Summary of Study ST002283

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 PR001463. The data can be accessed directly via it's Project DOI: 10.21228/M8MH6X 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 IDST002283
Study TitleThe “ForensOMICS” approach to forensic post-mortem interval estimation: combining metabolomics, lipidomics and proteomics for the analysis human skeletal remains
Study SummaryThe combined use of multiple omics methods to answer complex system biology questions is growing in biological and medical sciences, as the importance of studying interrelated biological processes in their entirety is increasingly recognized. We applied a combination of metabolomics, lipidomics and proteomics to human bone to investigate the potential of this multi-omics approach to estimate the time elapsed since death (i.e., the post-mortem interval, PMI). This “ForensOMICS” approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors in a fresh stage of decomposition before placement of the bodies to decompose outdoors at the human taphonomy facility managed by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219, 790, 834 and 872 days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic and proteomic profiles from the pre- and post-placement bone samples. Multivariate analysis was used to investigate the three omics blocks by means of Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers that could effectively describe post-mortem changes and classify the individuals based on their PMI. The resulting model showed that pre-placement bone metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement profiles. Metabolites associated with the pre-placement samples, suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules from the three groups that show excellent potential for estimation of the PMI, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different post-mortem stability, in future studies we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by including more stable proteins.
Institute
University of Central Lancashire
Last NameBonicelli
First NameAndrea
AddressFylde Rd, Preston PR1 2HE
Emailabonicelli@uclan.ac.uk
Phone07383974949
Submit Date2022-09-06
Num Groups5
Total Subjects4
Num Females4
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-10-13
Release Version1
Andrea Bonicelli Andrea Bonicelli
https://dx.doi.org/10.21228/M8MH6X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001463
Project DOI:doi: 10.21228/M8MH6X
Project Title:ForensOMICS
Project Type:Untargeted metabolomics
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:Fylde Rd, Preston, Lancashire, PR1 2HE, United Kingdom
Email:abonicelli@uclan.ac.uk
Phone:07383974949
Project Comments:raw data ID DataTrackID3449
Contributors:Andrea Bonicelli

Subject:

