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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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2
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Lancaster NM, Sinitcyn P, Forny P, Peters-Clarke TM, Fecher C, Smith AJ, Shishkova E, Arrey TN, Pashkova A, Robinson ML, Arp N, Fan J, Hansen J, Galmozzi A, Serrano LR, Rojas J, Gasch AP, Westphall MS, Stewart H, Hock C, Damoc E, Pagliarini DJ, Zabrouskov V, Coon JJ. Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568149. [PMID: 38045259 PMCID: PMC10690147 DOI: 10.1101/2023.11.21.568149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology was benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We applied this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detected 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of novel phosphorylation events relevant to mitochondrial and brain biology.
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Sun Q, Zhou X, Yang L, Xu H, Zhou X. Integration of Phosphoproteomics and Transcriptome Studies Reveals ABA Signaling Pathways Regulate UV-B Tolerance in Rhododendron chrysanthum Leaves. Genes (Basel) 2023; 14:1153. [PMID: 37372333 DOI: 10.3390/genes14061153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The influence of UV-B stress on the growth, development, and metabolism of alpine plants, such as the damage to DNA macromolecules, the decline in photosynthetic rate, and changes in growth, development, and morphology cannot be ignored. As an endogenous signal molecule, ABA demonstrates a wide range of responses to UV-B radiation, low temperature, drought, and other stresses. The typical effect of ABA on leaves is to reduce the loss of transpiration by closing the stomata, which helps plants resist abiotic and biological stress. The Changbai Mountains have a harsh environment, with low temperatures and thin air, so Rhododendron chrysanthum (R. chrysanthum) seedlings growing in the Changbai Mountains can be an important research object. In this study, a combination of physiological, phosphorylated proteomic, and transcriptomic approaches was used to investigate the molecular mechanisms by which abiotic stress leads to the phosphorylation of proteins in the ABA signaling pathway, and thereby mitigates UV-B radiation to R. chrysanthum. The experimental results show that a total of 12,289 differentially expressed genes and 109 differentially phosphorylated proteins were detected after UV-B stress in R. chrysanthum, mainly concentrated in plant hormone signaling pathways. Plants were treated with ABA prior to exposure to UV-B stress, and the results showed that ABA mitigated stomatal changes in plants, thus confirming the key role of endogenous ABA in plant adaptation to UV-B. We present a model that suggests a multifaceted R. chrysanthum response to UV-B stress, providing a theoretical basis for further elaboration of the mechanism of ABA signal transduction regulating stomata to resist UV-B radiation.
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Affiliation(s)
- Qi Sun
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Xiangru Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Liping Yang
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Hongwei Xu
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
| | - Xiaofu Zhou
- Jilin Provincial Key Laboratory of Plant Resource Science and Green Production, Jilin Normal University, Siping 136000, China
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4
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
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Emenike B, Nwajiobi O, Raj M. Covalent Chemical Tools for Profiling Post-Translational Modifications. Front Chem 2022; 10:868773. [PMID: 35860626 PMCID: PMC9289218 DOI: 10.3389/fchem.2022.868773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
Nature increases the functional diversity of the proteome through posttranslational modifications (PTMs); a process that involves the proteolytic processing or catalytic attachment of diverse functional groups onto proteins. These modifications modulate a host of biological activities and responses. Consequently, anomalous PTMs often correlate to a host of diseases, hence there is a need to detect these transformations, both qualitatively and quantitatively. One technique that has gained traction is the use of robust chemical strategies to label different PTMs. By utilizing the intrinsic chemical reactivity of the different chemical groups on the target amino acid residues, this strategy can facilitate the delineation of the overarching and inclusionary roles of these different modifications. Herein, we will discuss the current state of the art in post-translational modification analysis, with a direct focus on covalent chemical methods used for detecting them.
