1
|
Lertruangpanya K, Roytrakul S, Surarit R, Horsophonphong S. Comparative proteomic analysis of dental pulp from supernumerary and normal permanent teeth. Clin Oral Investig 2024; 28:321. [PMID: 38758416 PMCID: PMC11101566 DOI: 10.1007/s00784-024-05698-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVES To obtain and compare the protein profiles of supernumerary and normal permanent dental pulp tissues. MATERIALS AND METHODS Dental pulp tissues were obtained from supernumerary and normal permanent teeth. Proteins were extracted and analyzed by liquid chromatography-tandem mass spectrometry (LC/MS-MS). Protein identification and quantification from MS data was performed with MaxQuant. Statistical analysis was conducted using Metaboanalyst to identify differentially expressed proteins (DEPs) (P-value < 0.05, fold-change > 2). Gene Ontology enrichment analyses were performed with gProfiler. RESULTS A total of 3,534 proteins were found in normal dental pulp tissue and 1,093 in supernumerary dental pulp tissue, with 174 DEPs between the two groups. This analysis revealed similar functional characteristics in terms of cellular component organization, cell differentiation, developmental process, and response to stimulus, alongside exclusive functions unique to normal permanent dental pulp tissues such as healing, vascular development and cell death. Upon examination of DEPs, these proteins were associated with the processes of wound healing and apoptosis. CONCLUSIONS This study provides a comprehensive understanding of the protein profile of dental pulp tissue, including the first such profiling of supernumerary permanent dental pulp. There are functional differences between the proteomic profiles of supernumerary and normal permanent dental pulp tissue, despite certain biological similarities between the two groups. Differences in protein expression were identified, and the identified DEPs were linked to the healing and apoptosis processes. CLINICAL RELEVANCE This discovery enhances our knowledge of supernumerary and normal permanent pulp tissue, and serves as a valuable reference for future studies on supernumerary teeth.
Collapse
Affiliation(s)
- Kritkamon Lertruangpanya
- Department of Pediatric Dentistry, Faculty of Dentistry, Mahidol University, 6 Yothi Road, Ratchathewi, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Rudee Surarit
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
- Faculty of Dentistry, Siam University, Bangkok, Thailand
| | - Sivaporn Horsophonphong
- Department of Pediatric Dentistry, Faculty of Dentistry, Mahidol University, 6 Yothi Road, Ratchathewi, Bangkok, Thailand.
| |
Collapse
|
2
|
Lange PF, Schilling O, Huesgen PF. Positional proteomics: is the technology ready to study clinical cohorts? Expert Rev Proteomics 2023; 20:309-318. [PMID: 37869791 DOI: 10.1080/14789450.2023.2272046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/22/2023] [Indexed: 10/24/2023]
Abstract
INTRODUCTION Positional proteomics provides proteome-wide information on protein termini and their modifications, uniquely enabling unambiguous identification of site-specific, limited proteolysis. Such proteolytic cleavage irreversibly modifies protein sequences resulting in new proteoforms with distinct protease-generated neo-N and C-termini and altered localization and activity. Misregulated proteolysis is implicated in a wide variety of human diseases. Protein termini, therefore, constitute a huge, largely unexplored source of specific analytes that provides a deep view into the functional proteome and a treasure trove for biomarkers. AREAS COVERED We briefly review principal approaches to define protein termini and discuss recent advances in method development. We further highlight the potential of positional proteomics to identify and trace specific proteoforms, with a focus on proteolytic processes altered in disease. Lastly, we discuss current challenges and potential for applying positional proteomics in biomarker and pre-clinical research. EXPERT OPINION Recent developments in positional proteomics have provided significant advances in sensitivity and throughput. In-depth analysis of proteolytic processes in clinical cohorts thus appears feasible in the near future. We argue that this will provide insights into the functional state of the proteome and offer new opportunities to utilize proteolytic processes altered or targeted in disease as specific diagnostic, prognostic and companion biomarkers.
Collapse
Affiliation(s)
- Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
- Institute of Biochemistry, Department for Chemistry, University of Cologne, Cologne, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| |
Collapse
|
3
|
Haack AM, Overall CM, Auf dem Keller U. Degradomics technologies in matrisome exploration. Matrix Biol 2022; 114:1-17. [PMID: 36280126 DOI: 10.1016/j.matbio.2022.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Consisting of a defined set of extracellular proteins secreted from resident cells and with minor contributions from serum proteins, the extracellular matrix (ECM) is an essential component of all tissues. Maintaining tissue homeostasis, structural support and cellular control through cell-ECM communication, the ECM has come to be viewed as not just a passive structural entity but rather as a dynamic signaling conduit between cells and the extracellular compartment. Proteins and their cleavage products mediate this communication, and aberrant signaling, either directly or indirectly distorting the ECM, results in pathological conditions including cancer, inflammation, fibrosis, and neurodegenerative diseases. Characterization of ECM components, the matrisome, the extracellular environment and their changes in disease is therefore of importance to understand and mitigate by developing novel therapeutics. Liquid chromatography-mass spectrometry (LC-MS) proteomics has been integral to protein and proteome research for decades and long superseded the obsolescent gel-based approaches. A continuous effort has ensured progress with increased sensitivity and throughput as more advanced equipment has been developed hand in hand with specialized enrichment, detection, and identification methods. Part of this effort lies in the field of degradomics, a branch of proteomics focused on discovering novel protease substrates by identification of protease-generated neo-N termini, the N-terminome, and characterizing the responsible protease networks. Various methods to do so have been developed, some specialized for specific tissue types, others for particular proteases, throughput, or ease of use. This review aims to provide an overview of the state-of-the-art proteomics techniques that have successfully been recently utilized to characterize proteolytic cleavages in the ECM and thereby guided new research and understanding of the ECM and matrisome biology.