Subject ID:SU002369
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:61-91
Gender:Female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Age PMI Deposition State
SA218507D3_TF_D_Lip_Neg61 2-10 Pre deposition Fresh
SA218508D3_TF_C_Lip_Neg61 2-10 Pre deposition Fresh
SA218509D3_TF_A_Hilic_Neg61 2-10 Pre deposition Fresh
SA218510D3_TF_E_Lip_Neg61 2-10 Pre deposition Fresh
SA218511D3_TF_D_Hilic_Pos61 2-10 Pre deposition Fresh
SA218512D3_TF_B_Hilic_Pos61 2-10 Pre deposition Fresh
SA218513D3_TF_C_Hilic_Pos61 2-10 Pre deposition Fresh
SA218514D3_TF_C_Hilic_Neg61 2-10 Pre deposition Fresh
SA218515D3_TF_E_Hilic_Pos61 2-10 Pre deposition Fresh
SA218516D3_TF_E_Hilic_Neg61 2-10 Pre deposition Fresh
SA218517D3_TF_C_Lip_Pos61 2-10 Pre deposition Fresh
SA218518D3_TF_D_Lip_Pos61 2-10 Pre deposition Fresh
SA218519D3_TF_E_Lip_Pos61 2-10 Pre deposition Fresh
SA218520D3_TF_B_Lip_Pos61 2-10 Pre deposition Fresh
SA218521D3_TF_A_Lip_Pos61 2-10 Pre deposition Fresh
SA218522D3_TF_A_Hilic_Pos61 2-10 Pre deposition Fresh
SA218523D3_TF_B_Lip_Neg61 2-10 Pre deposition Fresh
SA218524D3_TF_A_Lip_Neg61 2-10 Pre deposition Fresh
SA218525D3_TF_D_Hilic_Neg61 2-10 Pre deposition Fresh
SA218526D3_TF_B_Hilic_Neg61 2-10 Pre deposition Fresh
SA218527D3_TS_A_Lip_Pos61 834 Burial Skeletonised
SA218528D3_TS_E_Lip_Neg61 834 Burial Skeletonised
SA218529D3_TS_B_Lip_Pos61 834 Burial Skeletonised
SA218530D3_TS_C_Lip_Pos61 834 Burial Skeletonised
SA218531D3_TS_E_Lip_Pos61 834 Burial Skeletonised
SA218532D3_TS_D_Lip_Pos61 834 Burial Skeletonised
SA218533D3_TS_D_Lip_Neg61 834 Burial Skeletonised
SA218534D3_TS_C_Lip_Neg61 834 Burial Skeletonised
SA218535D3_TS_B_Hilic_Neg61 834 Burial Skeletonised
SA218536D3_TS_A_Hilic_Neg61 834 Burial Skeletonised
SA218537D3_TS_C_Hilic_Neg61 834 Burial Skeletonised
SA218538D3_TS_A_Lip_Neg61 834 Burial Skeletonised
SA218539D3_TS_B_Lip_Neg61 834 Burial Skeletonised
SA218540D3_TS_E_Hilic_Neg61 834 Burial Skeletonised
SA218541D3_TS_D_Hilic_Neg61 834 Burial Skeletonised
SA218542D3_TS_D_Hilic_Pos61 834 Burial Skeletonised
SA218543D3_TS_B_Hilic_Pos61 834 Burial Skeletonised
SA218544D3_TS_A_Hilic_Pos61 834 Burial Skeletonised
SA218545D3_TS_E_Hilic_Pos61 834 Burial Skeletonised
SA218546D3_TS_C_Hilic_Pos61 834 Burial Skeletonised
SA218547D2_TF_E_Lip_Neg67 2-10 Pre deposition Fresh
SA218548D2_TF_D_Lip_Neg67 2-10 Pre deposition Fresh
SA218549D2_TF_A_Hilic_Pos67 2-10 Pre deposition Fresh
SA218550D2_TF_B_Hilic_Pos67 2-10 Pre deposition Fresh
SA218551D2_TF_C_Hilic_Pos67 2-10 Pre deposition Fresh
SA218552D2_TF_C_Lip_Neg67 2-10 Pre deposition Fresh
SA218553D2_TF_E_Lip_Pos67 2-10 Pre deposition Fresh
SA218554D2_TF_B_Lip_Pos67 2-10 Pre deposition Fresh
SA218555D2_TF_C_Lip_Pos67 2-10 Pre deposition Fresh
SA218556D2_TF_E_Hilic_Neg67 2-10 Pre deposition Fresh
SA218557D2_TF_D_Lip_Pos67 2-10 Pre deposition Fresh
SA218558D2_TF_A_Lip_Pos67 2-10 Pre deposition Fresh
SA218559D2_TF_D_Hilic_Neg67 2-10 Pre deposition Fresh
SA218560D2_TF_E_Hilic_Pos67 2-10 Pre deposition Fresh
SA218561D2_TF_B_Hilic_Neg67 2-10 Pre deposition Fresh
SA218562D2_TF_A_Hilic_Neg67 2-10 Pre deposition Fresh
SA218563D2_TF_C_Hilic_Neg67 2-10 Pre deposition Fresh
SA218564D2_TF_B_Lip_Neg67 2-10 Pre deposition Fresh
SA218565D2_TF_D_Hilic_Pos67 2-10 Pre deposition Fresh
SA218566D2_TF_A_Lip_Neg67 2-10 Pre deposition Fresh
SA218567D2_TS_E_Hilic_Pos67 790 Burial Skeletonised
SA218568D2_TS_B_Lip_Pos67 790 Burial Skeletonised
SA218569D2_TS_A_Lip_Pos67 790 Burial Skeletonised
SA218570D2_TS_D_Lip_Neg67 790 Burial Skeletonised
SA218571D2_TS_C_Hilic_Pos67 790 Burial Skeletonised
SA218572D2_TS_B_Hilic_Pos67 790 Burial Skeletonised
SA218573D2_TS_E_Lip_Neg67 790 Burial Skeletonised
SA218574D2_TS_C_Lip_Pos67 790 Burial Skeletonised
SA218575D2_TS_C_Lip_Neg67 790 Burial Skeletonised
SA218576D2_TS_A_Hilic_Pos67 790 Burial Skeletonised
SA218577D2_TS_D_Hilic_Neg67 790 Burial Skeletonised
SA218578D2_TS_C_Hilic_Neg67 790 Burial Skeletonised
SA218579D2_TS_B_Hilic_Neg67 790 Burial Skeletonised
SA218580D2_TS_A_Hilic_Neg67 790 Burial Skeletonised
SA218581D2_TS_E_Hilic_Neg67 790 Burial Skeletonised
SA218582D2_TS_E_Lip_Pos67 790 Burial Skeletonised
SA218583D2_TS_B_Lip_Neg67 790 Burial Skeletonised
SA218584D2_TS_D_Hilic_Pos67 790 Burial Skeletonised
SA218585D2_TS_D_Lip_Pos67 790 Burial Skeletonised
SA218586D2_TS_A_Lip_Neg67 790 Burial Skeletonised
SA218587D4_TF_B_Lip_Pos77 2-10 Pre deposition Fresh
SA218588D4_TF_A_Lip_Pos77 2-10 Pre deposition Fresh
SA218589D4_TF_C_Lip_Pos77 2-10 Pre deposition Fresh
SA218590D4_TF_D_Lip_Pos77 2-10 Pre deposition Fresh
SA218591D4_TF_E_Lip_Pos77 2-10 Pre deposition Fresh
SA218592D4_TF_B_Hilic_Neg77 2-10 Pre deposition Fresh
SA218593D4_TF_D_Hilic_Pos77 2-10 Pre deposition Fresh
SA218594D4_TF_C_Hilic_Pos77 2-10 Pre deposition Fresh
SA218595D4_TF_C_Lip_Neg77 2-10 Pre deposition Fresh
SA218596D4_TF_E_Hilic_Pos77 2-10 Pre deposition Fresh
SA218597D4_TF_E_Lip_Neg77 2-10 Pre deposition Fresh
SA218598D4_TF_B_Lip_Neg77 2-10 Pre deposition Fresh
SA218599D4_TF_A_Lip_Neg77 2-10 Pre deposition Fresh
SA218600D4_TF_C_Hilic_Neg77 2-10 Pre deposition Fresh
SA218601D4_TF_A_Hilic_Neg77 2-10 Pre deposition Fresh
SA218602D4_TF_D_Lip_Neg77 2-10 Pre deposition Fresh
SA218603D4_TF_B_Hilic_Pos77 2-10 Pre deposition Fresh
SA218604D4_TF_E_Hilic_Neg77 2-10 Pre deposition Fresh
SA218605D4_TF_D_Hilic_Neg77 2-10 Pre deposition Fresh
SA218606D4_TF_A_Hilic_Pos77 2-10 Pre deposition Fresh
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Collection:

