Body fluid identification by mass spectrometry

Discovery of specific protein markers in multiple body fluids and their application in forensic science

Identification of multiple body fluids is crucial for the reconstruction and corroboration of crime event. However, for the body fluids with high component similarities, such as peripheral blood and menstrual blood, reliable distinguishing markers are still lacking. Furthermore, a comprehensive protein marker assay for multiple body fluids is urgently necessary for complex crime events. Herein, we established a highly specific and detectable method for discovering protein markers in peripheral blood, menstrual blood, saliva, semen and vaginal fluid through integrating in-depth discovery proteomics and a two-step targeted screening approach. Four menstrual blood markers with high endometrial specificities were identified for differentiation from peripheral blood and exhibited moderate protein concentrations for reproducible analysis with a protein quantitation CV value of 8.66%. Finally, a targeted discrimination method with 16 protein markers was established. We successfully identified 47 blind samples with 100% specificity and detection rate, sourced from five types of body fluids and presented on matrices such as cotton, tissues, slides or fluid. Overall, this work developed an effective method for discovering body fluid biomarkers, obtained specific protein markers to identify five kinds of body fluids and their targeted monitoring will show great significance for forensic science.

Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains

Recent advances in next-generation sequencing have opened up new possibilities for applying the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts of the body to identify body fluids from biological evidence. Despite promising results, microbiome-based methods have not been integrated into forensic practice due to the lack of standardized protocols and systematic testing of methods on forensically relevant samples. Our study addresses critical decisions in establishing these protocols, focusing on bioinformatics choices and the use of machine learning to present microbiome results in case reports for forensically relevant and challenging samples. In our study, we propose using operational taxonomic units (OTUs) for read data processing and generating heterogeneous training data sets for training a random forest classifier. We incorporated six forensically relevant classes: saliva, semen, skin from hand, penile skin, urine, and vaginal/menstrual fluid, and our classifier achieved a high weighted average F1 score of 0.89. Systematic testing on mock forensic samples, including mixed-source samples and underwear, revealed reliable detection of at least one component of the mixture and the identification of vaginal fluid from underwear substrates. Additionally, when investigating the sexually shared microbiome (sexome) of heterosexual couples, our classifier could potentially infer the nature of sexual activity. We therefore highlight the value of the sexome for assessing the nature of sexual activities in forensic investigations while delineating areas that warrant further research.IMPORTANCEMicrobiome-based analyses combined with machine learning offer potential avenues for use in forensic science and other applied fields, yet standardized protocols remain lacking. Moreover, machine learning classifiers have shown promise for predicting body sites in forensics, but they have not been systematically evaluated on complex mixed-source samples. Our study addresses key decisions for establishing standardized protocols and, to our knowledge, is the first to report classification results from uncontrolled mixed-source samples, including sexome (sexually shared microbiome) samples. In our study, we explore both the strengths and limitations of classifying the mixed-source samples while also providing options for tackling the limitations.

Proteomics for forensic identification of saliva and vomit in a case of alleged rape

In crime investigations, the unambiguous identification of biological traces can be decisive for framing the events. In this study, we applied proteomics to analyze scant amounts of biological residues in the context of an alleged rape case, focusing on the detection of traces of vomit. We used high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and two distinct proteomic workflows to identify proteins and possible proteolytic peptides in biological residues from clothing, bedding, and car upholstery from the alleged crime scene. Specifically, a fragment of pillowcase contained a protein pattern indicative of human saliva and a complex panel of peptides resulting from extensive hydrolysis of salivary proteins. The presence of partly digested proteins from bovine meat, wheat, and eggs, along with salivary and gastric enzymes, demonstrated the presence of vomit on the alleged victim's trousers, also providing insights into the recently consumed meal. A drop of cow's milk on the seat of the suspect's car was likely irrelevant to the criminal act. Other fabric samples showed only common contaminants, excluding significant biological traces or food-derived proteins. These findings support the judicial decision regarding consent to sexual intercourse, for which DNA individualization lacks evidentiary power, and establish a reference for annotating saliva and vomit traces in forensic investigations.

Identification of extracellular matrix proteins in plasma as a potential biomarker for intervertebral disc degeneration

PURPOSE

Recently, there has been significant focus on extracellular matrix proteolysis due to its importance in the pathological progression of intervertebral disc degeneration (IVDD). The present study investigates the circulating levels of extracellular matrix proteins in the plasma of IVDD and determines their potential relevance as biomarkers in disc degeneration.

METHODS

Global proteomic analysis was performed in the plasma samples of 10 healthy volunteers (HV) and 10 diseased subjects (DS) after depletion of highly abundant proteins such as albumin and IgG.