Collapse
Affiliation(s)
- Aleksander M Haack
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, DK-2800 Kongens Lyngby, Denmark.
| |
Collapse
|
4
|
Richert R, Ducret M, Alliot-Licht B, Bekhouche M, Gobert S, Farges JC. A critical analysis of research methods and experimental models to study pulpitis. Int Endod J 2022; 55 Suppl 1:14-36. [PMID: 35034368 DOI: 10.1111/iej.13683] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
Pulpitis is the inflammatory response of the dental pulp to a tooth insult, whether it is microbial, chemical, or physical in origin. It is traditionally referred to as reversible or irreversible, a classification for therapeutic purposes that determines the capability of the pulp to heal. Recently, new knowledge about dental pulp physiopathology led to orientate therapeutics towards more frequent preservation of pulp vitality. However, full adoption of these vital pulp therapies by dental practitioners will be achieved only following better understanding of cell and tissue mechanisms involved in pulpitis. The current narrative review aimed to discuss the contribution of the most significant experimental models developed to study pulpitis. Traditionally, in vitro two(2D)- or three(3D)-dimensional cell cultures or in vivo animal models were used to analyse the pulp response to pulpitis inducers at cell, tissue or organ level. In vitro 2D cell cultures were mainly used to decipher the specific roles of key actors of pulp inflammation such as bacterial by-products, pro-inflammatory cytokines, odontoblasts or pulp stem cells. However, these simple models did not reproduce the 3D organisation of the pulp tissue and, with rare exceptions, did not consider interactions between resident cell types. In vitro tissue/organ-based models were developed to better reflect the complexity of the pulp structure. Their major disadvantage is that they did not allow the analysis of blood supply and innervation participation. On the contrary, in vivo models have allowed researchers to identify key immune, vascular and nervous actors of pulpitis and to understand their function and interplay in the inflamed pulp. However, inflammation was mainly induced by iatrogenic dentine drilling associated with simple pulp exposure to the oral environment or stimulation by individual bacterial by-products for short periods. Clearly, these models did not reflect the long and progressive development of dental caries. Lastly, the substantial diversity of the existing models makes experimental data extrapolation to the clinical situation complicated. Therefore, improvement in the design and standardization of future models, for example by using novel molecular biomarkers, databased models and artificial intelligence, will be an essential step in building an incremental knowledge of pulpitis in the future.
Collapse
Affiliation(s)
- Raphaël Richert
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Mécanique des Contacts et Structures, UMR 5259, Villeurbanne, France
| | - Maxime Ducret
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Brigitte Alliot-Licht
- Université de Nantes, Faculté d'Odontologie, Nantes, France.,CHU de Nantes, Odontologie Conservatrice et Pédiatrique, Service d, Nantes, France
| | - Mourad Bekhouche
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Stéphanie Gobert
- Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Jean-Christophe Farges
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| |
Collapse
|
5
|
Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes. Genomics 2021; 114:292-304. [PMID: 34915127 DOI: 10.1016/j.ygeno.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022]
Abstract
Mycobacterium tuberculosis (MTB) is a severe causing agent of tuberculosis (TB). Although H37Rv, the type strain of M. tuberculosis was sequenced in 1998, annotation errors of encoding genes have been frequently reported in hundreds of papers. This phenomenon is particularly severe at the 5' end of the genes. Here, we applied a TMPP [(N-Succinimidyloxycarbonylmethyl) tris (2,4,6-trimethoxyphenyl) phosphonium bromide] labeling combined with StageTip separating strategy on M. tuberculosis H37Rv to characterize the N-terminal start sites of its annotated encoding genes. Totally, 1047 proteins were identified with 2058 TMPP labeled N-terminal peptides from all the 2625 mass spectrometer (MS) sequenced proteins. Comparative genomics analysis allowed the re-annotation of 43 proteins' N-termini in H37Rv and 762 proteins in Mycobacteriaceae. All revised N-termini start sites were distributed in 5'-UTR of annotated genes due to over-annotation of previous N-terminal initiation codon, especially the ATG. In addition, we identified and verified a novel gene Rv1078A in +3 frame different from the annotated gene Rv1078 in +2 frame. Altogether, our findings contribute to the better understanding of N-terminal of H37Rv and other species from Mycobacteriaceae that can assist future studies on biological study.
Collapse
|
6
|
Koudelka T, Winkels K, Kaleja P, Tholey A. Shedding light on both ends: An update on analytical approaches for N- and C-terminomics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119137. [PMID: 34626679 DOI: 10.1016/j.bbamcr.2021.119137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 02/04/2023]
Abstract
Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
Collapse
Affiliation(s)
- Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| |
Collapse
|
7
|
Hynek R, Michalus I, Cejnar P, Šantrůček J, Seidlová S, Kučková Š, Sázelová P, Kašička V. In-bone protein digestion followed by LC-MS/MS peptide analysis as a new way towards the routine proteomic characterization of human maxillary and mandibular bone tissue in oral surgery. Electrophoresis 2021; 42:2552-2562. [PMID: 34453862 DOI: 10.1002/elps.202100211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/12/2021] [Accepted: 08/26/2021] [Indexed: 11/11/2022]
Abstract
Proteomic characterization of alveolar bones in oral surgery represents an analytical challenge due to their insoluble character. The implementation of a straightforward technique could lead to the routine use of proteomics in this field. This work thus developed a simple technique for the characterization of bone tissue for human maxillary and mandibular bones. It is based on the direct in-bone tryptic digestion of proteins in both healthy and pathological human maxillary and mandibular bone samples. The released peptides were then identified by the LC-MS/MS. Using this approach, a total of 1120 proteins were identified in the maxillary bone and 1151 proteins in the mandibular bone. The subsequent partial least squares-discrimination analysis (PLS-DA) of protein data made it possible to reach 100% discrimination between the samples of healthy alveolar bones and those of the bone tissue surrounding the inflammatory focus. These results indicate that the in-bone protein digestion followed by the LC-MS/MS and subsequent statistical analysis can provide a deeper insight into the field of oral surgery at the molecular level. Furthermore, it could also have a diagnostic potential in the differentiation between the proteomic patterns of healthy and pathological alveolar bone tissue. Data are available via ProteomeXchange with the identifier PXD026775.