Collection ID:CO002362
Collection Summary:Bone samples (ca. 1 cm3) of the anterior midshaft tibia (left) were collected prior to placement of the body outdoors, and again upon retrieval of the completely skeletonized remains (right). Each body was in “fresh” stage of decomposition when pre-placement samples were taken, and in “skeletonization” stage when post-placement samples were collected, based on scoring of the gross morphological changes37. The duration of each placement and the deposition context are reported in Table 1. The soft tissue was incised with a disposable scalpel, and a 12 V Dremel cordless lithium-ion drill with a diamond wheel drill bit was used at max. 5000 revolutions to collect ~1 cm3 of bone. Sampling instruments were cleaned with bleach and deionised water between each individual sample collection. A total of eight samples were collected in Ziploc bags, transferred immediately to a -80 °C freezer, and subsequently shipped overnight on dry ice to the Forensic Science Unit at Northumbria University, U.K. The samples were then transferred to a lockable freezer at -20 °C as per UK Human Tissue Act regulations (licence number 12495). The bone samples were defrosted, and fine powder was obtained with a Dremel drill equipped with diamond-tipped drill bits operated at speed 5000 rpms, to avoid heat damage caused by the friction with the bone. The collected powder was homogenised and stored in 2 mL protein LoBind tubes (Eppendorf UK Limited, Stevenage, UK) at -80 °C until extraction and testing. The powder sample was later divided into 25 mg aliquots. The research and bone sample analyses were reviewed and approved by the Ethics committee at Northumbria University (ref. 11623).
Sample Type:Bone
Storage Conditions:-20℃

