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Datta KK, Chatterjee A, Gowda H. Phosphotyrosine Profiling Using SILAC. Methods Mol Biol 2023; 2603:117-125. [PMID: 36370274 DOI: 10.1007/978-1-0716-2863-8_9] [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] [Indexed: 06/16/2023]
Abstract
Tyrosine phosphorylation on proteins is an important posttranslational modification that regulates various processes in cells. Mass spectrometry-based phosphotyrosine profiling can reveal tyrosine kinase signaling activity in cells. Using quantitative proteomics strategies such as stable isotope labeling with amino acids in cell culture (SILAC) allows comparison of tyrosine kinase signaling activity across two to -three different conditions. In this book chapter, we discuss the reagents required and a step-by-step protocol to carry out phosphotyrosine profiling using SILAC.
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Affiliation(s)
- Keshava K Datta
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Harsha Gowda
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia.
- Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.
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2
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Vitorino R, Choudhury M, Guedes S, Ferreira R, Thongboonkerd V, Sharma L, Amado F, Srivastava S. Peptidomics and proteogenomics: background, challenges and future needs. Expert Rev Proteomics 2021; 18:643-659. [PMID: 34517741 DOI: 10.1080/14789450.2021.1980388] [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] [Indexed: 10/20/2022]
Abstract
INTRODUCTION With available genomic data and related information, it is becoming possible to better highlight mutations or genomic alterations associated with a particular disease or disorder. The advent of high-throughput sequencing technologies has greatly advanced diagnostics, prognostics, and drug development. AREAS COVERED Peptidomics and proteogenomics are the two post-genomic technologies that enable the simultaneous study of peptides and proteins/transcripts/genes. Both technologies add a remarkably large amount of data to the pool of information on various peptides associated with gene mutations or genome remodeling. Literature search was performed in the PubMed database and is up to date. EXPERT OPINION This article lists various techniques used for peptidomic and proteogenomic analyses. It also explains various bioinformatics workflows developed to understand differentially expressed peptides/proteins and their role in disease pathogenesis. Their role in deciphering disease pathways, cancer research, and biomarker discovery using biofluids is highlighted. Finally, the challenges and future requirements to overcome the current limitations for their effective clinical use are also discussed.
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Affiliation(s)
- Rui Vitorino
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manisha Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
| | - Sofia Guedes
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Francisco Amado
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
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Li H, Zhou R, Xu S, Chen X, Hong Y, Lu Q, Liu H, Zhou B, Liang X. Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow. J Proteome Res 2020; 19:2226-2235. [DOI: 10.1021/acs.jproteome.9b00723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Ruo Zhou
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Shaohang Xu
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Baojin Zhou
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
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Madugundu AK, Na CH, Nirujogi RS, Renuse S, Kim KP, Burns KH, Wilks C, Langmead B, Ellis SE, Collado‐Torres L, Halushka MK, Kim M, Pandey A. Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells. Proteomics 2019; 19:e1800315. [PMID: 30983154 PMCID: PMC6812510 DOI: 10.1002/pmic.201800315] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/17/2019] [Indexed: 01/11/2023]
Abstract
Understanding the molecular profile of every human cell type is essential for understanding its role in normal physiology and disease. Technological advancements in DNA sequencing, mass spectrometry, and computational methods allow us to carry out multiomics analyses although such approaches are not routine yet. Human umbilical vein endothelial cells (HUVECs) are a widely used model system to study pathological and physiological processes associated with the cardiovascular system. In this study, next-generation sequencing and high-resolution mass spectrometry to profile the transcriptome and proteome of primary HUVECs is employed. Analysis of 145 million paired-end reads from next-generation sequencing confirmed expression of 12 186 protein-coding genes (FPKM ≥0.1), 439 novel long non-coding RNAs, and revealed 6089 novel isoforms that were not annotated in GENCODE. Proteomics analysis identifies 6477 proteins including confirmation of N-termini for 1091 proteins, isoforms for 149 proteins, and 1034 phosphosites. A database search to specifically identify other post-translational modifications provide evidence for a number of modification sites on 117 proteins which include ubiquitylation, lysine acetylation, and mono-, di- and tri-methylation events. Evidence for 11 "missing proteins," which are proteins for which there was insufficient or no protein level evidence, is provided. Peptides supporting missing protein and novel events are validated by comparison of MS/MS fragmentation patterns with synthetic peptides. Finally, 245 variant peptides derived from 207 expressed proteins in addition to alternate translational start sites for seven proteins and evidence for novel proteoforms for five proteins resulting from alternative splicing are identified. Overall, it is believed that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.
