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Non-invasive screening of breast cancer from fingertip smears-a proof of concept study. Sci Rep 2023; 13:1868. [PMID: 36725900 PMCID: PMC9892587 DOI: 10.1038/s41598-023-29036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/30/2023] [Indexed: 02/03/2023] Open
Abstract
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.
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2
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Baniasad M, Reed AJ, Lai SM, Zhang L, Schulte KQ, Smith AR, LeSassier DS, Weber KL, Hewitt FC, Woerner AE, Gardner MW, Wysocki VH, Freitas MA. Optimization of proteomics sample preparation for forensic analysis of skin samples. J Proteomics 2021; 249:104360. [PMID: 34481086 DOI: 10.1016/j.jprot.2021.104360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/28/2021] [Accepted: 08/22/2021] [Indexed: 01/11/2023]
Abstract
We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples. Human skin cells are a proteinaceous matrix that can enable forensic identification of individuals. We performed a systematic optimization of proteomic sample preparation for a protein-based human forensic identification application. Digestion parameters, including incubation duration, temperature, and the type and concentration of surfactant, were systematically varied to maximize digestion completeness. Through replicate digestions, parameter optimization was performed to maximize repeatability and increase the number of identified peptides and proteins. Final digestion conditions were selected based on the parameters that yielded the greatest percent of peptides with zero missed tryptic cleavages, which benefit the analysis of genetically variable peptides (GVPs). We evaluated the final digestion conditions for identification of GVPs by applying MS-based proteomics on a mixed-donor sample. The results were searched against a human proteome database appended with a database of GVPs constructed from known non-synonymous single nucleotide polymorphisms (SNPs) that occur at known population frequencies. The aim of this study was to demonstrate the potential of our proteomics sample preparation for future implementation of GVP analysis by forensic laboratories to facilitate human identification. SIGNIFICANCE: Genetically variable peptides (GVPs) can provide forensic evidence that is complementary to traditional DNA profiling and be potentially used for human identification. An efficient protein extraction and reproducible digestion method of skin proteins is a key contributor for downstream analysis of GVPs and further development of this technology in forensic application. In this study, we optimized the enzymatic digestion conditions, such as incubation time and temperature, for skin samples. Our study is among the first attempts towards optimization of proteomics sample preparation for protein-based skin identification in forensic applications such as touch samples. Our digestion method employs RapiGest (an acid-labile surfactant), trypsin enzymatic digestion, and an incubation time of 16 h at 37 °C.
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Affiliation(s)
- Maryam Baniasad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Andrew J Reed
- Mass Spectrometry and Proteomics Facility, Campus Chemistry Instrument Center, The Ohio State University, Columbus, OH, USA
| | - Stella M Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Liwen Zhang
- Mass Spectrometry and Proteomics Facility, Campus Chemistry Instrument Center, The Ohio State University, Columbus, OH, USA
| | | | | | | | | | | | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Michael A Freitas
- Mass Spectrometry and Proteomics Facility, Campus Chemistry Instrument Center, The Ohio State University, Columbus, OH, USA; The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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3
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Deriš H, Cindrić A, Lauber M, Petrović T, Bielik A, Taron CH, Wingerden M, Lauc G, Trbojević-Akmačić I. Robustness and repeatability of GlycoWorks RapiFluor-MS IgG N-glycan profiling in a long-term high-throughput glycomic study. Glycobiology 2021; 31:1062-1067. [PMID: 34132802 DOI: 10.1093/glycob/cwab050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/16/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022] Open
Abstract
Protein glycosylation is the attachment of a carbohydrate moiety to a protein backbone affecting both structure and function of the protein. Abnormal glycosylation is associated with various diseases, and some of the changes in glycosylation are detectable even before symptom development. As such, glycans have emerged as compelling new biomarker candidates. A wide range of analytical methods exist for small-scale glycan analyses. However, there is a growing need for highly robust and reproducible high-throughput techniques that allow for large-scale glycoprofiling. Here we describe the evaluation of robustness and repeatability of immunoglobulin G (IgG) N-glycan analysis using the GlycoWorks RapiFluor-MS N-Glycan Kit followed by hydrophilic interaction ultra-high-performance liquid chromatography (HILIC-UHPLC) from 335 technical replicates of human plasma randomly distributed across 67 96-well plates. The data was collected over a five-month period using multiple UHPLC systems and chromatographic columns. Following relative IgG N-glycan quantification in acquired chromatograms, data analysis showed that the most abundant peaks that together made up for three fourths of the detected IgG N-glycome all had coefficients of variation (CVs) lower than 2 percent. The highest CVs ranging from 16 to 29 percent accompanied low abundance glycan peaks with the individual relative peak area below 1 percent that together made up for less than 2 percent of the detected IgG N-glycome. These results show that the tested method is very robust and repeatable, making it suitable for the IgG N-glycan analysis of a large number of samples in a high-throughput manner over a longer period of time.