Collapse
Affiliation(s)
- Radovan Hynek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Iva Michalus
- First Faculty of Medicine, Charles University, Kateřinská 32, Prague 2, 121 08, Czech Republic
| | - Pavel Cejnar
- Department of Computing and Control Engineering, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Jiří Šantrůček
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Sabina Seidlová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Štěpánka Kučková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic
| | - Petra Sázelová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo 542/2, Prague 6, 166 10, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo 542/2, Prague 6, 166 10, Czech Republic
| |
Collapse
|
8
|
Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
Collapse
Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
| |
Collapse
|
9
|
Proteomic analysis of human dental pulp in different clinical diagnosis. Clin Oral Investig 2020; 25:3285-3295. [PMID: 33159586 DOI: 10.1007/s00784-020-03660-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/27/2020] [Indexed: 01/20/2023]
Abstract
OBJECTIVES The present study aimed to identify proteins obtained from pulp tissue and correlate with each clinical diagnosis (healthy pulp, inflamed pulp, and necrotic pulp). MATERIALS AND METHODS A total of forty-five molars were used. Three biological replicas were evaluated. Lysis and sonication were used for protein extraction. Protein quantification was assessed by using the Bradford technique, and shotgun proteome analysis was performed by nanoUPLC-MSE using a Synapt G2 mass spectrometer. Mass spectra data were processed using the Waters PLGS software, and protein identification was done using the human Uniprot database appended to the PLGS search engine. RESULTS A total of 123 different proteins were identified in all evaluated pulp conditions. Among these, 66 proteins were observed for healthy pulp, 66 for inflamed pulp, and 91 for necrotic pulp. Most protein identification was related to immune response, multi-organism process, platelet activation, and stress in inflamed pulp samples compared to healthy pulp. Proteins related to cellular component organization or biogenesis, developmental process, growth, immune response, multi-organism process, response to stimulus, signaling, stress, and transport were identified in cases of apical periodontitis compared to inflamed pulp. CONCLUSIONS The progression of the disease to inflamed pulp promoted a high abundance of proteins related to the immune system and stress. Comparing the necrotic pulp with inflamed pulp conditions, a high abundance of proteins was noticed related to metabolism, transport, and response between organisms. CLINICAL RELEVANCE This finding may assist in future studies of new markers, understanding of tissue engineering, and development of future products.
Collapse
|
10
|
Ju S, Kwon Y, Kim JM, Park D, Lee S, Lee JW, Hwang CS, Lee C. iNrich, Rapid and Robust Method to Enrich N-Terminal Proteome in a Highly Multiplexed Platform. Anal Chem 2020; 92:6462-6469. [DOI: 10.1021/acs.analchem.9b05653] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Yumi Kwon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jeong-Mok Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Daechan Park
- Department of Biological Sciences, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Seonjeong Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
- Department of Converging Science and Technology, KHU-KIST, Kyung Hee University, Seoul 02447, Republic of Korea
| |
Collapse
|
11
|
Jobin PG, Solis N, Machado Y, Bell PA, Rai SK, Kwon NH, Kim S, Overall CM, Butler GS. Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage. J Biol Chem 2019; 295:2186-2202. [PMID: 31771979 PMCID: PMC7039567 DOI: 10.1074/jbc.ra119.010486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/03/2019] [Indexed: 12/19/2022] Open
Abstract
Tyrosyl-tRNA synthetase ligates tyrosine to its cognate tRNA in the cytoplasm, but it can also be secreted through a noncanonical pathway. We found that extracellular tyrosyl-tRNA synthetase (YRS) exhibited proinflammatory activities. In addition to acting as a monocyte/macrophage chemoattractant, YRS initiated signaling through Toll-like receptor 2 (TLR2) resulting in NF-κB activation and release of tumor necrosis factor α (TNFα) and multiple chemokines, including MIP-1α/β, CXCL8 (IL8), and CXCL1 (KC) from THP1 monocyte and peripheral blood mononuclear cell–derived macrophages. Furthermore, YRS up-regulated matrix metalloproteinase (MMP) activity in a TNFα-dependent manner in M0 macrophages. Because MMPs process a variety of intracellular proteins that also exhibit extracellular moonlighting functions, we profiled 10 MMPs for YRS cleavage and identified 55 cleavage sites by amino-terminal oriented mass spectrometry of substrates (ATOMS) positional proteomics and Edman degradation. Stable proteoforms resulted from cleavages near the start of the YRS C-terminal EMAPII domain. All of the MMPs tested cleaved at ADS386↓387LYV and VSG405↓406LVQ, generating 43- and 45-kDa fragments. The highest catalytic efficiency for YRS was demonstrated by MMP7, which is highly expressed by monocytes and macrophages, and by neutrophil-specific MMP8. MMP-cleaved YRS enhanced TLR2 signaling, increased TNFα secretion from macrophages, and amplified monocyte/macrophage chemotaxis compared with unprocessed YRS. The cleavage of YRS by MMP8, but not MMP7, was inhibited by tyrosine, a substrate of the YRS aminoacylation reaction. Overall, the proinflammatory activity of YRS is enhanced by MMP cleavage, which we suggest forms a feed-forward mechanism to promote inflammation.