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Comprehensive Evaluation of Different TiO2-Based Phosphopeptide Enrichment and Fractionation Methods for Phosphoproteomics. Cells 2022; 11:cells11132047. [PMID: 35805136 PMCID: PMC9265536 DOI: 10.3390/cells11132047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Protein phosphorylation is an essential post-translational modification that regulates multiple cellular processes. Due to their low stoichiometry and ionization efficiency, it is critical to efficiently enrich phosphopeptides for phosphoproteomics. Several phosphopeptide enrichment methods have been reported; however, few studies have comprehensively compared different TiO2-based phosphopeptide enrichment methods using complex proteomic samples. Here, we compared four TiO2-based phosphopeptide enrichment methods that used four non-phosphopeptide excluders (glutamic acid, lactic acid, glycolic acid, and DHB). We found that these four TiO2-based phosphopeptide enrichment methods had different enrichment specificities and that phosphopeptides enriched by the four methods had different physicochemical characteristics. More importantly, we discovered that phosphopeptides had a higher deamidation ratio than peptides from cell lysate and that phosphopeptides enriched using the glutamic acid method had a higher deamidation ratio than the other three methods. We then compared two phosphopeptide fractionation methods: ammonia- or TEA-based high pH reversed-phase (HpH-RP). We found that fewer phosphopeptides, especially multi-phosphorylated peptides, were identified using the ammonia-based method than using the TEA-based method. Therefore, the TEA-based HpH-RP fractionation method performed better than the ammonia method. In conclusion, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
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Ino Y, Nishi M, Yamaoka Y, Miyakawa K, Jeremiah SS, Osada M, Kimura Y, Ryo A. Phosphopeptide enrichment using Phos-tag technology reveals functional phosphorylation of the nucleocapsid protein of SARS-CoV-2. J Proteomics 2022; 255:104501. [PMID: 35093569 PMCID: PMC8800104 DOI: 10.1016/j.jprot.2022.104501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/28/2022]
Abstract
Phosphorylation of viral proteins serves as a regulatory mechanism during the intracellular life cycle of infected viruses. There is therefore a pressing need to develop a method to efficiently purify and enrich phosphopeptides derived from viral particles in biological samples. In this study, we utilized Phos-tag technology to analyze the functional phosphorylation of the nucleocapsid protein (N protein; NP) of severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral particles were collected from culture supernatants of SARS-CoV-2-infected VeroE6/TMPRSS2 cells by ultracentrifugation, and phosphopeptides were purified by Phos-tag magnetic beads for LC-MS/MS analysis. Analysis revealed that NP was reproducibly phosphorylated at serine 79 (Ser79). Multiple sequence alignment and phylogenetic analysis showed that the Ser79 was a distinct phospho-acceptor site in SARS-CoV-2 but not in other beta-coronaviruses. We also found that the prolyl-isomerase Pin1 bound to the phosphorylated Ser79 in NP and positively regulated the production of viral particles. These results suggest that SARS-CoV-2 may have acquired the potent virus-host interaction during its evolution mediated by viral protein phosphorylation. Moreover, Phos-tag technology can provide a useful means for analyzing the functional phosphorylation of viral proteins. Significance In this study, we aimed to investigate the functional phosphorylation of SARS-CoV-2 NP. For this purpose, we used Phos-tag technology to purify and enrich virus-derived phosphopeptides with high selectivity and reproducibility. This method can be particularly useful in analyzing viral phosphopeptides from cell culture supernatants that often contain high concentrations of fetal bovine serum and supplements. We newly identified an NP phosphorylation site at Ser79, which is important for Pin1 binding. Furthermore, we showed that the interaction between Pin1 and phosphorylated NP could enhance viral replication in a cell culture model.
