Proteomics as a new tool to study fingermark ageing in forensics

Towards a comprehensive understanding of the muscle proteome in Schizothorax labiatus: Insights from seasonal variations, metabolic responses, and reproductive signatures in the River Jhelum

Proteomics is a very advanced technique used for defining correlations, compositions and activities of hundreds of proteins from organisms as well as effectively used in identifying particular proteins with varying peptide lengths and amino acid counts. In the present study, an endeavour has been put forth to create muscle proteome expression of snow trout, Schizothorax labiatus. Liquid chromatography-mass spectrometry (LC-MS) using label free quantification (LFQ) technique has extensively been carried out to explore changes in protein metabolism and its composition to discriminate across species, clarify functions and pinpoint protein biomarkers from organisms. In LFQ technique, the abundances of proteins are determined based on the signal intensities of their corresponding peptides in mass spectrometry. The main benefit of using this method is that it doesn't require pre-labelling proteins with isotopic tags, which streamlines the experimental procedure and gets rid of any bias that might have been caused by the labelling process. LFQ techniques frequently offer a wider dynamic range, making it possible to detect and quantify proteins over a broad range of abundances obtained from the complex biological materials including fish muscle. The results of proteomic analysis could provide an insight in understanding about how various proteins are expressed in response to environmental challenges. For proteomic study, two different weight groups of S. labiatus were taken from River Jhelum based on biological, physiological and logistical factors. These groups corresponded to different life stages, such as younger size and adults/brooders in order to capture potential variations in the muscle proteome related to growth and development. The proteomic analysis of S. labiatus depicted that an overall of 220 proteins in male and 228 in female fish of group 1 were noted. However, when male and female S. labiatus were examined based on spectral count and peptide abundance using ProteinLynx Global Software, a total of 10 downregulated and 32 upregulated proteins were found. In group 2 of S. labiatus, a total of 249 proteins in male and 301 in female fish were documented. When the two genders of S. labiatus were likened to one another by LFQ technique, a total of 41 downregulated and 06 upregulated proteins were identified. The variability in the protein numbers between two fish weight groups reflected biological differences, influenced by factors such as age, developmental stages, physiological condition and reproductive activities. During the study, it was observed that S. labiatus exhibited downregulated levels of proteins that were involved in feeding and growth. The contributing factors to this manifestation could be explained by lower feeding and metabolic activity of fish and decreased food availability during winter in River Jhelum. Contrarily, the fish immune response proteins were found to be significantly over-expressed in S. labiatus, indicating that the environment was more likely to undergo increased microbial infection, pollution load and anthropogenic activities. In addition, it was also discovered that there was an upregulated expression of the reproductive proteins in S. labiatus, which could be linked to the fish's pre-spawning time as the fish used in this study was collected in the winter season which is the pre-spawning period of the fish. Therefore, the present study would be useful in obtaining new insights regarding the molecular makeup of species, methods of adaptation and reactions to environmental stresses. This information contributes to our understanding of basic science and may have applications in environmental monitoring, conservation and preservation of fish species.

Microbes in fingerprints: A source for dating crime evidence?

Interest in the human microbiome has grown in recent years because of increasing applications to biomedicine and forensic science. However, the potential for dating evidence at a crime scene based upon time-dependent changes in microbial signatures has not been established, despite a relatively straightforward scientific process for isolating the microbiome. We hypothesize that modifications in microbial diversity, abundance, and succession can provide estimates of the time a surface was touched for investigative purposes. In this proof-of-concept research, the sequencing and analysis of the 16 S rRNA gene from microbes present in fresh and aged latent fingerprints deposited by three donors with pre- and post-washed hands is reported. The stability of major microbial phyla is confirmed while the dynamics of less abundant groups is described up to 21 days post-deposition. Most importantly, a phylum is suggested as the source for possible biological markers to date fingerprints: Deinococcus-Thermus.