RESULTS

We identified 144 and 135 matrix-associated proteins in plasma samples from healthy volunteers (HV) and patients with disc degeneration (DS), respectively. Among these, 49 of the matrix-associated proteins were identical to the proteins found in intervertebral disc (IVD) tissues retrieved from the in-house library. Applying stringent parameters, we selected 28 proteins, with 26 present in DS and 21 in HV. 19 proteins were found common between the groups, two of which-aggrecan (ACAN) and fibulin 1 (FBLN1) - showed statistically significant differences. Specifically, ACAN was up-regulated and FBLN1 was down-regulated in the DS-plasma. In particular, DS-plasma exhibited specific expression of collagen type 2a1 (COL2A1), native to the nucleus pulposus.

CONCLUSION

The distinct presence of collagen type 2a1 and the elevated expression of aggrecan in IVDD plasma may serve as the basis for the development of a potential biomarker for monitoring the progression of disc degeneration.

Mass spectrometry-based proteomics for source-level attribution after DNA extraction

Biological traces recovered from crime scenes serve as vital evidence in forensic investigations. While DNA evidence is frequently used to address the sub-source level of the hierarchy of propositions, the biological source of the DNA can be highly probative at the source level. Current body fluid detection methods pose certain limitations, such as reports of false positive results from some of the presumptive and/or confirmatory tests in current use. These tests are also individual tests for the detection of one body fluid, meaning that if the sample is suspected to be a mixture of multiple body fluids, then different tests would need to be conducted to confirm the body fluid(s) present, which may exhaust small amounts of available biological trace. Proteomics applications for the identification of body fluids have been previously explored, and potential biomarkers indicative of body fluids discovered from liquid-chromatography tandem mass spectrometry (LC-MS/MS) methods have been reported. This work focuses on developing a mass spectrometry-based proteomics approach for the identification of body fluids by targeting discriminating peptide biomarkers from the non-DNA component left over after DNA extraction of samples. The non-DNA component is typically a waste product but with unappreciated evidential value. Our methodology for the purification of proteins from the post-DNA extraction waste includes an acetone precipitation and single-pot solid-phase-enhanced sample preparation (SP3) technique, microwave-assisted trypsin digestion, and LC-MS/MS analysis of the resultant peptides. Preliminary results from this proof-of-concept study include a list of potentially discriminating proteins and peptides for blood, saliva, and semen developed from the analysis of post-DNA extraction waste. Our method allows for multiple analytes to be targeted simultaneously from a DNA profiling waste stream and we anticipate that it could eventually be incorporated into standard forensic laboratory workflows.

Phenotypic profiling based on body fluid traces discovered at the scene of crime: Raman spectroscopy of urine stains for race differentiation

Modern criminal investigations heavily rely on trace bodily fluid evidence as a rich source of DNA. DNA profiling of such evidence can result in the identification of an individual if a matching DNA profile is available. Alternatively, phenotypic profiling based on the analysis of body fluid traces can significantly narrow down the pool of suspects in a criminal investigation. Urine stain is a frequently encountered specimen at the scene of crime. Raman spectroscopy offers great potential as a universal confirmatory method for the identification of all main body fluids, including urine. In this proof-of-concept study, Raman spectroscopy combined with advanced statistics was used for race differentiation based on the analysis of urine stains. Specifically, a Random Forest (RF) model was built, which allowed for differentiating Caucasian (CA) and African American (AA) descent donors with 90% accuracy based on Raman spectra of dried urine samples. Raman spectra were collected from samples of 28 donors varying in age and sex. This novel technology offers great potential as a universal forensic tool for phenotypic profiling of a potential suspect immediately at the scene of a crime, providing invaluable information for a criminal investigation.

Applications of MALDI mass spectrometry in forensic science

Forensic chemistry literature has grown exponentially, with many analytical techniques being used to provide valuable information to help solve criminal cases. Among them, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), particularly MALDI MS imaging (MALDI MSI), has shown much potential in forensic applications. Due to its high specificity, MALDI MSI can analyze a wide variety of compounds in complex samples without extensive sample preparation, providing chemical profiles and spatial distributions of given analyte(s). This review introduces MALDI MS(I) to forensic scientists with a focus on its basic principles and the applications of MALDI MS(I) to the analysis of fingerprints, drugs of abuse, and their metabolites in hair, medicine samples, animal tissues, and inks in documents.