Collapse
Affiliation(s)
- Parker G Jobin
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nestor Solis
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Yoan Machado
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Peter A Bell
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Simran K Rai
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V5T 4S6, Canada
| | - Nam Hoon Kwon
- College of Pharmacy, Seoul National University, 151-742, Seoul, Republic of Korea; Medicinal Bioconvergence Research Center, Seoul National University, 151-742, Seoul, Republic of Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, 151-742, Seoul, Republic of Korea; Medicinal Bioconvergence Research Center, Seoul National University, 151-742, Seoul, Republic of Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
| | - Georgina S Butler
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
12
|
Weng SSH, Demir F, Ergin EK, Dirnberger S, Uzozie A, Tuscher D, Nierves L, Tsui J, Huesgen PF, Lange PF. Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples. Mol Cell Proteomics 2019; 18:2335-2347. [PMID: 31471496 PMCID: PMC6823850 DOI: 10.1074/mcp.tir119.001560] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Protein N termini unambiguously identify truncated, alternatively translated or modified proteoforms with distinct functions and reveal perturbations in disease. Selective enrichment of N-terminal peptides is necessary to achieve proteome-wide coverage for unbiased identification of site-specific regulatory proteolytic processing and protease substrates. However, many proteolytic processes are strictly confined in time and space and therefore can only be analyzed in minute samples that provide insufficient starting material for current enrichment protocols. Here we present High-efficiency Undecanal-based N Termini EnRichment (HUNTER), a robust, sensitive and scalable method for the analysis of previously inaccessible microscale samples. HUNTER achieved identification of >1000 N termini from as little as 2 μg raw HeLa cell lysate. Broad applicability is demonstrated by the first N-terminome analysis of sorted human primary immune cells and enriched mitochondrial fractions from pediatric cancer patients, as well as protease substrate identification from individual Arabidopsis thaliana wild type and Vacuolar Processing Enzyme-deficient mutant seedlings. We further implemented the workflow on a liquid handling system and demonstrate the feasibility of clinical degradomics by automated processing of liquid biopsies from pediatric cancer patients.
Collapse
Affiliation(s)
- Samuel S H Weng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Enes K Ergin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Sabrina Dirnberger
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Anuli Uzozie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Domenic Tuscher
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Lorenz Nierves
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Janice Tsui
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Philipp F Lange
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital, Vancouver, Canada.
| |
Collapse
|
13
|
Bell PA, Solis N, Kizhakkedathu JN, Matthew I, Overall CM. Proteomic and N-Terminomic TAILS Analyses of Human Alveolar Bone Proteins: Improved Protein Extraction Methodology and LysargiNase Digestion Strategies Increase Proteome Coverage and Missing Protein Identification. J Proteome Res 2019; 18:4167-4179. [DOI: 10.1021/acs.jproteome.9b00445] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
14
|
Zelanis A, Oliveira AK, Prudova A, Huesgen PF, Tashima AK, Kizhakkedathu J, Overall CM, Serrano SMT. Deep Profiling of the Cleavage Specificity and Human Substrates of Snake Venom Metalloprotease HF3 by Proteomic Identification of Cleavage Site Specificity (PICS) Using Proteome Derived Peptide Libraries and Terminal Amine Isotopic Labeling of Substrates (TAILS) N-Terminomics. J Proteome Res 2019; 18:3419-3428. [PMID: 31337208 DOI: 10.1021/acs.jproteome.9b00325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Snakebite is a major medical concern in many parts of the world with metalloproteases playing important roles in the pathological effects of Viperidae venoms, including local tissue damage, hemorrhage, and coagulopathy. Hemorrhagic Factor 3 (HF3), a metalloprotease from Bothrops jararaca venom, induces local hemorrhage and targets extracellular matrix (ECM) components, including collagens and proteoglycans, and plasma proteins. However, the full substrate repertoire of this metalloprotease is unknown. We report positional proteomic studies identifying >2000 N-termini, including neo-N-termini of HF3 cleavage sites in mouse embryonic fibroblast secretome proteins. Terminal amine isotopic labeling of substrates (TAILS) analysis identified a preference for Leu at the P1' position among candidate HF3 substrates including proteins of the ECM and focal adhesions and the cysteine protease inhibitor cystatin-C. Interestingly, 190 unique peptides matched to annotated cleavage sites in the TopFIND N-termini database, suggesting that these cleavages occurred at a site prone to cleavage or might have been generated by other proteases activated upon incubation with HF3, including caspases-3 and -7, cathepsins D and E, granzyme B, and MMPs 2 and 9. Using Proteomic identification of cleavage site specificity (PICS), a tryptic library derived from THP-1 monocytic cells was used as HF3 substrates for identifying protease cleavage sites and sequence preferences in peptides. A total of 799 unique cleavage sites were detected and, in accordance with TAILS analysis using native secreted protein substrates of MEF cells, revealed a clear preference for Leu at P1'. Taken together, these results greatly expand the known substrate degradome of HF3 and reveal potential new targets, which may serve as a basis to better elucidate the complex pathophysiology of snake envenomation.
Collapse
Affiliation(s)
- André Zelanis
- Department of Science and Technology , Federal University of São Paulo (ICT-UNIFESP) , São José dos Campos , SP 12231-280 , Brazil.,Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| | - Ana K Oliveira
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| | - Anna Prudova
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada
| | - Pitter F Huesgen
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , Juelich 52425 , Germany
| | - Alexandre K Tashima
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| | - Jayachandran Kizhakkedathu
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada
| | - Christopher M Overall
- Centre for Blood Research , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada.,Department of Oral Biological and Medical Sciences, Faculty of Dentistry , University of British Columbia , Vancouver , BC V6T 1Z3 , Canada
| | - Solange M T Serrano
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS) , Instituto Butantan , São Paulo , SP 05503-000 , Brazil
| |
Collapse
|
15
|
Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev Proteomics 2019; 15:515-535. [PMID: 29893147 DOI: 10.1080/14789450.2018.1483340] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.
Collapse
Affiliation(s)
- Ruzanna Mnatsakanyan
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Gerta Shema
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Mark Basik
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Gerald Batist
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Christoph H Borchers
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,c University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria , Victoria , British Columbia V8Z 7X8 , Canada.,d Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , V8P 5C2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Albert Sickmann
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,f Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum , Germany.,g Department of Chemistry , College of Physical Sciences, University of Aberdeen , Aberdeen AB24 3FX , Scotland , United Kingdom
| | - René P Zahedi
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| |
Collapse
|
16
|
Liberato T, Fukushima I, Kitano ES, Serrano SM, Chammas R, Zelanis A. Proteomic profiling of the proteolytic events in the secretome of the transformed phenotype of melanocyte-derived cells using Terminal Amine Isotopic Labeling of Substrates. J Proteomics 2019; 192:291-298. [DOI: 10.1016/j.jprot.2018.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 12/27/2022]
|
17
|
Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
Collapse
Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| |
Collapse
|
18
|
Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J Proteome Res 2018; 17:4031-4041. [PMID: 30099871 PMCID: PMC6387656 DOI: 10.1021/acs.jproteome.8b00441] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.