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Affiliation(s)
- Helena Deriš
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Ana Cindrić
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Matthew Lauber
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Tea Petrović
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia
| | - Alicia Bielik
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938-2723, United States
| | - Christopher H Taron
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938-2723, United States
| | - Marleen Wingerden
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757-3696, United States
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, 10000 Zagreb, Croatia.,University of Zagreb, Faculty of Pharmacy and Biochemistry, 10000 Zagreb, Croatia
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4
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
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.
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5
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Huo Y, Liu K, Lou X. Strong additive and synergistic effects of polyoxyethylene nonionic surfactant-assisted protein MALDI imaging mass spectrometry. Talanta 2020; 222:121524. [PMID: 33167234 DOI: 10.1016/j.talanta.2020.121524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
Protein MALDI imaging mass spectrometry (MALDI-IMS) holds a great promise to acquire spatial distribution information of proteins on biological tissue, but it suffers from the small number of proteins detected by direct MALDI-IMS detection. Ionic surfactants have been extensively used for protein extraction to improve the number of proteins detected in tissue samples by LC-MS analysis, but seldom by direct MALDI-IMS detection. Nonionic surfactants are milder than ionic surfactants and protein native structures are remained after extraction, which favors the spatial resolution of direct MALDI-IMS. However, nonionic surfactants are less effective than ionic surfactants. In this report, we utilized polyoxyethylene nonionic surfactants (PNS) to pre-incubate the tissue section, followed by the on-tissue trypsin digestion and then direct MALDI detection of in-situ formed peptides. For the first time, we observed that the additive effect of PNS and the synergistic effect of the mixed PNS in improving the number of peptides detected. Specifically, the peptides detected were 73.0-90.7% distinct when the different PNS (Tween 80 or Triton X-100 alone or their mixture) was used. Taking advantage of this additive effect, the 96 proteins including 12 transmembrane proteins were detected, corresponding to a ~10-fold improvement compared to MALDI-IMS without surfactant. When the mixed surfactants were used to replace Tween 80 and Triton X-100 alone, the optimized surfactant concentration decreased 20-100-fold and the number of peptides detected with m/z > 2500 Da was improved 15-fold. The additive and synergistic effects of PNS suggested that the interaction mode between each PNS and proteins is highly variable. Benefiting from the strong additive effect and diversity of PNS, further improvement of the number of proteins detected by MALDI-IMS is clearly feasible.
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Affiliation(s)
- Yumeng Huo
- Department of Chemistry, Capital Normal University, Beijing, 100048, China
| | - Kehui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, 100048, China.