MALDI MSI Separation of Same Donor's Fingermarks Based on Time of Deposition-A Proof-of-Concept Study

Despite the advent of DNA profiling, fingerprints still play an important role in suspect identification. However, if single crime scene marks may be challenging to identify, overlapping fingermarks, understandably, pose an even greater challenge. In the last decade, mass spectrometry-imaging methods have provided a possible solution to the separation of fingermarks from two or more donors, based on the differential chemical composition. However, there are no studies attempting to separate overlapping marks from the same donor. This is important in relation to fingermark deposition at different times, which could be critical, for example, to ascertain legitimate access to the scene. In the work presented here, we investigate whether Matrix-Assisted Laser Desorption Ionisation Mass Spectrometry Imaging can separate the same donor's fingermarks deposited at different times based on intra-donor fingermark composition variability. Additionally, the hypothesis that the different times of deposition could be also determined was investigated in the view of linking the suspect at the scene at different times; the dating window of MALDI MSI within the selected molecular range was explored. Results show that it is possible to separate overlapping fingermarks from the same donor in most cases, even from natural marks. Fresh marks (0 days) could be separated from those of fourteen days of age, though the latter could not be distinguished from the set aged for seven days. Due to the use of only one donor, these are to be considered preliminary data, though findings are interesting enough to warrant further investigation of the capabilities and limitations of this approach using a larger cohort of donors.

Non-invasive screening of breast cancer from fingertip smears-a proof of concept study

Breast cancer is a global health issue affecting 2.3 million women per year, causing death in over 600,000. Mammography (and biopsy) is the gold standard for screening and diagnosis. Whilst effective, this test exposes individuals to radiation, has limitations to its sensitivity and specificity and may cause moderate to severe discomfort. Some women may also find this test culturally unacceptable. This proof-of-concept study, combining bottom-up proteomics with Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS) detection, explores the potential for a non-invasive technique for the early detection of breast cancer from fingertip smears. A cohort of 15 women with either benign breast disease (n = 5), early breast cancer (n = 5) or metastatic breast cancer (n = 5) were recruited from a single UK breast unit. Fingertips smears were taken from each patient and from each of the ten digits, either at the time of diagnosis or, for metastatic patients, during active treatment. A number of statistical analyses and machine learning approaches were investigated and applied to the resulting mass spectral dataset. The highest performing predictive method, a 3-class Multilayer Perceptron neural network, yielded an accuracy score of 97.8% when categorising unseen MALDI MS spectra as either the benign, early or metastatic cancer classes. These findings support the need for further research into the use of sweat deposits (in the form of fingertip smears or fingerprints) for non-invasive screening of breast cancer.

Proteomic Applications in Aquatic Environment Studies

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Unlocking the potential of forensic traces: Analytical approaches to generate investigative leads

Forensic investigation involves gathering the information necessary to understand the criminal events as well as linking objects or individuals to an item, location or other individual(s) for investigative purposes. For years techniques such as presumptive chemical tests, DNA profiling or fingermark analysis have been of great value to this process. However, these techniques have their limitations, whether it is a lack of confidence in the results obtained due to cross-reactivity, subjectivity and low sensitivity; or because they are dependent on holding reference samples in a pre-existing database. There is currently a need to devise new ways to gather as much information as possible from a single trace, particularly from biological traces commonly encountered in forensic casework. This review outlines the most recent advancements in the forensic analysis of biological fluids, fingermarks and hair. Special emphasis is placed on analytical methods that can expand the information obtained from the trace beyond what is achieved in the usual practices. Special attention is paid to those methods that accurately determine the nature of the sample, as well as how long it has been at the crime scene, along with individualising information regarding the donor source of the trace.

Exploring the problem of determining human age from fingermarks using MALDI MS-machine learning combined approaches

For over a century fingerprints have been predominantly used as a means of biometric identification. Notwithstanding, the unique pattern of lines that can contribute to identifying a suspect is made up of molecules originating from touch chemistry (contaminants) as well as from within the body. It is the latter class of molecules that could provide additional information about a suspect, such as lifestyle, as well as physiological, pharmacological and pathological states. An example of the physiological state (and semi-biometric information) is the sex of an individual; recent investigations have demonstrated the opportunity to determine the sex of an individual with an 86% accuracy of prediction based on the peptidic/protein profile of their fingerprints. In the study presented here, the first of its kind, a range of supervised learning predictive methods have been evaluated to explore the depth of the issue connected to human age determination from fingermarks exploiting again the differential presence of peptides and small proteins. A number of observations could be made providing (i) an understanding of the more appropriate study design for this kind of investigation, (ii) the most promising prediction model to test within future work and (iii) the deeper issues relating to this type of determination and concerning a mismatch between chronological and biological ages. Particularly resolving point (iii) is crucial to the success in determining the age of an individual from the molecular composition of their fingermark.

Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation

Our current knowledge on protein deamidation results from a journey that started almost 100 years ago, when a handful of researchers first described the non-enzymatic "desamidation" of glutamine, and the effect of different anions on the catalytic rate of the reaction. Since then, the field has tremendously expended and now finds outreach in very diverse areas. In light of all the recent articles published in these areas, it seemed timely to propose an integrated review on the subject, including a short historical overview of the landmark discoveries in the field, highlighting the current global positioning of protein deamidation in biology and non-biology fields, and concluding with a workflow for those asking if a protein can deamidate, and identify the residues involved. This review is essentially intended to provide newcomers in the field with an overview of how deamidation has penetrated our society and what tools are currently at hand to identify and quantify protein deamidation.

Trends in deamidation across archaeological bones, ceramics and dental calculus

The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.

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.

Improving the visualization of fingermarks using multi-target immunolabeling

The development of fingermarks is an important step in visualizing ridge patterns for individualization purposes. Immunolabeling can be applied to fingermarks to selectively and sensitively detect antigens in fingermarks, and can be used as a developing method to visualize fingermarks. In this study we investigated single (the detection of one antigen) and multiple targeting approaches (the detection of multiple antigens simultaneously) to improve fingermark development. The detection of dermcidin, an antimicrobial peptide, was used as the gold standard to compare single and multi-target detection of keratins, albumin and/or dermcidin. Single detection of dermcidin and albumin mostly resulted in clear ridge details and/or pore detection, whereas the single keratin detection resulted in a poor visualization of the fingermarks. The multi-target approach in which both dermcidin and albumin were targeted, resulted in improved fingermark development compared to single dermcidin detection. Therefore, we recommend the use of multi-target detection consisting of anti-dermcidin and anti-albumin when using immunolabeling as fingermark development technique. Additionally, the optimized multi-target approach was tested as a pre- and post-development technique in combination with powder dusting and cyanoacrylate fuming. Immunolabeling has not been implemented yet in forensic case work, however we expect that immunolabeling can be used to redevelop poorly developed and/or smudged fingermarks in the nearby future. Currently, an ongoing pilot-study is being conducted in collaboration with the Dutch police.

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.

Advances in fingermark age determination techniques

Fingermarks have long been recognized as one of the most reliable and valuable evidence for personal identification. In practice, fingerprint analysis primarily concentrates on latent fingerprint visualization. However, fingerprint visualization techniques do not always enable individualization when fingermarks collected in crime scenes are fragmentary, ambiguous, or deformed. Age determination techniques based on physical and chemical composition changes in fingerprints over time have attracted researchers' attention in recent years. Nevertheless, the components of fingerprints are liable to factors including donor features, deposition conditions, substrate properties, environmental conditions and revealing methods. All the influences mainly contribute to unreliable outcomes of age estimation. Recent developments in fingermark age determination have moved forward to more precise approaches. The advanced methods can be classified into two categories including techniques based on the modifications of physical characteristics and chemical composition characteristics. Herein, the review includes the five types of variables that influence the aging process. The methodologies are subsequently highlighted along with their advantages and disadvantages. Furthermore, photography, optical, microscopy and electrochemical methods, and vibrational spectroscopy and mass spectrometry (MS) techniques are summarized in detail, with an emphasis on their utilization.

Fatty acids as biomimetic replication agents for luminescent metal-organic framework patterns

Luminescent metal-organic frameworks (MOFs) are known to spontaneously self-assemble on human fingerprints. Here, we investigate the different chemical components of fingerprints and determine that MOF growth is predominantly induced by insoluble fatty acids. This finding shows that these simple biomolecules can be employed for the precise positioning of luminescent MOFs.

Fractionation of DNA and protein from individual latent fingerprints for forensic analysis

Human touch samples represent a significant portion of forensic DNA casework. Yet, the generally low abundance of genetic material combined with the predominantly extracellular nature of DNA in these samples makes DNA-based forensic analysis exceptionally challenging. Human proteins present in these same touch samples offer an abundant and environmentally-robust alternative. Proteogenomic methods, using protein sequence variants arising from nonsynonymous DNA mutations, have recently been applied to forensic analysis and may represent a viable option looking forward. However, DNA analysis remains the gold standard and any proteomics-based methods would need to consider how DNA could be co-extracted from samples without significant loss. Herein, we describe a simple workflow for the collection, enrichment and fractionation of DNA and protein in latent fingerprint samples. This approach ensures that DNA collected from a latent fingerprint can be analyzed by traditional DNA casework methods, while protein can be proteolytically digested and analyzed via standard liquid chromatography-tandem mass spectrometry-based proteomics methods from the same touch sample. Sample collection from non-porous surfaces (i.e., glass) is performed through the application of an anionic surfactant over the fingermark. The sample is then split into separate DNA and protein fractions following centrifugation to enrich the protein fraction by pelleting skin cells. The results indicate that this workflow permits analysis of DNA within the sample, yet highlights the challenge posed by the trace nature of DNA in touch samples and the potential for DNA to degrade over time. Protein deposited in touch samples does not appear to share this limitation, with robust protein quantities collected across multiple human donors. The quantity and quality of protein remains robust regardless of fingerprint age. The proteomic content of these samples is consistent across individual donors and fingerprint age, supporting the future application of genetically variable peptide (GVP) analysis of touch samples for forensic identification.