Collapse
Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC Canada V6T 1Z3
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Room 425, Building #114, Yonsei University,50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Siqi Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, United States
| | - Michael Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive, 3165 Porter Drive, Palo Alto, 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Macquarie University, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| |
Collapse
|
19
|
Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
Collapse
Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| |
Collapse
|
20
|
Huang J, Wang J, Li Q, Zhang Y, Zhang X. Enzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun Approach. J Proteome Res 2017; 17:212-221. [DOI: 10.1021/acs.jproteome.7b00521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jingnan Huang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Wang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingqing Li
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| |
Collapse
|
21
|
Paik YK, Omenn GS, Hancock WS, Lane L, Overall CM. Advances in the Chromosome-Centric Human Proteome Project: looking to the future. Expert Rev Proteomics 2017; 14:1059-1071. [PMID: 29039980 DOI: 10.1080/14789450.2017.1394189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on 'missing proteins (MPs)', which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs. Areas covered: We will cover the scope, historic background, progress, challenges and future prospects of C-HPP. This review also addresses the question of how we can best improve the methodological approaches, select the optimal biological samples, and recommend stringent protocols for the identification and characterization of MPs. A new strategy for functional analysis of some of those annotated proteins having unknown function will also be discussed. Expert commentary: If the project moves well by reshaping the original goals, the current working modules and team work in the proposed extended planning period, it is anticipated that a progressively more detailed draft of an accurate chromosome-based proteome map will become available with functional information.
Collapse
Affiliation(s)
- Young-Ki Paik
- a Yonsei Proteome Research Center and Department of Biochemistry , Yonsei University , Seoul , Korea
| | - Gilbert S Omenn
- b Department of Computational Medicine & Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - William S Hancock
- c Department of Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , USA
| | - Lydie Lane
- d Department of Human Protein Sciences, Faculty of Medicine , University of Geneva , Geneva , Switzerland.,e Swiss Institute of Bioinformatics , Geneva , Switzerland
| | - Christopher M Overall
- f Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , University of British Columbia , Vancouver , Canada
| |
Collapse
|
22
|
Abbey SR, Eckhard U, Solis N, Marino G, Matthew I, Overall CM. The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes. J Dent Res 2017; 97:338-346. [PMID: 29035686 DOI: 10.1177/0022034517736054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The proteome and N-terminome of the human odontoblast cell layer were identified for the first time by shotgun proteomic and terminal amine isotopic labeling of substrates (TAILS) N-terminomic analyses, respectively, and compared with that of human dental pulp stroma from 26 third molar teeth. After reverse-phase liquid chromatography-tandem mass spectrometry, >170,000 spectra from the shotgun and TAILS analyses were matched by 4 search engines to 4,888 and 12,063 peptides in the odontoblast cell layer and pulp stroma, respectively. Within these peptide groups, 1,543 and 5,841 protein N-termini, as well as 895 and 2,423 unique proteins, were identified with a false discovery rate of ≤1%. Thus, the human dental pulp proteome was expanded by 974 proteins not previously identified among the 4,123 proteins in our 2015 dental pulp study. Further, 222 proteins of the odontoblast cell layer were not found in the pulp stroma, suggesting many of these proteins are synthesized only by odontoblasts. When comparing the proteomes of older and younger donors, differences were more apparent in the odontoblast cell layer than in the dental pulp stroma. In the odontoblast cell layer proteome, we found proteomic evidence for dentin sialophosphoprotein, which is cleaved into dentin sialoprotein and dentin phosphoprotein. By exploring the proteome of the odontoblast cell layer and expanding the known dental pulp proteome, we found distinct proteome differences compared with each other and with dentin. Moreover, between 61% and 66% of proteins also occurred as proteoforms commencing with a neo-N-terminus not annotated in UniProt. Hence, TAILS increased proteome coverage and revealed considerable proteolytic processing, by identifying stable proteoforms in these dynamic dental tissues. All mass spectrometry raw data have been deposited to ProteomeXchange with the identifier <PXD006557>, with the accompanying metadata at Mendeley Data ( https://data.mendeley.com/datasets/b57zfh6wmy/1 ).
Collapse
Affiliation(s)
- S R Abbey
- 1 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - U Eckhard
- 1 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada.,2 Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - N Solis
- 1 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada.,2 Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - G Marino
- 1 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada.,2 Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada
| | - I Matthew
- 1 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - C M Overall
- 1 Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada.,2 Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.,3 Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
23
|
Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P. Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. J Proteome Res 2017; 16:4352-4363. [PMID: 28959888 DOI: 10.1021/acs.jproteome.7b00340] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide diversity and sequence coverage compared with Trypsin. Therefore, a multiprotease strategy was used for searching more MPs in the same human testis tissues separated by 10% SDS-PAGE, followed by high resolution LC-MS/MS system (Q Exactive HF). A total of 7838 proteins were identified. Among them, three PE2 MPs in neXtProt 2017-01 have been identified: beta-defensin 123 ( Q8N688 , chr 20q), cancer/testis antigen family 45 member A10 ( P0DMU9 , chr Xq), and Histone H2A-Bbd type 2/3 ( P0C5Z0 , chr Xq). However, because only one unique peptide of ≥9 AA was identified in beta-defensin 123 and Histone H2A-Bbd type 2/3, respectively, further analysis indicates that each falls under the exceptions clause of the HPP Guidelines v2.1. After a spectrum quality check, isobaric PTM and single amino acid variant (SAAV) filtering, and verification with a synthesized peptide, and based on overlapping peptides from different proteases, these three MPs should be considered as exemplary examples of MPs found by exceptional criteria. Other MPs were considered as candidates but need further validation. All MS data sets have been deposited to the ProteomeXchange with identifier PXD006465.