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Affiliation(s)
- Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Mayuko Nishi
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yutaro Yamaoka
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Suzukawa 21, Isehara-shi, Kanagawa 259-1146, Japan
| | - Kei Miyakawa
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Sundararaj Stanleyraj Jeremiah
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Makoto Osada
- Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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8
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Iannetta AA, Hicks LM. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. Methods Mol Biol 2022; 2499:1-41. [PMID: 35696073 DOI: 10.1007/978-1-0716-2317-6_1] [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: 06/15/2023]
Abstract
Post-translational modifications (PTMs) regulate complex biological processes through the modulation of protein activity, stability, and localization. Insights into the specific modification type and localization within a protein sequence can help ascertain functional significance. Computational models are increasingly demonstrated to offer a low-cost, high-throughput method for comprehensive PTM predictions. Algorithms are optimized using existing experimental PTM data, thus accurate prediction performance relies on the creation of robust datasets. Herein, advancements in mass spectrometry-based proteomics technologies to maximize PTM coverage are reviewed. Further, requisite experimental validation approaches for PTM predictions are explored to ensure that follow-up mechanistic studies are focused on accurate modification sites.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Cui F, Qian X, Ying W. Integrated Strategy for Unbiased Profiling of the Histidine Phosphoproteome. Anal Chem 2021; 93:15584-15589. [PMID: 34787389 DOI: 10.1021/acs.analchem.1c03374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Histidine phosphorylation (pHis), which plays a key role in signal transduction in bacteria and lower eukaryotes, has been shown to be involved in tumorigenesis. Due to its chemical instability, substoichiometric properties, and lack of specific enrichment reagents, there is a lack of approaches for specific and unbiased enrichment of pHis-proteins/peptides. In this study, an integrated strategy was established and evaluated as an unbiased tool for exploring the histidine phosphoproteome. First, taking advantage of the lower charge states of pHis-peptides versus the non-modified naked peptides at weak acid solution (∼pH 2.7), strong cation exchange (SCX) chromatography was used to differentiate modified and non-modified naked peptides. Furthermore, selective enrichment of the pHis-peptide was performed by applying Cu-IDA beads enrichment. Finally, stable isotope dimethyl labeling was introduced to guarantee high-confidence assignment of pHis-peptides. Using this integrated strategy, 563 different pHis-peptides (H = 1) in 385 proteins were identified from HeLa lysates. Motif analysis revealed that pHis prefers hydrophobic amino acids and has the consensus motif-HxxK, which covered the reports from different approaches. Thus, our method may provide an unbiased and effective tool to reveal histidine phosphoproteome and to study the biological process and function of histidine phosphorylation.
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Affiliation(s)
- Fangfang Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, No. 38, Life Park Road, Changping District, Beijing, 102206, China
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10
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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Rolfs F, Piersma SR, Dias MP, Jonkers J, Jimenez CR. Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate. Mol Cell Proteomics 2021; 20:100078. [PMID: 33819647 PMCID: PMC8111777 DOI: 10.1016/j.mcpro.2021.100078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/21/2022] Open
Abstract
In daily practice, different types of biomolecules are usually extracted for large-scale "omics" analysis with tailored protocols. However, when sample material is limited, an all-in-one strategy is preferable. Although lysis of cells and tissues with urea is widely used for phosphoproteomic applications, DNA, RNA, and proteins can be simultaneously extracted from small samples using acid guanidinium thiocyanate-phenol-chloroform (AGPC). Use of AGPC for mass spectrometry-based phosphoproteomics was reported but has not yet been thoroughly evaluated against a classical phosphoproteomic protocol. Here we compared urea- with AGPC-based protein extraction, profiling phosphorylations in the DNA damage response pathway after ionizing irradiation of U2OS cells as proof of principle. On average we identified circa 9000 phosphosites per sample with both extraction methods. Moreover, we observed high similarity of phosphosite characteristics (e.g., 94% shared class 1 identifications) and deduced kinase activities (e.g., ATM, ATR, CHEK1/2, PRKDC). We furthermore extended our comparison to murine and human tissue samples yielding similar and highly correlated results for both extraction protocols. AGPC-based sample extraction can thus replace common cell lysates for phosphoproteomic workflows and may thus be an attractive way to obtain input material for multiple omics workflows, yielding several data types from a single sample.
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Key Words
- agpc, acid guanidinium thiocyanate–phenol–chloroform
- hcc, hepatocellular carcinoma
- inka, integrative inferred kinase activity
- ir, irradiated
- mbr, match between runs
- nt, untreated
- ps, phosphosite(s)
- ptm-sea, posttranslational modification signature enrichment analysis
- ptyr, phosphotyrosine
- rnab, rna-bee
- u2os, u2 osteosarcoma
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Affiliation(s)
- Frank Rolfs
- Amsterdam UMC, OncoProteomics Laboratory, Department Medical Oncology, Location VUmc, Amsterdam, the Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode institute, Amsterdam, the Netherlands
| | - Sander R Piersma
- Amsterdam UMC, OncoProteomics Laboratory, Department Medical Oncology, Location VUmc, Amsterdam, the Netherlands
| | - Mariana Paes Dias
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Oncode institute, Amsterdam, the Netherlands.
| | - Connie R Jimenez
- Amsterdam UMC, OncoProteomics Laboratory, Department Medical Oncology, Location VUmc, Amsterdam, the Netherlands.