Applications of Raman spectroscopy in the analysis of biological evidence

During the past few decades, Raman spectroscopy has progressed and captivated added attention in the field of science. However, the application of Raman spectroscopy is not limited to the field of forensic science and analytical chemistry; it is one of the emerging spectroscopic techniques, utilized in the field of forensic science which in turn could be a supporting tool in the law and justice system. The advantage of Raman spectroscopy over the other conventional techniques is that it is rapid, reliable, and non-destructive in nature with minimal or no sample preparation. The quantitative and qualitative analysis of evidence from biological and non-biological origins could easily be performed by using Raman spectroscopy. The forensic domain is highly complex with multidisciplinary branches, and therefore a plethora of techniques are utilized for the detection, identification, and differentiation of innumerable pieces of evidence for the purpose of law and justice. Herein, a systematic review is carried out on the application of Raman spectroscopy in the realm of forensic biology and serology considering its usefulness in practical perspectives. This review paper highlights the significance of modern techniques, including micro-Raman spectroscopy, confocal Raman spectroscopy, surface-enhanced Raman spectroscopy, and paper-based surface-enhanced Raman spectroscopy, in the field of Raman spectroscopy. These techniques have demonstrated notable advancements in terms of their applications and capabilities. Furthermore, to comprehensively capture the progress in the development of Raman spectroscopy, all the published papers which could be retrieved from the available databases from the year 2007 to 2022 were incorporated.

Detection of Oral Fluid Stains on Common Substrates Using SEM and ATR-FTIR Spectroscopy for Forensic Purposes

Attenuated total reflectance (ATR) Fourier-transform infrared (FTIR) spectroscopy has been pursued as a novel approach to detect and differentiate biological materials with high specificity owing to its ability to record unique spectral patterns corresponding to the biochemical composition of a specimen. This study expands the application of ATR-FTIR for detecting oral fluid (OF) stains on various common substrates, including four porous and six nonporous substrates. For nonporous substrates, the spectral contribution from the substrate was minimal, and no background subtraction from the substrate bands was required (except for mirrors). For porous substrates, the contribution from the surface was pronounced and was addressed via background subtraction. The results indicated that major OF bands were detected on all the surfaces, even six months after OF deposition. Furthermore, scanning electron microscopy (SEM) was used to probe the morphologies of OF stains on various substrates. SEM micrographs revealed characteristic salt crystals and protein aggregates formed by the dried OF, which were observed for fresh samples and samples after six months post-deposition. Overall, this study demonstrated the great potential of SEM and ATR-FTIR spectroscopy for detecting OF traces on porous and nonporous substrates for up to six months for forensic purposes.

Seminal plasma proteomics as putative biomarkers for male infertility diagnosis

Male infertility represents a significant global public health issue that is currently emerging as a prominent research focus. Presently, laboratories adhere to the guidelines outlined by the World Health Organization (WHO) manuals for conducting routine semen analysis to diagnose male infertility. However, the accuracy of results in predicting sperm quality and fertility is limited because some individuals with a normal semen analysis report, an unremarkable medical history, and a physical examination may still experience infertility. As a result, the importance of employing more advanced techniques to investigate sperm function and male fertility in the treatment of male infertility and/or subfertility becomes apparent. The standard test for evaluating human semen has been improved by more complex tests that look at things like reactive oxygen species (ROS) levels, total antioxidant capacity (TAC), sperm DNA fragmentation levels, DNA compaction, apoptosis, genetic testing, and the presence and location of anti-sperm antibodies. Recent discoveries of novel biomarkers have significantly enriched our understanding of male fertility. Moreover, the notable biological diversity among samples obtained from the same individual complicates the efficacy of routine semen analysis. Therefore, unraveling the molecular mechanisms involved in fertilization is pivotal in expanding our understanding of factors contributing to male infertility. By understanding how these proteins work and what role they play in sperm activity, we can look at the expression profile in men who can't have children to find diagnostic biomarkers. This review examines the various sperm and seminal plasma proteins associated with infertility, as well as proteins that are either deficient or exhibit aberrant expression, potentially contributing to male infertility causes.

Profiling age and body fluid DNA methylation markers using nanopore adaptive sampling

DNA methylation plays essential roles in regulating physiological processes, from tissue and organ development to gene expression and aging processes and has emerged as a widely used biomarker for the identification of body fluids and age prediction. Currently, methylation markers are targeted independently at specific CpG sites as part of a multiplexed assay rather than through a unified assay. Methylation detection is also dependent on divergent methodologies, ranging from enzyme digestion and affinity enrichment to bisulfite treatment, alongside various technologies for high-throughput profiling, including microarray and sequencing. In this pilot study, we test the simultaneous identification of age-associated and body fluid-specific methylation markers using a single technology, nanopore adaptive sampling. This innovative approach enables the profiling of multiple CpG marker sites across entire gene regions from a single sample without the need for specialized DNA preparation or additional biochemical treatments. Our study demonstrates that adaptive sampling achieves sufficient coverage in regions of interest to accurately determine the methylation status, shows a robust consistency with whole-genome bisulfite sequencing data, and corroborates known CpG markers of age and body fluids. Our work also resulted in the identification of new sites strongly correlated with age, suggesting new possible age methylation markers. This study lays the groundwork for the systematic development of nanopore-based methodologies in both age prediction and body fluid identification, highlighting the feasibility and potential of nanopore adaptive sampling while acknowledging the need for further validation and expansion in future research.

Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification

Rescoring of peptide spectrum matches originating from database search engines enabled by peptide property predictors is exceeding the performance of peptide identification from traditional database search engines. In contrast to the peptide spectrum match scores calculated by traditional database search engines, rescoring peptide spectrum matches generates scores based on comparing observed and predicted peptide properties, such as fragment ion intensities and retention times. These newly generated scores enable a more efficient discrimination between correct and incorrect peptide spectrum matches. This approach was shown to lead to substantial improvements in the number of confidently identified peptides, facilitating the analysis of challenging datasets in various fields such as immunopeptidomics, metaproteomics, proteogenomics, and single-cell proteomics. In this review, we summarize the key elements leading up to the recent introduction of multiple data-driven rescoring pipelines. We provide an overview of relevant post-processing rescoring tools, introduce prominent data-driven rescoring pipelines for various applications, and highlight limitations, opportunities, and future perspectives of this approach and its impact on mass spectrometry-based proteomics.

Discrimination of human and animal bloodstains using hyperspectral imaging

Blood is the most encountered type of biological evidence in violent crimes and contains pertinent information to a forensic investigation. The false presumption that blood encountered at a crime scene is human may not be realised until after costly and sample-consuming tests are performed. To address the question of blood origin, the novel application of visible-near infrared hyperspectral imaging (HSI) is used for the detection and discrimination of human and animal bloodstains. The HSI system used is a portable, non-contact, non-destructive method for the determination of blood origin. A support vector machine (SVM) binary classifier was trained for the discrimination of bloodstains of human (n = 20) and five animal species: pig (n = 20), mouse (n = 16), rat (n = 5), rabbit (n = 5), and cow (n = 20). On an independent test set, the SVM model achieved accuracy, precision, sensitivity, and specificity values of 96, 97, 95, and 96%, respectively. Segmented images of bloodstains aged over a period of two months were produced, allowing for the clear visualisation of the discrimination of human and animal bloodstains. The inclusion of such a system in a forensic investigation workflow not only removes ambiguity surrounding blood origin, but can potentially be used in tandem with HSI bloodstain age determination methods for rapid on-scene forensic analysis.

Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects

Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.

Identification of blood species based on surface-enhanced Raman scattering spectroscopy and convolutional neural network

The identification of blood species is of great significance in many aspects such as forensic science, wildlife protection, and customs security and quarantine. Conventional Raman spectroscopy combined with chemometrics is an established method for identification of blood species. However, the Raman spectrum of trace amount of blood could hardly be obtained due to the very small cross-section of Raman scattering. In order to overcome this limitation, surface-enhanced Raman scattering (SERS) was adopted to analyze trace amount of blood. The 785 nm laser was selected as the optimal laser to acquire the SERS spectra, and the blood SERS spectra of 19 species were measured. The convolutional neural network (CNN) was used to distinguish the blood of 19 species including human. The recognition accuracy of the blood species was obtained with 98.79%. Our study provides an effective and reliable method for identification and classification of trace amount of blood.

Development of a rapid, in-situ analysis method using sheath-flow probe electrospray ionisation-mass spectrometry for the direct identification of cocaine metabolites in dried blood spots

RATIONALE

Small amounts of biofluid samples are frequently found at crime scenes; however, existing gold standard methods such as LC-MS frequently require destructive extraction of the sample before a time-consuming analysis which puts strain on forensic analysis providers and can preclude further sample analysis. This study presents the application of sheath-flow probe electrospray ionization-mass spectrometry (sfPESI-MS) to the direct analysis of drug metabolites in dried blood spots (DBS) as a high throughput, minimally destructive alternative.

METHODS

A rapid direct analysis method using a sfPESI ionisation source coupled to an Orbitrap Exactive mass spectrometer was applied to detect cocaine metabolites (benzoylecgonine, BZE, cocaethylene, CE, and ecgonine methyl ester, EME) from DBS. An optimisation study exploring the use of different chemical modifiers (formic acid and sodium acetate) in the sfPESI probe extraction solvent was conducted to enhance the sensitivity and reproducibility of the sfPESI-MS method.

RESULTS

Optimisation of the extraction solvent significantly enhanced the sensitivity and reproducibility of the sfPESI-MS method. A quantitative response over a five-point calibration range 0.5 to 10 μg/ml was obtained for BZE (R²  = 0.9979) and CE (R²  = 0.9948). Limits of detection (LOD) of 1.31, 0.29 and 0.15 μg/ml were achieved for EME, BZE and CE, respectively, from 48 h aged DBSs with % RSD (relative standard deviation) across the calibration range ranging between 19%-28% for [BZE + H]⁺ , 13%-21% for [CE + H]⁺ and 12%-29% for [EME + H]⁺ .