Collapse
Affiliation(s)
- Yihao Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Yang Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University , Guangzhou 510275, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yue Gao
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University , Wuhan 430072, China.,Graduate School, Anhui Medical University , Hefei 230032, China.,Tianjin Baodi Hospital , Tianjin 301800, China
| |
Collapse
|
24
|
Salmon CR, Giorgetti APO, Paes Leme AF, Domingues RR, Kolli TN, Foster BL, Nociti FH. Microproteome of dentoalveolar tissues. Bone 2017; 101:219-229. [PMID: 28527949 DOI: 10.1016/j.bone.2017.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/12/2017] [Accepted: 05/15/2017] [Indexed: 01/18/2023]
Abstract
Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues. Using the LCM-LC-MS/MS approach, a total of 243 proteins was identified from all tissues, 193 proteins in DC, 147 in AB, and 135 proteins DE. Ninety proteins (37% of total) were common to all tissues, whereas 52 proteins (21%) were overlapping in only two. Also, 101 (42%) proteins were exclusively detected in DC (60), AB (15), or DE (26). Identification in all tissues of expected ECM proteins including collagen alpha-1(I) chain (COL1A1), collagen alpha-1(XII) chain (COL12A1), biglycan (BGN), asporin (ASPN), lumican (LUM), and fibromodulin (FMOD), served to validate the approach. Principal component analysis (PCA) and hierarchical clustering identified a high degree of similarity in DC and AB proteomes, whereas DE presented a distinct dataset. Exclusively and differentially identified proteins were detected from all three tissues. The protein-protein interaction network (interactome) of DC was notable for its inclusion of several indicators of metabolic function (e.g. mitochondrial proteins, protein synthesis, and calcium transport), possibly reflecting cementocyte activity. The DE proteome included known and novel mineralization regulators, including matrix metalloproteinase 20 (MMP-20), 5' nucleotidase (NT5E), and secreted phosphoprotein 24 (SPP-24 or SPP-2). Application of the LCM-LC-MS/MS approach to dentoalveolar tissues would be of value in many experimental designs, including developmental studies of transgenic animals, investigation of treatment effects, and identification of novel regenerative factors.
Collapse
Affiliation(s)
- Cristiane R Salmon
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil
| | - Ana Paula O Giorgetti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil
| | - Adriana F Paes Leme
- National Biosciences Laboratory, Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil
| | - Romênia R Domingues
- National Biosciences Laboratory, Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil
| | - Tamara N Kolli
- Biosciences Division, College of Dentistry, Ohio State University, Columbus, OH, United States
| | - Brian L Foster
- Biosciences Division, College of Dentistry, Ohio State University, Columbus, OH, United States
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil.
| |
Collapse
|
25
|
Comprehensive analysis of human protein N-termini enables assessment of various protein forms. Sci Rep 2017; 7:6599. [PMID: 28747677 PMCID: PMC5529458 DOI: 10.1038/s41598-017-06314-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/09/2017] [Indexed: 01/10/2023] Open
Abstract
Various forms of protein (proteoforms) are generated by genetic variations, alternative splicing, alternative translation initiation, co- or post-translational modification and proteolysis. Different proteoforms are in part discovered by characterizing their N-terminal sequences. Here, we introduce an N-terminal-peptide-enrichment method, Nrich. Filter-aided negative selection formed the basis for the use of two N-blocking reagents and two endoproteases in this method. We identified 6,525 acetylated (or partially acetylated) and 6,570 free protein N-termini arising from 5,727 proteins in HEK293T human cells. The protein N-termini included translation initiation sites annotated in the UniProtKB database, putative alternative translational initiation sites, and N-terminal sites exposed after signal/transit/pro-peptide removal or unknown processing, revealing various proteoforms in cells. In addition, 46 novel protein N-termini were identified in 5′ untranslated region (UTR) sequence with pseudo start codons. Our data showing the observation of N-terminal sequences of mature proteins constitutes a useful resource that may provide information for a better understanding of various proteoforms in cells.
Collapse
|
26
|
Tholey A, Becker A. Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2191-2199. [PMID: 28711385 DOI: 10.1016/j.bbamcr.2017.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 02/06/2023]
Abstract
Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level. We briefly introduce major approaches of bottom-up proteomics used in the field of protease research and highlight the shortcomings of these methods. We then discuss the present state-of-the-art of top-down proteomics. Together with the discussion of known challenges we show the potential of this approach and present a number of successful applications of top-down proteomics in protease research. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
Collapse
Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Alexander Becker
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| |
Collapse
|
27
|
Demir F, Niedermaier S, Kizhakkedathu JN, Huesgen PF. Profiling of Protein N-Termini and Their Modifications in Complex Samples. Methods Mol Biol 2017; 1574:35-50. [PMID: 28315242 DOI: 10.1007/978-1-4939-6850-3_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Protein N termini are a unique window to the functional state of the proteome, revealing translation initiation sites, co-translation truncation and modification, posttranslational maturation, and further proteolytic processing into different proteoforms with distinct functions. As a direct readout of proteolytic activity, protein N termini further reveal proteolytic regulation of diverse biological processes and provide a route to determine specific substrates and hence the physiological functions for any protease of interest. Here, we describe our current protocol of the successful Terminal Amine Isotope Labeling of Substrates (TAILS) technique, which enriches protein N-terminal peptides from complex proteome samples by negative selection. Genome-encoded N termini, protease-generated neo-N termini, and endogenously modified N termini are all enriched simultaneously. Subsequent mass spectrometric analysis therefore profiles all protein N termini and their modifications present in a complex sample in a single experiment. We further provide a detailed protocol for the TAILS-compatible proteome preparation from plant material and discuss specific considerations for N terminome data analysis and annotation.
