Assessing protein sequencing in human single hair shafts of decreasing lengths

Jones, Katherine F.; Carlson, Traci L.; Eckenrode, Brian A.; Donfack, Joseph

doi:10.1016/j.fsigen.2019.102145

Cited by 10 publications

(19 citation statements)

References 23 publications

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“…In terms of meeting the Daubert standard, GVP analysis has also undergone testing and validation studies using real-world scenarios, such as pigmentation status, body site origin and time in storage, peer review, and reported error [3, 17, 27, 62, 63]. This research contributes further by establishing the use of peptide standards as an additional validation option to investigators [3, 17, 19, 27, 38, 64, 65]. To meet the SWGDAM developmental guidelines, GVP DNA markers have been characterized, species specificity is checked, sensitivity is currently being studied, stability of peptides has been demonstrated, precision and accuracy are reported in proteomic datasets, and population studies are currently being conducted [3, 19, 27, 38, 65].…”

Section: Resultsmentioning

confidence: 99%

“…This research contributes further by establishing the use of peptide standards as an additional validation option to investigators [3, 17, 19, 27, 38, 64, 65]. To meet the SWGDAM developmental guidelines, GVP DNA markers have been characterized, species specificity is checked, sensitivity is currently being studied, stability of peptides has been demonstrated, precision and accuracy are reported in proteomic datasets, and population studies are currently being conducted [3, 19, 27, 38, 65]. Of the targeted mass spectrometry approaches taken, the QQQ mass selection windows for primary and transition ions are broader and less selective than those used in parallel reaction monitoring.…”

Section: Resultsmentioning

confidence: 99%

“…A panel of 24 highly characterized GVPs from 12 loci was selected to represent a wide range of potential sensitivities, from rarely to frequently detected, and were well characterized over a range of studies and laboratory groups [3, 17, 19, 27, 38]. The peptides selected range from 8 to 21 amino acids in length and were all modified with stable isotopes at the C-terminal lysine (+8 Da) or arginine (+10 Da) (JPT peptide technologies, Acton, MA) (Table 1).…”

Section: Methodsmentioning

confidence: 99%

“…No reuse allowed without permission. studies are currently being conducted [3,19,27,38,65]. Of the targeted mass spectrometry approaches taken, the QQQ mass selection windows for primary and transition ions are broader and less selective than those used in parallel reaction monitoring.…”

Section: Analysis Of Performance For the Qqq Platformmentioning

confidence: 99%

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Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts

Goecker¹,

Legg²,

Salemi

et al. 2021

Preprint

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Protein is a major component of all biological evidence. Proteomic genotyping is the use of genetically variant peptides that contain single amino acid polymorphisms to infer the genotype of matching non-synonymous single nucleotide polymorphisms for the individual who originated the protein sample. This can be used to statistically associate an individual to evidence found at a crime scene. The utility of the inferred genotype increases as the detection of genetically variant peptides increases, which is the direct result of technology transfer to mass spectrometry platforms typically available. Digests of single (2 cm) human hair shafts from three European and two African subjects were analyzed using data dependent acquisition on a Q-Exactive Plus Hybrid Quadrupole-Orbitrap system, data independent acquisition and a variant of parallel reaction monitoring on a Orbitrap Fusion Lumos Tribrid system, and multiple reaction monitoring on an Agilent 6495 triple quadrupole system. In our hands, average genetically variant peptide detection from a selected 24 genetically variant peptide panel increased from 6.5 +/- 1.1 and 3.1 +/- 0.8 using data dependent and independent acquisition to 9.5 +/- 0.7 and 11.7 +/- 1.7 using parallel reaction monitoring and multiple reaction monitoring (p < 0.05). Parallel reaction monitoring resulted in a 1.3-fold increase in detection sensitivity, and multiple reaction monitoring resulted in a 1.6-fold increase in detection sensitivity. This increase in biomarker detection has a functional impact on the statistical association of a protein sample and an individual. Increased biomarker sensitivity, using Markov Chain Monte Carlo modeling, produced a median estimated random match probability of over 1 in 10 trillion from a single hair using targeted proteomics. For parallel reaction monitoring and multiple reaction monitoring, detected genetically variant peptides were validated by the inclusion of stable isotope labeled peptides in each sample, which served also as a detection trigger. This research accomplishes two aims: the demonstration of utility for alternative analytical platforms in proteomic genotyping, and the establishment of validation methods for the evaluation of inferred genotypes.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Analysis Of Performance For the Qqq Platformmentioning

confidence: 99%

See 2 more Smart Citations

Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts

Goecker¹,

Legg²,

Salemi

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…Protein extraction, in-solution trypsin digestion and sample clean-up followed by an unmodified in-house protocol developed during a previous research effort [13].…”

Section: Protein Extraction In-solution Trypsin Digestion and Sample Clean-upmentioning

confidence: 99%

Assessing Single-Source Reproducibility of Human Head Hair Peptide Profiling from Different Regions of the Scalp

Lawas

Jones

Mason

et al. 2021

Forensic Science International: Genetics

Self Cite

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Neither microscopical hair comparisons nor mitochondrial DNA sequencing alone, or together, constitutes a basis for personal identification. Due to these limitations, a complementary technique to compare questioned and known hair shafts was investigated. Recently, scientists from Lawrence Livermore National Laboratory's Forensic Science Center and other collaborators developed a peptide profiling technique, which can infer nonsynonymous single nucleotide polymorphisms (SNPs) preserved in hair shaft proteins as single amino acid polymorphisms (SAPs). In this study, peptide profiling was evaluated to determine if it can meet forensic expectations when samples are in limited quantities with the possibility that hair samples collected from different areas of a single donor's scalp (i.e., single source) might not exhibit the same SAP profile. The average dissimilarity, percent differences in SAP profiles within each source, ranged from 0% difference to 29%. This pilot study suggests that more work is needed before peptide profiling of hair can be considered for forensic comparisons.

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From flesh to bones: Multi‐omics approaches in forensic science

Procopio,

Bonicelli

2024

Proteomics

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Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high‐throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state‐of‐the‐art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi‐omics techniques for forensic investigations.

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Assessing protein sequencing in human single hair shafts of decreasing lengths

Cited by 10 publications

References 23 publications

Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts

Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts

Assessing Single-Source Reproducibility of Human Head Hair Peptide Profiling from Different Regions of the Scalp

From flesh to bones: Multi‐omics approaches in forensic science

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