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12
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Cell-cycle phospho-regulation of the kinetochore. Curr Genet 2021; 67:177-193. [PMID: 33221975 DOI: 10.1007/s00294-020-01127-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
The kinetochore is a mega-dalton protein assembly that forms within centromeric regions of chromosomes and directs their segregation during cell division. Here we review cell cycle-mediated phosphorylation events at the kinetochore, with a focus on the budding yeast Saccharomyces cerevisiae and the insight gained from forced associations of kinases and phosphatases. The point centromeres found in the budding yeast S. cerevisiae are one of the simplest such structures found in eukaryotes. The S. cerevisiae kinetochore comprises a single nucleosome, containing a centromere-specific H3 variant Cse4CENP-A, bound to a set of kinetochore proteins that connect to a single microtubule. Despite the simplicity of the budding yeast kinetochore, the proteins are mostly homologous with their mammalian counterparts. In some cases, human proteins can complement their yeast orthologs. Like its mammalian equivalent, the regulation of the budding yeast kinetochore is complex: integrating signals from the cell cycle, checkpoints, error correction, and stress pathways. The regulatory signals from these diverse pathways are integrated at the kinetochore by post-translational modifications, notably phosphorylation and dephosphorylation, to control chromosome segregation. Here we highlight the complex interplay between the activity of the different cell-cycle kinases and phosphatases at the kinetochore, emphasizing how much more we have to understand this essential structure.
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13
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14
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Juarez-Escobar J, Elizalde-Contreras JM, Loyola-Vargas VM, Ruiz-May E. A Phosphoproteomic Analysis Pipeline for Peels of Tropical Fruits. Methods Mol Biol 2021; 2139:179-196. [PMID: 32462587 DOI: 10.1007/978-1-0716-0528-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phosphorylation is a posttranslational reversible modification related to signaling and regulatory mechanisms. Protein phosphorylation is linked to structural changes that modulate protein activity, interaction, or localization and therefore the cell signaling pathways. The use of techniques for phosphoprotein enrichment along with mass spectrometry has become a powerful tool for the characterization of signal transduction in model organisms. However, limited efforts have focused on the establishment of protocols for the analysis of the phosphoproteome in nonmodel organisms such as tropical fruits. This chapter describes a potential pipeline for sample preparation and enrichment of phosphorylated proteins/peptides before MS analysis of peels of some species of tropical fruits.
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Affiliation(s)
- Janet Juarez-Escobar
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán (CICY), Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico.
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15
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Human growth hormone proteoform pattern changes in pituitary adenomas: Potential biomarkers for 3P medical approaches. EPMA J 2021; 12:67-89. [PMID: 33786091 DOI: 10.1007/s13167-021-00232-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/11/2021] [Indexed: 12/19/2022]
Abstract
Relevance Human growth hormone (hGH) is synthesized, stored, and secreted by somatotroph cells in the pituitary gland, and promotes human growth and metabolism. Compared to a normal pituitary, a GH-secreting pituitary adenoma can secrete excessive GH to cause pathological changes in body tissues. GH proteoform changes would be associated with GH-related disease pathogenesis. Purpose This study aimed to elucidate changes in GH proteoforms between GH-secreting pituitary adenomas and control pituitaries for the predictive diagnostics, targeted prevention, and personalization of medical services. Methods The isoelectric point (pI) and relative molecular mass (Mr) are two basic features of a proteoform that can be used to effectively array and detect proteoforms with two-dimensional gel electrophoresis (2DGE) and 2DGE-based western blot. GH proteoforms were characterized with liquid chromatography (LC) and mass spectrometry (MS). Phosphoproteomics, ubiquitinomics, acetylomics, and bioinformatics were used to analyze post-translational modifications (PTMs) of GH proteoforms in GH-secreting pituitary adenoma tissues and control pituitaries. Results Sixty-six 2D gel spots were found to contain hGH, including 46 spots (46 GH proteoforms) in GH-secreting pituitary adenomas and 35 spots (35 GH proteoforms) in control pituitaries. Further, 35 GH proteoforms in control pituitary tissues were matched with 35 of 46 GH proteoforms in GH-secreting pituitary adenoma tissues; and 11 GH proteoforms were presented in only GH-secreting pituitary adenoma tissues but not in control pituitary tissues. The matched 35 GH proteoforms showed quantitative changes in GH-secreting pituitary adenomas compared to the controls. The quantitative levels of those 46 GH proteoforms in GH-secreting pituitary adenomas were significantly different from those 35 GH proteoforms in control pituitaries. Meanwhile, different types of PTMs were identified among those GH proteoforms. Phosphoproteomics identified phosphorylation at residues Ser77, Ser132, Ser134, Thr174, and Ser176 in hGH. Ubiquitinomics identified ubiquitination at residue Lys96 in hGH. Acetylomics identified acetylation at reside Lys171 in hGH. Deamination was identified at residue Asn178 in hGH. Conclusion These findings provide the first hGH proteoform pattern changes in GH-secreting pituitary adenoma tissues compared to control pituitary tissues, and the status of partial PTMs in hGH proteoforms. Those data provide in-depth insights into biological roles of hGH in GH-related diseases, and identify hGH proteoform pattern biomarkers for treatment of a GH-secreting pituitary adenoma in the context of 3P medicine -predictive diagnostics, targeted prevention, and personalization of medical services. Supplementary information The online version contains supplementary material available at 10.1007/s13167-021-00232-7.