Treatment:

Treatment ID:TR002381
Treatment Summary:Anterior midshaft tibial bone was collected from four female body donors in a fresh stage of decomposition before placement of the bodies to decompose outdoors at the human taphonomy facility managed by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219, 790, 834 and 872 days)

Sample Preparation:

Sampleprep ID:SP002375
Sampleprep Summary:Chloroform (Chl), AnalaR NORMAPUR® ACS was purchased from VWR Chemicals (Lutterworth, UK). Water Optima™ LC/MS Grade, Methanol (MeOH) Optima™ LC/MS Grade, Pierce™ Acetonitrile (ACN), LC-MS Grade and Isopropanol (IPA), Optima™LC/MS Grade were purchased from Thermo Scientific (Hemel Hempstead, United Kingdom). In total two replicates for each of the six specimens were extracted according to a modified Folch et al. [17] as follow: 25 mg of bone powder was placed in tube A and 750μL of 2:1 (v/v) Chl:MeOH were added, vortexed for 30s and sonicated in ice for additional 20 min. 300μL of LC-MS grade water was added to induce phase separation and sonicate for another 15 mins. The sample were then centrifuged at 10°C for 5 mins at 2000 RPM. The respective upper and lower fractions were collected and transferred to fresh Eppendorf tubes and the samples were re-extracted with a second time using 750μL of 2:1 (v/v) Chl:MeOH. The two respective fractions were combined and concentrated. The organic lipid fraction was preconcentrated using a vacuum concentrator at 55oC for 2.5 hours or until all organic solvents has been removed. The aqueous metabolite fractions were flash frozen in liquid nitrogen and preconcentrated using a lyophilizer cold trap -65oC over night to remove all water content. The respective dry fractions were then stored at -80 until analysis. The metabolite fraction was resuspended in 100μL in 95:5 ACN/water (v/v) and sonicated for 15 mins and centrifuged for 15 min at 15K RPM at 4oC and supernatant was then transferred to 1.5mL autosampler vials with 200μL microinsert and caped. 20μL of each sample were collected and pooled to create the pooled QC. The lipid extracts were resuspended in 100μL of 1:1:2 (v/v) water:ACN:IPA and sonicated for sonicated for 15 min and centrifuged for 15 min at 15K RPM at 10oC and supernatant was then transferred to 1.5mL autosampler vials with 200μL microinsert and caped. 20μL of each sample were collected and pooled to create the pooled QC. The sample set was then submitted for analysis
Processing Storage Conditions:On ice
Extraction Method:Chloroform methanol biphasic extraction
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003728 AN003729 AN003730 AN003731
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Obitrap ID-X Tribrid Obitrap ID-X Tribrid Obitrap ID-X Tribrid Obitrap ID-X Tribrid
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Area integration Area integration Area integration Area integration

Chromatography:

Chromatography ID:CH002761
Chromatography Summary:Hilic ESI+
Methods Filename:AB_Human_Bone_Chromatography.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45°C
Flow Gradient:95% B at T0 hold for 1.5 min, linear decrease to 50% B at 11 min, hold for 4 mins
Flow Rate:200 μL/min
Injection Temperature:300°C
Sample Injection:3μL
Solvent A:100% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:100% acetonitrile; 10 mM ammonium formate; 0.1% formic acid
Preconditioning:4.5 mins B
Chromatography Type:HILIC
  