Changes in latent fingermark glyceride composition as a function of sample age using UPLC-IMS-QToF-MSE

The composition of fingermark residue has been an important topic in forensic science, mainly in efforts to better understand and eventually improve the efficacy of latent fingermark detection methods. While the lipid fraction has been extensively studied, there is currently little information about how the glyceride fraction of latent fingermarks is chemically altered over time following deposition. A previously reported untargeted ultra performance liquid chromatography-ion mobility spectrometry-quadrupole time-of-flight mass spectrometry (UPLC-IMS-QToF-MS^E) method was used to investigate changes over time in fingermark di- and triglycerides. Charged latent fingermark samples from 5 donors were analysed up to 28 days following deposition. Significant changes in glyceride composition occurred with increased sample age, attributed primarily to the oxidation of unsaturated triglycerides through ozonolysis. Considerably fewer unsaturated TGs were identified in samples 7 and 28 days following deposition, while mono- and diozonides of these lipids were identified as major components of aged samples. Additional compounds were identified as possible aldehyde and carboxylic acid derivatives resulting from the reaction of water with ozonolysis intermediates. While the onset of these processes occurred rapidly following deposition, continuing oxidation over time was seen via the progressive ozonolysis of diunsaturated triglycerides. These results represent a further step towards understanding the factors affecting fingermark composition, ageing and subsequent detection under operational conditions.

Interpol review of fingermarks and other body impressions 2016-2019

This review paper covers the forensic-relevant literature in fingerprint and bodily impression sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20 Review%20 Papers%202019. pdf.

Developing front-end devices for improved sample preparation in MS-based proteome analysis

Chemical analysis has long relied on instrumentation, from the simplest (eg, burets) to the more sophisticated (eg, mass spectrometers) to facilitate precision measurements. Regardless of their complexity, the development of a new instrumental device can be a valued approach to address problems in science. In this perspective, we outline the process of novel device design, from early phase conception to the manufacturing and testing of the tool or gadget. Focus is placed on the development of improved front-end devices to facilitate protein sample manipulations ahead of mass spectrometry, which therefore augment the proteomics workflow. Highlighted are some of the many training secrets, choices, and challenges that are inherent to the often iterative process of device design. In hopes of inspiring others to pursue instrument design to address relevant research questions, we present a summary list of points to consider prior to innovating their own devices.

Artificial fingerprints for cross-comparison of forensic DNA and protein recovery methods

Quantitative genomic and proteomic evaluation of human latent fingerprint depositions represents a challenge within the forensic field, due to the high variability in the amount of DNA and protein initially deposited. To better assess recovery techniques for touch depositions, we present a method to produce simple and customizable artificial fingerprints. These artificial fingerprint samples include the primary components of a typical latent fingerprint, specifically sebaceous fluid, eccrine perspiration, extracellular DNA, and proteinaceous epidermal skin material (i.e., shed skin cells). A commercially available emulsion of sebaceous and eccrine perspiration material provides a chemically-relevant suspension solution for fingerprint deposition, simplifying artificial fingerprint production. Extracted human genomic DNA is added to accurately mimic the extracellular DNA content of a typical latent print and comparable DNA yields are recovered from the artificial prints relative to human prints across surface types. Capitalizing on recent advancements in the use of protein sequence identification for human forensic analysis, these samples also contain a representative quantity of protein, originating from epidermal skin cells collected from the fingers and palms of volunteers. Proteomic sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis indicates a high level of protein overlap between artificial and latent prints. Data are available via ProteomeXchange with identifier PXD015445. By including known quantities of DNA and protein into each artificial print, this method enables total DNA and protein recovery to be quantitatively assessed across different sample collection and extraction methods to better evaluate extraction efficiency. Collectively, these artificial fingerprint samples are simple to make, highly versatile and customizable, and accurately represent the biochemical composition and biological signatures of human fingerprints.