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.

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Study IDST002558
Study TitleExtraction and Untargeted Analysis of Metabolome from Undemineralised Cortical Bone Matrix for Forensic Application
Study SummaryUntargeted 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
DepartmentNatural Sciences
Last NameBonicelli
First NameAndrea
Address1 North Cliff street
Emailabonicelli@uclan.ac.uk
Phone07383974949
Submit Date2023-03-15
Num Groups3
Total Subjects1
Num Males1
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-03-17
Release Version1
Andrea Bonicelli Andrea Bonicelli
https://dx.doi.org/10.21228/M8DX4F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA257238BLK B_RP_posBlank Blank
SA257239BLK C_Hilic_posBlank Blank
SA257240BLK B_Hilic_posBlank Blank
SA257241BLK A_RP_posBlank Blank
SA257242BLK C_Hilic_negBlank Blank
SA257243BLK A_Hilic_negBlank Blank
SA257244BLK B_Hilic_negBlank Blank
SA257245BLK A_Hilic_posBlank Blank
SA257246BLK C_RP_posBlank Blank
SA257247BLK A_RP_negBlank Blank
SA257248BLK C_RP_negBlank Blank
SA257249BLK B_RP_negBlank Blank
SA257250A1_Hilic_posChlor_Meth Sample
SA257251A5_Hilic_negChlor_Meth Sample
SA257252A3_Hilic_negChlor_Meth Sample
SA257253A4_Hilic_negChlor_Meth Sample
SA257254A2_RP_posChlor_Meth Sample
SA257255A3_RP_posChlor_Meth Sample
SA257256A2_Hilic_negChlor_Meth Sample
SA257257A3_RP_negChlor_Meth Sample
SA257258A2_RP_negChlor_Meth Sample
SA257259A4_RP_negChlor_Meth Sample
SA257260A5_RP_negChlor_Meth Sample
SA257261A4_RP_posChlor_Meth Sample
SA257262A5_RP_posChlor_Meth Sample
SA257263A1_RP_negChlor_Meth Sample
SA257264A1_RP_posChlor_Meth Sample
SA257265A4_Hilic_posChlor_Meth Sample
SA257266A1_Hilic_negChlor_Meth Sample
SA257267A3_Hilic_posChlor_Meth Sample
SA257268A5_Hilic_posChlor_Meth Sample
SA257269A2_Hilic_posChlor_Meth Sample
SA257270C1_RP_posMeth_ACN Sample
SA257271C1_Hilic_posMeth_ACN Sample
SA257272C2_Hilic_posMeth_ACN Sample
SA257273C4_Hilic_posMeth_ACN Sample
SA257274C3_Hilic_posMeth_ACN Sample
SA257275C3_RP_posMeth_ACN Sample
SA257276C4_RP_posMeth_ACN Sample
SA257277C1_RP_negMeth_ACN Sample
SA257278C2_RP_negMeth_ACN Sample
SA257279C4_RP_negMeth_ACN Sample
SA257280C5_RP_negMeth_ACN Sample
SA257281C5_RP_posMeth_ACN Sample
SA257282C5_Hilic_posMeth_ACN Sample
SA257283C3_RP_negMeth_ACN Sample
SA257284C2_RP_posMeth_ACN Sample
SA257285C4_Hilic_negMeth_ACN Sample
SA257286C2_Hilic_negMeth_ACN Sample
SA257287C1_Hilic_negMeth_ACN Sample
SA257288C5_Hilic_negMeth_ACN Sample
SA257289C3_Hilic_negMeth_ACN Sample
SA257290B5_RP_negMeth_Water Sample
SA257291B4_RP_negMeth_Water Sample
SA257292B3_RP_negMeth_Water Sample
SA257293B5_Hilic_posMeth_Water Sample
SA257294B1_Hilic_negMeth_Water Sample
SA257295B2_Hilic_negMeth_Water Sample
SA257296B5_Hilic_negMeth_Water Sample
SA257297B4_Hilic_negMeth_Water Sample
SA257298B3_Hilic_negMeth_Water Sample
SA257299B4_Hilic_posMeth_Water Sample
SA257300B3_Hilic_posMeth_Water Sample
SA257301B1_RP_posMeth_Water Sample
SA257302B1_Hilic_posMeth_Water Sample
SA257303B1_RP_negMeth_Water Sample
SA257304B2_RP_negMeth_Water Sample
SA257305B2_RP_posMeth_Water Sample
SA257306B3_RP_posMeth_Water Sample
SA257307B2_Hilic_posMeth_Water Sample
SA257308B5_RP_posMeth_Water Sample
SA257309B4_RP_posMeth_Water Sample
SA257310QC05_Hilic_posQC QC
SA257311QC08_Hilic_posQC QC
SA257312QC01_RP_negQC QC
SA257313QC02_RP_negQC QC
SA257314QC03_RP_negQC QC
SA257315QC04_RP_negQC QC
SA257316QC07_Hilic_posQC QC
SA257317QC06_RP_negQC QC
SA257318QC05_RP_negQC QC
SA257319QC08_RP_negQC QC
SA257320QC07_RP_negQC QC
SA257321QC06_Hilic_posQC QC
SA257322QC07_RP_posQC QC
SA257323QC01_Hilic_posQC QC
SA257324QC04_Hilic_negQC QC
SA257325QC03_Hilic_negQC QC
SA257326QC02_Hilic_posQC QC
SA257327QC03_Hilic_posQC QC
SA257328QC06_Hilic_negQC QC
SA257329QC07_Hilic_negQC QC
SA257330QC08_Hilic_negQC QC
SA257331QC02_Hilic_negQC QC
SA257332QC01_Hilic_negQC QC
SA257333QC05_RP_posQC QC
SA257334QC06_RP_posQC QC
SA257335QC05_Hilic_negQC QC
SA257336QC04_RP_posQC QC
SA257337QC03_RP_posQC QC
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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 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

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: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
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