CONCLUSIONS

A rapid (< 20 s) quantitative method for the direct analysis of cocaine metabolites from DBS which requires no prior sample preparation was developed. Although the LOD achieved for BZE (LOD: 0.29 μg/ml) was above the UK threshold limit of exposure for drug driving (0.05 μg/ml), the method may be suitable for use in identifying overdose in forensic analysis.

Long time stability of 35 small endogenous biomolecules in dried urine spotted on various surfaces and environmental conditions

Analysis of endogenous biomolecules is an important aspect of many forensic investigations especially with focus on DNA analysis for perpetrator/victim identification and protein analysis for body fluid identification. Recently, small endogenous biomolecules have been used for differentiation of synthetic "fake" urine from authentic urine and might be also useful for biofluid identification. Therefore, the aim of this study was to adapt and optimize a method for analysis of small EBs and to investigate long time stability of 35 small endogenous biomolecules (including acylcarnitines with their isomers and metabolites as well as amino acids with their metabolites) in spotted urine samples. Urine samples were spotted on seven different surfaces (Whatman 903 Protein Saver Cards, cotton swabs, cotton glove, denim, underwear, and smooth and rough flagstone) and stored under six environmental conditions (reference condition, sunlight, LED light, 4 °C, 37 °C, humidity of 95%). At certain time points (d0, d7, d28 and d56) samples were analyzed in triplicates by an optimized extraction and LC-HRMS approach. In addition, the urine marker Tamm-Horsfall-Protein was determined on cotton swabs at the same time points using a commercial lateral flow test. Twenty-one of 35 small endogenous biomolecules were stable on most materials/surfaces and under most storage conditions. Significant lower endogenous biomolecule peak areas were found for rough flagstone and underwear as well as for high humidity storage. Kynurenic acid proved to be photo labile. While high long time stabilities were found for 19 of 28 acylcarnitines, nine acylcarnitines showed aberrant stability patterns without evident structural reason. For Tamm-Horsfall-Protein degradation within 28 days was observed even under reference conditions. The presented study demonstrated the value of sensitive LC-HRMS analysis for small endogenous biomolecules / pattern. However, further studies will be indispensable for unambiguous body fluid identification by small endogenous biomolecules.

Determination of the Time since Deposition of Blood Traces Utilizing a Liquid Chromatography-Mass Spectrometry-Based Proteomics Approach

Knowledge about when a bloodstain was deposited at a crime scene can be of critical value in forensic investigation. A donor of a genetically identified bloodstain could be linked to a suspected time frame and the crime scene itself. Determination of the time since deposition (TsD) has been extensively studied before but has yet to reach maturity. We therefore conducted a proof-of-principle study to study time- and storage-dependent changes of the proteomes of dried blood stains. A bottom-up proteomics approach was employed, and high-resolution liquid-chromatography-mass-spectrometry (HR-LC-MS) and data-independent acquisition (DIA) were used to analyze samples aged over a 2 month period and two different storage conditions. In multivariate analysis, samples showed distinct clustering according to their TsD in both principal component analysis (PCA) and in partial least square discriminant analysis (PLS DA). The storage condition alters sample aging and yields different separation-driving peptides in hierarchical clustering and in TsD marker peptide selection. Certain peptides and amino acid modifications were identified and further assessed for their applicability in assessing passed TsD. A prediction model based on data resampling (Jackknife) was applied, and prediction values for selected peptide ratios were created. Depending on storage conditions and actual sample age, mean prediction performances ranges in between 70 and 130% for the majority of peptides and time points. This places this study as a first in investigating LC-MS based bottom-up proteomics approaches for TsD determination.

Forensic Discrimination of Differentially Sourced Animal Blood Using a Bottom-Up Proteomics Based MALDI MS Approach

Recently published work has reported the development and application of a bottom-up proteomic approach to distinguish between human and animal blood (down to animal species level), by rapid screening using Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS). In that study, it was additionally observed that intravenous animal blood exhibits different spectral profiles from blood collected within the animal chest cavity as well as from the diluted blood collected within packets of meat. In this follow-up study we explored the resulting hypothesis that, depending on how blood is shed or collected, protein biomarker profiles vary to the extent of systematically permitting a distinction between possible sources of blood (for example, flesh wound versus packaged meat). This intelligence may be important in reconstructing the dynamics of the crime. The combination of statistical analysis and tandem mass spectrometry has yielded additional animal blood markers as well as confirming the ability to correctly determine the animal species from which blood derived, regardless of the retailer selling it (amongst the five investigated). These data confirm the initial hypothesis and demonstrate the opportunity for the proteomics-MALDI combined approach to provide additional intelligence to the investigation of violent crimes when examining blood evidence.