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Yeh K, Burr WS, Stock NL, Stotesbury T. Preliminary analysis of latent fingerprints recovered from underneath bloodstains using matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI FT-ICR MSI). Forensic Chem 2020. [DOI: 10.1016/j.forc.2020.100274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Borja T, Karim N, Goecker Z, Salemi M, Phinney B, Naeem M, Rice R, Parker G. Proteomic genotyping of fingermark donors with genetically variant peptides. Forensic Sci Int Genet 2019; 42:21-30. [DOI: 10.1016/j.fsigen.2019.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/09/2019] [Accepted: 05/26/2019] [Indexed: 01/31/2023]
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8
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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9
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Cole LM, Clench MR, Francese S. Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:77-123. [PMID: 31236840 DOI: 10.1007/978-3-030-12298-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science.This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies.In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution.With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies.Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest.
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Affiliation(s)
- L M Cole
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - M R Clench
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - S Francese
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK.
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10
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Oonk S, Schuurmans T, Pabst M, de Smet LCPM, de Puit M. Proteomics as a new tool to study fingermark ageing in forensics. Sci Rep 2018; 8:16425. [PMID: 30401937 PMCID: PMC6219553 DOI: 10.1038/s41598-018-34791-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/26/2018] [Indexed: 01/10/2023] Open
Abstract
Fingermarks are trace evidence of great forensic importance, and their omnipresence makes them pivotal in crime investigation. Police and law enforcement authorities have exploited fingermarks primarily for personal identification, but crucial knowledge on when fingermarks were deposited is often lacking, thereby hindering crime reconstruction. Biomolecular constituents of fingermark residue, such as amino acids, lipids and proteins, may provide excellent means for fingermark age determination, however robust methodologies or detailed knowledge on molecular mechanisms in time are currently not available. Here, we address fingermark age assessment by: (i) drafting a first protein map of fingermark residue, (ii) differential studies of fresh and aged fingermarks and (iii), to mimic real-world scenarios, estimating the effects of donor contact with bodily fluids on the identification of potential age biomarkers. Using a high-resolution mass spectrometry-based proteomics approach, we drafted a characteristic fingermark proteome, of which five proteins were identified as promising candidates for fingermark age estimation. This study additionally demonstrates successful identification of both endogenous and contaminant proteins from donors that have been in contact with various bodily fluids. In summary, we introduce state-of-the-art proteomics as a sensitive tool to monitor fingermark aging on the protein level with sufficient selectivity to differentiate potential age markers from body fluid contaminants.
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Affiliation(s)
- Stijn Oonk
- Netherlands Forensic Institute, Digital Technology and Biometrics, Laan van Ypenburg 6, 2497 GB, Den Haag, Netherlands. .,Delft University of Technology, Faculty of Applied Sciences, Department of Chemical Engineering, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| | - Tom Schuurmans
- Netherlands Forensic Institute, Digital Technology and Biometrics, Laan van Ypenburg 6, 2497 GB, Den Haag, Netherlands
| | - Martin Pabst
- Delft University of Technology, Faculty of Applied Sciences, Department of Biotechnology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Louis C P M de Smet
- Delft University of Technology, Faculty of Applied Sciences, Department of Chemical Engineering, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,Wageningen University & Research, Laboratory of Organic Chemistry, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Marcel de Puit
- Netherlands Forensic Institute, Digital Technology and Biometrics, Laan van Ypenburg 6, 2497 GB, Den Haag, Netherlands. .,Delft University of Technology, Faculty of Applied Sciences, Department of Chemical Engineering, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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11
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Pleik S, Spengler B, Ram Bhandari D, Luhn S, Schäfer T, Urbach D, Kirsch D. Ambient-air ozonolysis of triglycerides in aged fingerprint residues. Analyst 2018; 143:1197-1209. [PMID: 29431747 DOI: 10.1039/c7an01506b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In forensic science, reconstructing the timing of events occurring during a criminal offense is of great importance. In some cases, the time when particular evidence was left on a crime scene is a critical matter. The ability to estimate the fingerprint age would raise the evidentiary value of fingerprints tremendously. For this purpose the most promising approach is the analysis of changes in the chemical compositions of fingerprint residues in the course of aging. The focus of our study is the identification of human specific compounds in fingerprint residues, characterized by a significant aging behavior that could analytically be used for the age determination of fingerprints in future. The first challenge is the sensitive detection of trace amounts of relevant human specific fingerprint compounds. Highly sensitive LC-MS methods were developed for the reliable structure identification of unsaturated triglycerides and their natural degradation products in order to proof the aging mechanism that takes place in fingerprint residues. Thus our results build the fundamental basis for further forensic method development and potential application in forensic investigation. Ozonolysis was found to be one of the major lipid degradation pathways in fingerprint residues in ambient air. High-resolution tandem mass spectrometry (HRMS2) was carried out to identify the ozonolysis products (TG48:0-monoozonide) formed under exposure to the highly reactive ozone in atmospheric air. The obtained products were confirmed by matrix assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Despite several challenges and limitations in the age estimation of fingerprints, the identification of individual degradation products of specific unsaturated lipids in aged fingerprint samples represents a significant analytical progress, resulting in a strong increase in the validity of chemical analysis of fingerprints.