Chromatography ID:CH002762
Chromatography Summary:Hilic ESI-
Methods Filename:AB_Human_Bone_Chromatography.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45°C
Flow Gradient:95% B at T0 hold for 1.5 min, linear decrease to 50% B at 11 min, hold for 4 mins
Flow Rate:200 μL/min
Injection Temperature:300°C
Sample Injection:5μL
Solvent A:100% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:100% acetonitrile; 10 mM ammonium formate; 0.1% formic acid
Preconditioning:4.5 mins B
Chromatography Type:HILIC
  
Chromatography ID:CH002763
Chromatography Summary:RP ESI+
Methods Filename:AB_Human_Bone_Chromatography.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45°C
Flow Gradient:60% B at T0 hold for 1.5 min, linear increase to 85% B at 7 min, increase to 95% B at 12.5 min and hold for 4.5 min
Flow Rate:200 μL/min
Injection Temperature:300°C
Sample Injection:3μL
Solvent A:40% water/60 % acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% formic acid; 10mM ammonium formate
Preconditioning:4.5 mins B
Chromatography Type:Reversed phase
  
Chromatography ID:CH002764
Chromatography Summary:RP ESI-
Methods Filename:AB_Human_Bone_Chromatography.pdf
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45°C
Flow Gradient:60% B at T0 hold for 1.5 min, linear increase to 85% B at 7 min, increase to 95% B at 12.5 min and hold for 4.5 min
Flow Rate:200 μL/min
Injection Temperature:300°C
Sample Injection:5μL
Solvent A:40% water/60 % acetonitrile; 0.1% ammonia; 10 mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 0.1% ammonia solution; 10mM ammonium formate
Preconditioning:4.5 mins B
Chromatography Type:Reversed phase

MS:

MS ID:MS003476
Analysis ID:AN003728
Instrument Name:Obitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Mass spectrometry (MS) data were acquired using the AcquieX acquisition workflow (data dependent analysis). The MS operating parameters were as follows: MS1 mass resolution 60K, for MS2 30K, stepped energy (HCD) 20, 25, 50, scan range 100-1000, RF len (%) 35, AGC gain, intensity threshold 2e4, 25% custom injection mode with an injection time of 54 ms. An extraction blank was used to create a background exclusion list and a pooled QC was used to create the inclusion list.
Ion Mode:POSITIVE
  
MS ID:MS003477
Analysis ID:AN003729
Instrument Name:Obitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Mass spectrometry (MS) data were acquired using the AcquieX acquisition workflow (data dependent analysis). The MS operating parameters were as follows: MS1 mass resolution 60K, for MS2 30K, stepped energy (HCD) 20, 25, 50, scan range 100-1000, RF len (%) 35, AGC gain, intensity threshold 2e4, 25% custom injection mode with an injection time of 54 ms. An extraction blank was used to create a background exclusion list and a pooled QC was used to create the inclusion list.
Ion Mode:NEGATIVE
  
MS ID:MS003478
Analysis ID:AN003730
Instrument Name:Obitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Mass spectrometry (MS) data were acquired using the AcquieX acquisition workflow (data dependent analysis). The MS operating parameters were as follows: MS1 mass resolution 60K, for MS2 30K, stepped energy (HCD) 20, 25, 50, scan range 100-1000, RF len (%) 35, AGC gain, intensity threshold 2e4, 25% custom injection mode with an injection time of 54 ms. An extraction blank was used to create a background exclusion list and a pooled QC was used to create the inclusion list.
Ion Mode:POSITIVE
  
MS ID:MS003479
Analysis ID:AN003731
Instrument Name:Obitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Mass spectrometry (MS) data were acquired using the AcquieX acquisition workflow (data dependent analysis). The MS operating parameters were as follows: MS1 mass resolution 60K, for MS2 30K, stepped energy (HCD) 20, 25, 50, scan range 100-1000, RF len (%) 35, AGC gain, intensity threshold 2e4, 25% custom injection mode with an injection time of 54 ms. An extraction blank was used to create a background exclusion list and a pooled QC was used to create the inclusion list.
Ion Mode:NEGATIVE
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