Collapse
Affiliation(s)
- Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany
| | - Stefan Niedermaier
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Department of Pathology & Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada, V6T 1Z3
- Department of Chemistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada, V6T 1Z3
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany.
| |
Collapse
|
28
|
Segura V, Garin-Muga A, Guruceaga E, Corrales FJ. Progress and pitfalls in finding the 'missing proteins' from the human proteome map. Expert Rev Proteomics 2016; 14:9-14. [PMID: 27885863 DOI: 10.1080/14789450.2017.1265450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map. Areas covered: This review focuses on the description of the missing proteome based on the HUPO standards, the analysis of the reasons explaining the difficulty of detecting missing proteins and the strategies currently used in the search for missing proteins. The present and future of the quest for the missing proteins is critically revised hereafter. Expert commentary: An overarching multidisciplinary effort is currently being done under the HUPO umbrella to allow completion of the human proteome map. It is expected that the detection of missing proteins will grow in the coming years since the methods and the best tissue/cell type sample for their search are already on the table.
Collapse
Affiliation(s)
- Victor Segura
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Alba Garin-Muga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Elizabeth Guruceaga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Fernando J Corrales
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| |
Collapse
|
29
|
Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J Proteome Res 2016; 15:3951-3960. [PMID: 27487407 PMCID: PMC5129622 DOI: 10.1021/acs.jproteome.6b00511] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list-the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [ www.thehpp.org/guidelines ]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 aa in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven (B/D)-HPP has created comprehensive SRM resources, generated popular protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.
Collapse
Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Human Protein Science, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Emma K. Lundberg
- SciLifeLab Stockholm and School of Biotechnology, KTH, Karolinska Institutet Science Park, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Ronald C. Beavis
- Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Christopher M. Overall
- Biochemistry and Molecular Biology, and Oral Biological and Medical Sciences University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC V6T 1Z3, Canada
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| |
Collapse
|
30
|
Lycette BE, Glickman JW, Roth SJ, Cram AE, Kim TH, Krizanc D, Weir MP. N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries. J Proteome Res 2016; 15:2891-9. [PMID: 27498768 DOI: 10.1021/acs.jproteome.5b00996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We identified tryptic peptides in yeast cell lysates that map to translation initiation sites downstream of the annotated start sites using the peptide-spectrum matching algorithms OMSSA and Mascot. To increase the accuracy of peptide-spectrum matching, both algorithms were run using several standardized parameter sets, and Mascot was run utilizing a, b, and y ions from collision-induced dissociation. A large fraction (22%) of the detected N-terminal peptides mapped to translation initiation downstream of the annotated initiation sites. Expression of several truncated proteins from downstream initiation in the same reading frame as the full-length protein (frame 1) was verified by western analysis. To facilitate analysis of the larger proteome of Drosophila, we created a streamlined sequence library from which all duplicated trypsin fragments had been removed. OMSSA assessment using this "stripped" library revealed 171 peptides that map to downstream translation initiation sites, 76% of which are in the same reading frame as the full-length annotated proteins, although some are in different reading frames creating new protein sequences not in the annotated proteome. Sequences surrounding implicated downstream AUG start codons are associated with nucleotide preferences with a pronounced three-base periodicity N1^G2^A3.
Collapse
Affiliation(s)
- Brynne E Lycette
- Department of Biology, Wesleyan University , Middletown, Connecticut 06459, United States.,Department of Mathematics and Computer Science, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Jacob W Glickman
- Department of Biology, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Samuel J Roth
- Department of Biology, Wesleyan University , Middletown, Connecticut 06459, United States.,Department of Mathematics and Computer Science, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Abigail E Cram
- Department of Biology, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Tae Hee Kim
- Department of Biology, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Danny Krizanc
- Department of Mathematics and Computer Science, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Michael P Weir
- Department of Biology, Wesleyan University , Middletown, Connecticut 06459, United States
| |
Collapse
|
31
|
Proteomic analysis of human tooth pulp proteomes – Comparison of caries-resistant and caries-susceptible persons. J Proteomics 2016; 145:127-136. [DOI: 10.1016/j.jprot.2016.04.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/08/2016] [Accepted: 04/17/2016] [Indexed: 01/13/2023]
|
32
|
TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors. Cell Rep 2016; 16:1762-1773. [PMID: 27477282 DOI: 10.1016/j.celrep.2016.06.086] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/31/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022] Open
Abstract
Deregulated cathepsin proteolysis occurs across numerous cancers, but in vivo substrates mediating tumorigenesis remain ill-defined. Applying 8-plex iTRAQ terminal amine isotopic labeling of substrates (TAILS), a systems-level N-terminome degradomics approach, we identified cathepsin B, H, L, S, and Z in vivo substrates and cleavage sites with the use of six different cathepsin knockout genotypes in the Rip1-Tag2 mouse model of pancreatic neuroendocrine tumorigenesis. Among 1,935 proteins and 1,114 N termini identified by TAILS, stable proteolytic products were identified in wild-type tumors compared with one or more different cathepsin knockouts (17%-44% of 139 cleavages). This suggests a lack of compensation at the substrate level by other cathepsins. The majority of neo-N termini (56%-83%) for all cathepsins was consistent with protein degradation. We validated substrates, including the glycolytic enzyme pyruvate kinase M2 associated with the Warburg effect, the ER chaperone GRP78, and the oncoprotein prothymosin-alpha. Thus, the identification of cathepsin substrates in tumorigenesis improves the understanding of cathepsin functions in normal physiology and cancer.
