QC | QC |
Collection:
| Collection ID: | CO002652 |
| Collection Summary: | Bone sample (∼1cm3) of the anterior midshaft tibia (left) were collected by means of a 12V Dremel cordless lithium-ion drill with a diamond impregnated wheel drill bit was used at maximum 5000 revolutions from an 82 years old male individual belonging to the Forensic Anthropology Center - Texas State University collection. |
| Sample Type: | Bone |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002671 |
| Treatment Summary: | No treatment was applied to the material. |
Sample Preparation:
| Sampleprep ID: | SP002665 |
| Sampleprep Summary: | The bone piece was further powdered using a Spex SamplePrep 6775-115 Freezer/Mill Small Cryogenic Grinder operated in liquid nitrogen at speed 10 with 3min pre-cooling, 2min run and 2min cooling protocol. The powder was stored in a cryovial at -80◦C until further processing. Biphasic Extraction 50mg of bone powder was placed in a 2mL Pre-Filled Bead Mill Tubes (ceramic 1.4 mm in diameter) and 900µL of 2:1 (% v/v) Chlor:MeOH were added. Samples were vortexed for 30s and and homogenised (4x20s bursts at 7200RPMs, pause 2min between bursts) in a Precellys evolution. To induce phase separation, 400µL of LC‐MS grade water was added and homogenised (4x20s bursts at 7200RPMs, pause 2min between bursts). The samples were then centrifuged at 4°C for 10min at 2000RPMs and rest in ice for 5min. 600µL lower fraction (organic) was collected and transferred to fresh Eppendorf tubes and the samples were re‐extracted for a second time using 500µL of 2:1 (% v/v) Chlor:MeOH and the tube homogenised (4x20s bursts at 7200RPMs, pause 2min between bursts). The two respective fractions were combined and concentrated. 600µL lower fraction (organic) was collected and transferred the previous Eppendorf tube. This was centrifuged at 13000rpm, 4°C for 10min and 1ml of the supernatant was collected and dried under nitrogen flow. 350µL of aqueous phase in a fresh Eppendorf tube and centrifuge at 13000rpm, 4°C for 10min and 300µL transferred to a fresh tube and dried under nitrogen flow. Dry extracts were store at -80°C until testing. Methanol-Water Extraction 50mg of bone powder was placed in a 2mL Pre-Filled Bead Mill Tubes (ceramic 1.4 mm in diameter) and 750µL of 8:2 (% v/v) MeOH:Water were added. Samples were vortexed for 30s and and homogenised (4x20s bursts at 7200RPMs, pause 2min between bursts) in a Precellys Evolution. The homogenisation tube was centrifuged at 13000RPMs, 4°C for 10min, 700µL were moved to a fresh tube. 750µL of 8:2 (% v/v) MeOH:Water were added and the homogenisation step was repeated. The homogenisation tube was centrifuged at 13000RPMs, 4°C for 10min, 700µL were moved to the same collection tube. The tube with the two extracts was centrifuged at 13000RPMs, 4°C for 10min and 1.2mL of supernatant were transferred in a fresh tube and dried under nitrogen flow. Dry extracts were store at -80°C until testing. Methanol-Acetonitrile-Water Extraction 50mg of bone powder was placed in a 2mL Pre-Filled Bead Mill Tubes (ceramic 1.4 mm in diameter) and 750µL of 2:2:1 (% v/v/v) MeOH:AC:Water were added. Samples were vortexed for 30s and and homogenised (4x20s bursts at 7200RPMs, pause 2min between bursts) in a Precellys Evolution. The homogenisation tube was centrifuged at 13000RPMs, 4°C for 10min, 700µL were moved to a fresh tube. 750µL of 2:2:1 (% v/v/v) MeOH:ACN:Water were added and the homogenisation step was repeated. The homogenisation tube was centrifuged at 13000RPMs, 4°C for 10min, 700uL were moved to the same collection tube. The tube with the two extracts was centrifuged at 13000RPMs, 4°C for 10min and 1.2mL of supernatant were transferred in a fresh tube and dried under nitrogen flow. Dry extracts were store at -80°C until testing. |
| Processing Storage Conditions: | Described in summary |
| Extract Storage: | -80℃ |
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 | QTOF | QTOF | QTOF | QTOF |
| 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 |
Chromatography:
| Chromatography ID: | CH003124 |
| Chromatography Summary: | Hilic ESI+ |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um) |
| Column Temperature: | 50 °C |
| Flow Gradient: | 0 min 98% B 3 min 98% B 23 min 5% B 24 min 5% B 24 min 98% B |
| Flow Rate: | 0.25 ml/min |
| Sample Injection: | 5 μL |
| Solvent A: | 10 mM ammonium formate and 0.1 % formic acid in water |
| Solvent B: | 9:1 acetonitrile / 10 mM ammonium formate and 0.1 % formic acid in water |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003125 |
| Chromatography Summary: | Hilic ESI- |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Agilent InfinityLab Poroshell 120 HILIC-Z (150 x 2.1mm,2.7um) |
| Column Temperature: | 50 °C |
| Flow Gradient: | 0 min 96% B 2 min 96% B 22 min 65% B 24 min 65% B 24 min 96% B |
| Flow Rate: | 0.25 ml/min |
| Sample Injection: | 5 μL |
| Solvent A: | 10 mM ammonium acetate, pH 9 with ammonium hydroxide and 10 µM medronic acid |
| Solvent B: | 85:15 acetonitrile / 10 mM ammonium acetate, pH 9 with ammonium hydroxide and 10 µM medronic acid in water |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH003126 |
| Chromatography Summary: | RP ESI+ |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Thermo Accucore C18 (150 x 2.1mm,2.6um) |
| Column Temperature: | 40 °C |
| Flow Gradient: | 0 min 5% B 1 min 5% B 8 min 100% B 10 min 100% B 10 min 5% B |
| Flow Rate: | 0.3 ml/min |
| Sample Injection: | 5 μL |
| Solvent A: | 0.1 % formic acid in water |
| Solvent B: | 0.1 % formic acid in 98:2 acetonitrile / water |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003127 |
| Chromatography Summary: | RP ESI- |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Thermo Accucore C18 (150 x 2.1mm,2.6um) |
| Column Temperature: | 40 °C |
| Flow Gradient: | 0 min 5% B 1 min 5% B 8 min 100% B 10 min 100% B 10 min 5% B |
| Flow Rate: | 0.3 ml/min |
| Sample Injection: | 5 μL |
| Solvent A: | 0.1 % formic acid in water |
| Solvent B: | 0.1 % formic acid in 98:2 acetonitrile / water |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003961 |
| Analysis ID: | AN004214 |
| Instrument Name: | ABI Sciex 6600 TripleTOF |
| Instrument Type: | QTOF |
| 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: | QTOF |
| 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: | QTOF |
| 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: | QTOF |
| 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 |