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Affiliation(s)
- Stefanie Pleik
- Forensic Science Institute, Federal Criminal Police Office, 65173 Wiesbaden, Germany.
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12
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Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging in the Study of Gastric Cancer: A Mini Review. Int J Mol Sci 2017; 18:ijms18122588. [PMID: 29194417 PMCID: PMC5751191 DOI: 10.3390/ijms18122588] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide and the disease outcome commonly depends upon the tumour stage at the time of diagnosis. However, this cancer can often be asymptomatic during the early stages and remain undetected until the later stages of tumour development, having a significant impact on patient prognosis. However, our comprehension of the mechanisms underlying the development of gastric malignancies is still lacking. For these reasons, the search for new diagnostic and prognostic markers for gastric cancer is an ongoing pursuit. Modern mass spectrometry imaging (MSI) techniques, in particular matrix-assisted laser desorption/ionisation (MALDI), have emerged as a plausible tool in clinical pathology as a whole. More specifically, MALDI-MSI is being increasingly employed in the study of gastric cancer and has already elucidated some important disease checkpoints that may help us to better understand the molecular mechanisms underpinning this aggressive cancer. Here we report the state of the art of MALDI-MSI approaches, ranging from sample preparation to statistical analysis, and provide a complete review of the key findings that have been reported in the literature thus far.
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13
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Zhou R, Basile F. Plasmonic Thermal Decomposition/Digestion of Proteins: A Rapid On-Surface Protein Digestion Technique for Mass Spectrometry Imaging. Anal Chem 2017; 89:8704-8712. [PMID: 28727443 DOI: 10.1021/acs.analchem.7b00430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method based on plasmon surface resonance absorption and heating was developed to perform a rapid on-surface protein thermal decomposition and digestion suitable for imaging mass spectrometry (MS) and/or profiling. This photothermal process or plasmonic thermal decomposition/digestion (plasmonic-TDD) method incorporates a continuous wave (CW) laser excitation and gold nanoparticles (Au-NPs) to induce known thermal decomposition reactions that cleave peptides and proteins specifically at the C-terminus of aspartic acid and at the N-terminus of cysteine. These thermal decomposition reactions are induced by heating a solid protein sample to temperatures between 200 and 270 °C for a short period of time (10-50 s per 200 μm segment) and are reagentless and solventless, and thus are devoid of sample product delocalization. In the plasmonic-TDD setup the sample is coated with Au-NPs and irradiated with 532 nm laser radiation to induce thermoplasmonic heating and bring about site-specific thermal decomposition on solid peptide/protein samples. In this manner the Au-NPs act as nanoheaters that result in a highly localized thermal decomposition and digestion of the protein sample that is independent of the absorption properties of the protein, making the method universally applicable to all types of proteinaceous samples (e.g., tissues or protein arrays). Several experimental variables were optimized to maximize product yield, and they include heating time, laser intensity, size of Au-NPs, and surface coverage of Au-NPs. Using optimized parameters, proof-of-principle experiments confirmed the ability of the plasmonic-TDD method to induce both C-cleavage and D-cleavage on several peptide standards and the protein lysozyme by detecting their thermal decomposition products with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The high spatial specificity of the plasmonic-TDD method was demonstrated by using a mask to digest designated sections of the sample surface with the heating laser and MALDI-MS imaging to map the resulting products. The solventless nature of the plasmonic-TDD method enabled the nonenzymatic on-surface digestion of proteins to proceed with undetectable delocalization of the resulting products from their precursor protein location. The advantages of this novel plasmonic-TDD method include short reaction times (<30 s/200 μm), compatibility with MALDI, universal sample compatibility, high spatial specificity, and localization of the digestion products. These advantages point to potential applications of this method for on-tissue protein digestion and MS-imaging/profiling for the identification of proteins, high-fidelity MS imaging of high molecular weight (>30 kDa) proteins, and the rapid analysis of formalin-fixed paraffin-embedded (FFPE) tissue samples.