High-throughput seminal fluid identification by automated immunoaffinity mass spectrometry

The identification of semen during a criminal investigation may be a critical component in the prosecution of a sexual assault. Commonly employed enzymatic and affinity-based methods for detection lack specificity, are time-consuming, and only provide a presumptive indication that semen is present where microscopic visualization is unable to meet the throughput demands. Contrary to traditional approaches, protein mass spectrometry provides true confirmatory results, but multiday sample preparation and nanoflow sample separation requirements have limited the practical applicability of these approaches. Aiming at streamlining sexual assault screening by mass spectrometry, the work here coupled a 60-minute rapid tryptic digestion, semenogelin-II peptide affinity purification on an Agilent AssayMap Bravo automation platform, and a 3-minute targeted LC-MS/MS method on an Agilent 6495 triple quadrupole mass spectrometer operating in multiple reaction monitoring mode for detecting semenogelin-II peptides in sexual assault samples. The developed assay was assessed using casework-type samples and was successful in detecting trace levels (0.0001 μl) of semen recovered from both cotton and vaginal swabs, as well as semen recovered from vaginal swabs during menses or adulterated with personal lubricants. This work represents a promising technique for high-throughput seminal fluid identification in sexual assault-type samples by mass spectrometry.

Cryoconcentration by Centrifugation–Filtration: A Simultaneous, Efficient and Innovative Method to Increase Thermosensitive Bioactive Compounds of Aqueous Maqui (Aristotelia chilensis (Mol.) Stuntz) Extract

Maqui (Aristotelia chilensis (Mol.) Stuntz) is a Chilean berry rich in antioxidants, which are mostly found in the pulp and skin of the fruit. The objective was to evaluate the cryoconcentration process by centrifugation–filtration as a simultaneous, efficient, and innovative method to increase the content of thermosensitive bioactive compounds of aqueous maqui extract. Cryoconcentration separated the concentrated solute from the aqueous maqui extract with an efficiency of more than 95%; it increased the content of total polyphenols and total anthocyanins and antioxidant capacity by 280%, 573%, and 226%, respectively. Although the concentrates obtained by evaporation at 50, 70, and 80 °C increased the content of bioactive compounds, they did so in a lower percentage than the cryoconcentrate. Furthermore, cyanidin 3,5-diglucoside was degraded at 70 and 80 °C. In conclusion, cryoconcentration by centrifugation–filtration as a simultaneous process efficiently separates the solutes from the frozen matrix of aqueous maqui extract, and it maintains and increases the contents of polyphenols and anthocyanins and antioxidant capacity. This method is recommended for concentrating natural berry extracts with thermosensitive compounds.

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime

Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.

Developmental validation of a multiplex proteomic assay for the identification of forensically relevant biological fluids

The aim of this study was to validate a multiplex proteomic assay for the identification of high-specificity protein biomarkers by multiple reaction monitoring mass spectrometry on a triple quadrupole mass spectrometer for the accurate, reliable, and confirmatory identification of bodily fluids commonly encountered in a forensic context. This includes the identification of peripheral blood, semen, saliva, urine, and vaginal/menstrual fluid. The assay is able to efficiently identify pure or mixed stains through the identification of target peptide fragments originating from tissue-specific proteins including: uromodulin from urine; prostatic acid phosphatase, prostate specific antigen and semenogelin-II for semen; statherin, submaxillary gland androgen-regulated protein 3B and amylase for saliva; cornulin, martrigel-induced gene C4 protein, suprabasin and neutrophil gelatinase-associated lipocalin for vaginal/menstrual fluid; and alpha-1 antitrypsin, hemopexin, and hemoglobin subunit beta for peripheral blood. Based on the results of the developmental validation studies which included an assessment of reproducibility and repeatability, sensitivity, species specificity, carryover, mixtures, as well as a series of casework type samples. Only a small selection of case samples was unable to unambiguously identify the target fluid including urine recovered from substrates as well as semen when mixed with personal lubricants. Overall, the mass spectrometry-based workflow offers significant advantages compared to existing serological methods.

Forensic proteomics

Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.

Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers

Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples.

Proteomics in Forensic Analysis: Applications for Human Samples

Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.

Forensic analysis of beverage stains using hyperspectral imaging

Documentation and analysis of crime scene evidences are of great importance in any forensic investigation. In this paper, we present the potential of hyperspectral imaging (HSI) to detect and analyze the beverage stains on a paper towel. To detect the presence and predict the age of the commonly used drinks in a crime scene, we leveraged the additional information present in the HSI data. We used 12 different beverages and four types of paper hand towel to create the sample stains in the current study. A support vector machine (SVM) is used to achieve the classification, and a convolutional auto-encoder is used to achieve HSI data dimensionality reduction, which helps in easy perception, process, and visualization of the data. The SVM classification model was re-established for a lighter and quicker classification model on the basis of the reduced dimension. We employed volume-gradient-based band selection for the identification of relevant spectral bands in the HSI data. Spectral data recorded at different time intervals up to 72 h is analyzed to trace the spectral changes. The results show the efficacy of the HSI techniques for rapid, non-contact, and non-invasive analysis of beverage stains.