Collapse
|
33
|
Butler GS, Connor AR, Sounni NE, Eckhard U, Morrison CJ, Noël A, Overall CM. Degradomic and yeast 2-hybrid inactive catalytic domain substrate trapping identifies new membrane-type 1 matrix metalloproteinase (MMP14) substrates: CCN3 (Nov) and CCN5 (WISP2). Matrix Biol 2016; 59:23-38. [PMID: 27471094 DOI: 10.1016/j.matbio.2016.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
Members of the CCN family of matricellular proteins are cytokines linking cells to the extracellular matrix. We report that CCN3 (Nov) and CCN5 (WISP2) are novel substrates of MMP14 (membrane-type 1-matrix metalloproteinase, MT1-MMP) that we identified using MMP14 "inactive catalytic domain capture" (ICDC) as a yeast two-hybrid protease substrate trapping platform in parallel with degradomics mass spectrometry screens for MMP14 substrates. CCN3 and CCN5, previously unknown substrates of MMPs, were biochemically validated as substrates of MMP14 and other MMPs in vitro-CCN5 was processed in the variable region by MMP14 and MMP2, as well as by MMP1, 3, 7, 8, 9 and 15. CCN1, 2 and 3 are proangiogenic factors yet we found novel opposing activity of CCN5 that was potently antiangiogenic in an aortic ring vessel outgrowth model. MMP14, a known regulator of angiogenesis, cleaved CCN5 and abrogated the angiostatic activity. CCN3 was also processed in the variable region by MMP14 and MMP2, and by MMP1, 8 and 9. In addition to the previously reported cleavages of CCN1 and CCN2 by several MMPs we found that MMPs 8, 9, and 1 process CCN1, and MMP8 and MMP9 also process CCN2. Thus, our study reveals additional and pervasive family-wide processing of CCN matricellular proteins/cytokines by MMPs. Furthermore, CCN5 cleavage by proangiogenic MMPs results in removal of an angiogenic brake held by CCN5. This highlights the importance of thorough dissection of MMP substrates that is needed to reveal higher-level control mechanisms beyond type IV collagen and other extracellular matrix protein remodelling in angiogenesis. SUMMARY We find CCN family member cleavage by MMPs is more pervasive than previously reported and includes CCN3 (Nov) and CCN5 (WISP2). CCN5 is a novel antiangiogenic factor, whose function is abrogated by proangiogenic MMP cleavage. By processing CCN proteins, MMPs regulate cell responses angiogenesis in connective tissues.
Collapse
Affiliation(s)
- Georgina S Butler
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Andrea R Connor
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Nor Eddine Sounni
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Ulrich Eckhard
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Charlotte J Morrison
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Agnès Noël
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada.
| |
Collapse
|
34
|
Paik YK, Omenn GS, Overall CM, Deutsch EW, Hancock WS. Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J Proteome Res 2016; 14:3409-14. [PMID: 26337862 DOI: 10.1021/acs.jproteome.5b00785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - William S Hancock
- Department of Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| |
Collapse
|
35
|
Advances of Proteomic Sciences in Dentistry. Int J Mol Sci 2016; 17:ijms17050728. [PMID: 27187379 PMCID: PMC4881550 DOI: 10.3390/ijms17050728] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/01/2016] [Accepted: 05/09/2016] [Indexed: 12/13/2022] Open
Abstract
Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.
Collapse
|
36
|
Eckhard U, Marino G, Butler GS, Overall CM. Positional proteomics in the era of the human proteome project on the doorstep of precision medicine. Biochimie 2016; 122:110-8. [DOI: 10.1016/j.biochi.2015.10.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/28/2015] [Indexed: 12/30/2022]
|
37
|
Eckhard U, Huesgen PF, Schilling O, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, auf dem Keller U, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14. Data Brief 2016; 7:299-310. [PMID: 26981551 PMCID: PMC4777984 DOI: 10.1016/j.dib.2016.02.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 11/19/2022] Open
Abstract
The data described provide a comprehensive resource for the family-wide active site specificity portrayal of the human matrix metalloproteinase family. We used the high-throughput proteomic technique PICS (Proteomic Identification of protease Cleavage Sites) to comprehensively assay 9 different MMPs. We identified more than 4300 peptide cleavage sites, spanning both the prime and non-prime sides of the scissile peptide bond allowing detailed subsite cooperativity analysis. The proteomic cleavage data were expanded by kinetic analysis using a set of 6 quenched-fluorescent peptide substrates designed using these results. These datasets represent one of the largest specificity profiling efforts with subsequent structural follow up for any protease family and put the spotlight on the specificity similarities and differences of the MMP family. A detailed analysis of this data may be found in Eckhard et al. (2015) [1]. The raw mass spectrometry data and the corresponding metadata have been deposited in PRIDE/ProteomeXchange with the accession number PXD002265.
Collapse
Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Pitter F. Huesgen
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Oliver Schilling
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Caroline L. Bellac
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Georgina S. Butler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer H. Cox
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Antoine Dufour
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Verena Goebeler
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Reinhild Kappelhoff
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ulrich auf dem Keller
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Theo Klein
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Philipp F. Lange
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Charlotte J. Morrison
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Anna Prudova
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David Rodriguez
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Amanda E. Starr
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yili Wang
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M. Overall
- Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
- Corresponding author at: Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada.Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British ColumbiaVancouverBCCanada
| |
Collapse
|
38
|
Eckhard U, Marino G, Abbey SR, Matthew I, Overall CM. TAILS N-terminomic and proteomic datasets of healthy human dental pulp. Data Brief 2015; 5:542-8. [PMID: 26587561 PMCID: PMC4625376 DOI: 10.1016/j.dib.2015.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/04/2022] Open
Abstract
The Data described here provide the in depth proteomic assessment of the human dental pulp proteome and N-terminome (Eckhard et al., 2015) [1]. A total of 9 human dental pulps were processed and analyzed by the positional proteomics technique TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminomics. 38 liquid chromatography tandem mass spectrometry (LC-MS/MS) datasets were collected and analyzed using four database search engines in combination with statistical downstream evaluation, to yield the by far largest proteomic and N-terminomic dataset of any dental tissue to date. The raw mass spectrometry data and the corresponding metadata have been deposited in ProteomeXchange with the PXD identifier <PXD002264>; Supplementary Tables described in this article are available via Mendeley Data (10.17632/555j3kk4sw.1).
Collapse
Affiliation(s)
- Ulrich Eckhard
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Giada Marino
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Simon R Abbey
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Ian Matthew
- Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada
| | - Christopher M Overall
- Centre for Blood Research, The Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada ; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, BC, Canada ; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|