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Affiliation(s)
- Rong Zhou
- Department of Chemistry, University of Wyoming , 1000 University Avenue, Laramie, Wyoming 82071, United States
| | - Franco Basile
- Department of Chemistry, University of Wyoming , 1000 University Avenue, Laramie, Wyoming 82071, United States
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14
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Peptide Imaging: Maximizing Peptide Yield, Optimization of the "Peptide Mass Fingerprint". Methods Mol Biol 2017. [PMID: 28523501 DOI: 10.1007/978-1-4939-7051-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In Matrix Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI), identification of observed proteins remains a challenge primarily due to the drop in sensitivity of time-of-flight (TOF) mass spectrometers beyond the mass range of 25-35 kDa (Francese et al. High Throughput Screen 12: 156-174, 2009) and inadequate mass resolving power at those molecular weights. To counteract this, a bottom-up proteomic approach is often employed. Proteolysis digests proteins into smaller peptide fragments, typically between 500 and 3000 Da which are easier to detect with a higher mass accuracy. Here, we describe the addition of a MS-compatible detergent to the endopeptidase trypsin, to enhance in situ proteolysis efficiency and peptide intensity.
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15
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A mass spectrometry-based forensic toolbox for imaging and detecting biological fluid evidence in finger marks and fingernail scrapings. Int J Legal Med 2017; 131:1413-1422. [DOI: 10.1007/s00414-017-1587-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/03/2017] [Indexed: 11/26/2022]
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16
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Systematic assessment of surfactants for matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Chim Acta 2017; 963:76-82. [DOI: 10.1016/j.aca.2017.01.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 11/18/2022]
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17
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Francese S, Bradshaw R, Denison N. An update on MALDI mass spectrometry based technology for the analysis of fingermarks – stepping into operational deployment. Analyst 2017. [DOI: 10.1039/c7an00569e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Expanded range of retrievable intelligence from fingermarksviaMALDI MS based methods and increased operational capabilities of the technology.
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Affiliation(s)
- S. Francese
- Centre for Mass Spectrometry Imaging
- Biomolecular Research Centre
- Sheffield Hallam University
- Sheffield
- UK
| | - R. Bradshaw
- Centre for Mass Spectrometry Imaging
- Biomolecular Research Centre
- Sheffield Hallam University
- Sheffield
- UK
| | - N. Denison
- Identification Services Yorkshire and the Humber Region
- Wakefield
- UK WF27UA
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18
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Deininger L, Patel E, Clench MR, Sears V, Sammon C, Francese S. Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks. Proteomics 2016; 16:1707-17. [DOI: 10.1002/pmic.201500544] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Lisa Deininger
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
| | - Ekta Patel
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
| | - Malcolm R. Clench
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
| | - Vaughn Sears
- Centre for Applied Science and Technology; Home Office; St Albans UK
| | - Chris Sammon
- Materials and Engineering Research Institute; Sheffield Hallam University; Sheffield UK
| | - Simona Francese
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
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