Direct seminal fluid identification by protease-free high-resolution mass spectrometry

Serological screening of sexual assault evidence has traditionally focused on enzyme activity and immunochromatographic assays that provide only a presumptive indication of seminal fluid and have limited sensitivity relative to DNA testing. Seminal fluid detection based on protein mass spectrometry represents a "Next Gen" serological technology that overcomes the specificity and sensitivity limitations of traditional serological screening but requires time-consuming sample preparation protocols. This paper describes a novel "peptidomics" approach to seminal fluid detection that eliminates the need for lengthy trypsin digestion. This streamlines sample preparation to a one-step process followed by high-resolution mass spectrometry to identify naturally occurring seminal fluid peptides and low-molecular weight proteins. Multiple protein biomarkers of seminal fluid were consistently and confidently identified based on the multiplexed detection of numerous endogenous peptides. These included Semenogelin I and II (90% and 86% sequence coverage, respectively); Prostate Specific Antigen/p30 (29% sequence coverage); and Prostatic Acid Phosphatase (24% sequence coverage). The performance of this streamlined peptidomics approach to seminal fluid identification in a forensic context was also assessed using simulated casework samples of the type typically collected as part of a sexual assault examination (e.g., oral and vaginal swabs stained with semen). The resulting data demonstrate that sub-microliter quantities of seminal fluid on cotton swabs can be recovered and reliably detected. This supports the forensic applicability of a peptidomic assay for seminal fluid identification with same-day sample preparation and analysis. Future development and streamlined multiplex peptidomic assays for additional biological stains can easily be envisaged.

mRNA profiling of mock casework samples: Results of a FoRNAP collaborative exercise

In recent years, forensic mRNA profiling has increasingly been used to identify the origin of human body fluids. By now, several laboratories have implemented mRNA profiling and also use it in criminal casework. In 2018 the FoRNAP (Forensic RNA Profiling) group was established among a number of these laboratories with the aim of sharing experiences, discussing optimization potential, identifying challenges and suggesting solutions with regards to mRNA profiling and casework. To compare mRNA profiling methods and results a collaborative exercise was organized within the FoRNAP group. Seven laboratories from four countries received 16 stains, comprising six pure body fluid / tissue stains and ten mock casework samples. The laboratories were asked to analyze the provided stains with their in-house method (PCR/CE or MPS) and markers of choice. Five laboratories used a DNA/RNA co-extraction strategy. Overall, up to 11 mRNA markers per body fluid were analyzed. We found that mRNA profiling using different extraction and analysis methods as well as different multiplexes can be applied to casework-like samples. In general, high input samples were typed with high accuracy by all laboratories, regardless of the method used. Irrespective of the analysis strategy, samples of low input or mixed stains were more challenging to analyze and interpret since, alike to DNA profiling, a higher number of markers dropped out and/or additional unexpected markers not consistent with the cell type in question were detected. It could be shown that a plethora of different but valid analysis and interpretation strategies exist and are successfully applied in the Forensic Genetics community. Nevertheless, efforts aiming at optimizing and harmonizing interpretation approaches in order to achieve a higher consistency between laboratories might be desirable in the future. The simultaneous extraction of DNA alongside RNA showed to be an effective approach to identify not only the body fluid present but also to identify the donor(s) of the stain. This allows investigators to gain valuable information about the origin of crime scene samples and the course of events in a crime case.

Pre-validation of a MALDI MS proteomics-based method for the reliable detection of blood and blood provenance

The reliable identification of blood, as well as the determination of its origin (human or animal) is of great importance in a forensic investigation. Whilst presumptive tests are rapid and deployed in situ, their very nature requires confirmatory tests to be performed remotely. However, only serological tests can determine blood provenance. The present study improves on a previously devised Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS)—proteomics based method for the reliable detection of blood by enabling the determination of blood provenance. The overall protocol was developed to be more specific than presumptive tests and faster/easier than the gold standard liquid chromatography (LC) MS/MS analysis. This is considered a pre-validation study that has investigated stains and fingermarks made in blood, other biofluids and substances that can elicit a false-positive response to colorimetric or presumptive tests, in a blind fashion. Stains and marks were either untreated or enhanced with a range of presumptive tests. Human and animal blood were correctly discriminated from other biofluids and non-biofluid related matrices; animal species determination was also possible within the system investigated. The procedure is compatible with the prior application of presumptive tests. The refined strategy resulting from iterative improvements through a trial and error study of 56 samples was applied to a final set of 13 blind samples. This final study yielded 12/13 correct identifications with the 13th sample being correctly identified as animal blood but with no species attribution. This body of work will contribute towards the validation of MALDI MS based methods and deployment in violent crimes involving bloodshed.