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Affiliation(s)
- Anil K. Madugundu
- Center for Molecular MedicineNational Institute of Mental Health and NeurosciencesHosur RoadBangalore560029KarnatakaIndia
- Institute of BioinformaticsInternational Technology ParkBangalore560066KarnatakaIndia
- Manipal Academy of Higher EducationManipal576104KarnatakaIndia
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
| | - Chan Hyun Na
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- NeurologyInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Raja Sekhar Nirujogi
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Santosh Renuse
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
| | - Kwang Pyo Kim
- Department of Applied ChemistryKyung Hee UniversityYonginGyeonggi17104Republic of Korea
| | - Kathleen H. Burns
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMD21205USA
- High Throughput Biology CenterJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Christopher Wilks
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
| | - Ben Langmead
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
| | - Shannon E. Ellis
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMD21205USA
| | - Leonardo Collado‐Torres
- Center for Computational BiologyJohns Hopkins UniversityBaltimoreMD21205USA
- Lieber Institute for Brain DevelopmentJohns Hopkins Medical CampusBaltimoreMD21205USA
| | - Marc K. Halushka
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Min‐Sik Kim
- Department of Applied ChemistryKyung Hee UniversityYonginGyeonggi17104Republic of Korea
- Department of New BiologyDGISTDaegu42988Republic of Korea
| | - Akhilesh Pandey
- Center for Molecular MedicineNational Institute of Mental Health and NeurosciencesHosur RoadBangalore560029KarnatakaIndia
- McKusick‐Nathans Institute of Genetic MedicineJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Center for Individualized Medicine and Department of Laboratory Medicine and PathologyMayo ClinicRochesterMN55905USA
- NeurologyInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Departments of PathologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of Biological ChemistryJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of OncologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
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Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C. Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics 2019; 20:56. [PMID: 30654742 PMCID: PMC6337836 DOI: 10.1186/s12864-019-5431-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 01/03/2019] [Indexed: 01/02/2023] Open
Abstract
Background Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. Results Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. Conclusions Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu. Data are available via ProteomeXchange under identifier PXD010618. Electronic supplementary material The online version of this article (10.1186/s12864-019-5431-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Ludovic Delage
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Alain Viari
- INRIA Grenoble-Rhône-Alpes, F-38330, Montbonnot-Saint-Martin, France
| | - Yves Vandenbrouck
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000, Grenoble, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Andrés Ritter
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France.,Present address: Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Dominique Marie
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | | | - Philippe Potin
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France. .,Protim, Univ Rennes, F-35042, Rennes cedex, France.
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Low TY, Mohtar MA, Ang MY, Jamal R. Connecting Proteomics to Next‐Generation Sequencing: Proteogenomics and Its Current Applications in Biology. Proteomics 2018; 19:e1800235. [DOI: 10.1002/pmic.201800235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/09/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - M. Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - Mia Yang Ang
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
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Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics. Proteomics 2018; 18:e1700150. [PMID: 29968278 DOI: 10.1002/pmic.201700150] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/23/2018] [Indexed: 01/15/2023]
Abstract
In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the database-driven approach is limited, mainly because of its static search space. In contrast, de novo sequencing derives peptide sequence information in an unbiased manner, using only the fragment ion information from the tandem mass spectra. In recent years, with the improvements in MS instrumentation, various new methods have been proposed for de novo sequencing. This review article provides an overview of existing de novo sequencing algorithms and software tools ranging from peptide sequencing to sequence-to-protein mapping. Various use cases are described for which de novo sequencing was successfully applied. Finally, limitations of current methods are highlighted and new directions are discussed for a wider acceptance of de novo sequencing in the community.
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Affiliation(s)
- Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Felix Hartkopf
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5020, Bergen, Norway
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
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