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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Li N, Zhan X. MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS. MASS SPECTROMETRY REVIEWS 2020; 39:471-498. [PMID: 32020673 DOI: 10.1002/mas.21618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Department of Oncology, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
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Uzdensky AB. Multifunctional Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Poverennaya EV, Kiseleva OI, Ivanov AS, Ponomarenko EA. Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms. BIOCHEMISTRY (MOSCOW) 2020; 85:68-79. [PMID: 32079518 DOI: 10.1134/s000629792001006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.
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Affiliation(s)
| | - O I Kiseleva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
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Lorentzian A, Uzozie A, Lange PF. Origins and clinical relevance of proteoforms in pediatric malignancies. Expert Rev Proteomics 2019; 16:185-200. [PMID: 30700156 DOI: 10.1080/14789450.2019.1575206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Cancer changes the proteome in complex ways that reach well beyond simple changes in protein abundance. Genomic and transcriptional variations and post-translational protein modification create functional variants of a protein, known as proteoforms. Childhood cancers have fewer genomic alterations but show equally dramatic phenotypic changes as malignant cells in adults. Therefore, unraveling the complexities of the proteome is even more important in pediatric malignancies. Areas covered: In this review, the biological origins of proteoforms and technological advancements in the study of proteoforms are discussed. Particular emphasis is given to their implication in childhood malignancies and the critical role of cancer-specific proteoforms for the next generation of cancer therapies and diagnostics. Expert opinion: Recent advancements in technology have led to a better understanding of the underlying mechanisms of tumorigenesis. This has been critical for the development of more effective and less harmful treatments that are based on direct targeting of altered proteins and deregulated pathways. As proteome coverage and the ability to detect complex proteoforms increase, the most need for change is in data compilation and database availability to mediate high-level data analysis and allow for better functional annotation of proteoforms.
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Affiliation(s)
- Amanda Lorentzian
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada
| | - Anuli Uzozie
- b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Philipp F Lange
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
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Kopylov AT, Ponomarenko EA, Ilgisonis EV, Pyatnitskiy MA, Lisitsa AV, Poverennaya EV, Kiseleva OI, Farafonova TE, Tikhonova OV, Zavialova MG, Novikova SE, Moshkovskii SA, Radko SP, Morukov BV, Grigoriev AI, Paik YK, Salekdeh GH, Urbani A, Zgoda VG, Archakov AI. 200+ Protein Concentrations in Healthy Human Blood Plasma: Targeted Quantitative SRM SIS Screening of Chromosomes 18, 13, Y, and the Mitochondrial Chromosome Encoded Proteome. J Proteome Res 2018; 18:120-129. [PMID: 30480452 DOI: 10.1021/acs.jproteome.8b00391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This work continues the series of the quantitative measurements of the proteins encoded by different chromosomes in the blood plasma of a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and a gene-centric approach, which is the basis for the implementation of the international Chromosome-centric Human Proteome Project (C-HPP), were applied for the quantitative measurement of proteins in human blood plasma. Analyses were carried out in the frame of C-HPP for each protein-coding gene of the four human chromosomes: 18, 13, Y, and mitochondrial. Concentrations of proteins encoded by 667 genes were measured in 54 blood plasma samples of the volunteers, whose health conditions were consistent with requirements for astronauts. The gene list included 276, 329, 47, and 15 genes of chromosomes 18, 13, Y, and the mitochondrial chromosome, respectively. This paper does not make claims about the detection of missing proteins. Only 205 proteins (30.7%) were detected in the samples. Of them, 84, 106, 10, and 5 belonged to chromosomes 18, 13, and Y and the mitochondrial chromosome, respectively. Each detected protein was found in at least one of the samples analyzed. The SRM SIS raw data are available in the ProteomeXchange repository (PXD004374, PASS01192).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sergey A Moshkovskii
- Institute of Biomedical Chemistry , Moscow 119435 , Russia.,Pirogov Russian National Research Medical University , Moscow 117997 , Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| | - Boris V Morukov
- Institute of Medico-Biological Problems , Moscow 123007 , Russia
| | | | - Young-Ki Paik
- Yonsei Proteome Research Center , Yonsei University , Seoul 03722 , Korea
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran , Iran.,Department of Molecular Sciences , Macquarie University , Sydney , New South Wales 2109 , Australia.,Department of Systems Biology , Agricultural Biotechnology Research Institute of Iran , Karaj , Iran
| | - Andrea Urbani
- Area of Diagnostic Laboratories , Fondazione Policlinico Gemelli-IRCCS , Rome 00168 , Italy.,Institute of Biochemistry and Clinical Biochemistry , Catholic University of the Sacred Heart , Rome 00168 , Italy
| | - Victor G Zgoda
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
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