Species identification of semen stains by ATR-FTIR spectroscopy

Semen stains are the most important biological evidence when identifying the aggressor in sexual assault cases. Current detecting assays of semen stains species identification were not confirmative enough. In this study, we investigated the potential of species identification of semen stains by using attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy combined with advanced chemometrics methods. The effect of substrates types and time since deposition (TSD) were considered in the study. A partial least squares-discriminant analysis (PLS-DA) classification model was established which demonstrated complete separation between human and other species (rabbit, dog, boar, bull, and ram). Validation was conducted which showed prediction abilities with 100% accuracy. Additionally, we found species identification could be achieved without sperm cells which proved ability of spectroscopic methods detecting the semen samples from the case of azoospermia. This work provides a powerful and practical tool for species identification of semen stains in real forensic casework.

Transcriptomic Prediction of Pig Liver-Enriched Gene 1 Functions in a Liver Cell Line

The newly identified liver-enriched gene 1 (LEG1) encodes a protein with a characteristic domain of unknown function 781 (DUF781/LEG1), constituting a protein family with only one member in mammals. A functional study in zebrafish suggested that LEG1 genes are involved in liver development, while the platypus LEG1 homolog, Monotreme Lactation Protein (MLP), which is enriched in the mammary gland and milk, acts as an antibacterial substance. However, no functional studies on eutherian LEG1s have been published to date. Thus, we here report the first functional prediction study at the cellular level. As previously reported, eutherian LEG1s can be classified into three paralogous groups. Pigs have all three LEG1 genes (pLEG1s), while humans and mice have retained only LEG1a. Hence, pLEG1s might represent an ideal model for studying LEG1 gene functions. RNA-seq was performed by the overexpression of pLEG1s and platypus MLP in HepG2 cells. Enrichment analysis showed that pLEG1a and pLEG1b might exhibit little function in liver cells; however, pLEG1c is probably involved in the endoplasmic reticulum (ER) stress response and protein folding. Additionally, gene set enrichment analysis revealed that platypus MLP shows antibacterial activity, confirming the functional study in platypus. Therefore, our study showed from the transcriptomic perspective that mammalian LEG1s have different functions in liver cells due to the subfunctionalization of paralogous genes.

Blood species identification based on deep learning analysis of Raman spectra

Blood analysis is an indispensable means of detection in criminal investigation, customs security and quarantine, anti-poaching of wildlife, and other incidents. Detecting the species of blood is one of the most important analyses. In order to classify species by analyzing Raman spectra of blood, a recognition method based on deep learning principle is proposed in this paper. This method can realize multi-identification blood species, by constructing a one-dimensional convolution neural network and establishing a Raman spectra database containing 20 kinds of blood. The network model is obtained through training, and then is employed to predict the testing set data. The average accuracy of blind detection is more than 97%. In this paper, we try to increase the diversity of data to improve the robustness of the model, optimize the network and adjust the hyperparameters to improve the recognition ability of the model. The evaluation results show that the deep learning model has high recognition performance to distinguish the species of blood.

Direct identification of forensic body fluids by MALDI-MS

The rapid identification of human body fluids is meaningful for forensic casework.

Human Organ Tissue Identification by Targeted RNA Deep Sequencing to Aid the Investigation of Traumatic Injury

Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers. The identifiable organs and tissues include brain, lung, liver, heart, kidney, intestine, stomach, skeletal muscle, adipose, and trachea. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific, with little cross-reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues. We also demonstrate the ability of the assay to successful identify the tissue source of origin using a single blind study.

Statistical approach for ATR-FTIR screening of semen in sexual evidence

Genetic identification has revolutionized the Forensic Sciences, especially in sexual aggression cases. For the successful extraction of the genetic information of a criminal, a crucial step is the prior detection of bodily fluids on evidence. In this article, a method for non-destructive screening of semen samples is reported. Using chemometric tools, bodily fluids can be detected and differentiated without damaging the sample, by correlating the infrared spectra of sexual evidence with previously recorded spectra from undamaged stains of individual bodily fluids. In modern hospitals/laboratories, the proposed method would not require additional equipment/material nor specialized personnel. Furthermore, the method provides qualitative and reliable results, without requiring human interpretation. Therefore, the proposed method opens a door for a low-cost, fully automated and efficient system for non-destructive screening of semen, which could be easily and massively implemented.