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16
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Muehlbauer LK, Hebert AS, Westphall MS, Shishkova E, Coon JJ. Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer. Anal Chem 2020; 92:15959-15967. [PMID: 33270415 DOI: 10.1021/acs.analchem.0c03415] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation on a global scale. Analysis of phosphopeptides requires enrichment, and even after the samples remain highly complex and exhibit broad dynamic range of abundance. Achieving maximal depth of coverage for phosphoproteomics therefore typically necessitates offline liquid chromatography prefractionation, a time-consuming and laborious approach. Here, we incorporate a recently commercialized aerodynamic high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the phosphoproteomic workflow. We characterize the effects of phosphorylation on the FAIMS separation, describe optimized compensation voltage settings for unlabeled phosphopeptides, and demonstrate the advantages of FAIMS-enabled gas-phase fractionation. Standard FAIMS single-shot analyses identified around 15-20% additional phosphorylation sites than control experiments without FAIMS. In comparison to liquid chromatography prefractionation, FAIMS experiments yielded similar or superior results when analyzing up to four discrete gas-phase fractions. Although using FAIMS led to a modest reduction in the precision of quantitative measurements when using label-free approaches, the data collected with FAIMS yielded a 26% increase in total reproducible measurements. Overall, we conclude that the new FAIMS technology is a valuable addition to any phosphoproteomic workflow, with greater benefits emerging from longer analyses and higher amounts of material.
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Affiliation(s)
- Laura K Muehlbauer
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Alexander S Hebert
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Michael S Westphall
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States
| | - Joshua J Coon
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, United States.,Morgridge Institute for Research, Madison, Wisconsin 53706, United States
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17
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Yu LR, Veenstra TD. Characterization of Phosphorylated Proteins Using Mass Spectrometry. Curr Protein Pept Sci 2020; 22:148-157. [PMID: 33231146 DOI: 10.2174/1389203721999201123200439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
Phosphorylation is arguably the most important post-translational modification that occurs within proteins. Phosphorylation is used as a signal to control numerous physiological activities ranging from gene expression to metabolism. Identifying phosphorylation sites within proteins was historically a challenge as it required either radioisotope labeling or the use of phospho-specific antibodies. The advent of mass spectrometry (MS) has had a major impact on the ability to qualitatively and quantitatively characterize phosphorylated proteins. In this article, we describe MS methods for characterizing phosphorylation sites within individual proteins as well as entire proteome samples. The utility of these methods is illustrated in examples that show the information that can be gained using these MS techniques.
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Affiliation(s)
- Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, 251 North Main Street, Cedarville, OH 45314, United States
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18
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Arribas Diez I, Govender I, Naicker P, Stoychev S, Jordaan J, Jensen ON. Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment. J Proteome Res 2020; 20:453-462. [PMID: 33226818 DOI: 10.1021/acs.jproteome.0c00508] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO2 magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO2-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO2 as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.
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Affiliation(s)
- Ignacio Arribas Diez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ireshyn Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa.,ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa
| | - Justin Jordaan
- ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa.,Rhodes University, Grahamstown 6139, South Africa
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
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19
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Chen SH, Lin YC, Shih MK, Wang LF, Liu SS, Hsu JL. LC-MS Quantification of Site-Specific Phosphorylation Degree by Stable-Isotope Dimethyl Labeling Coupled with Phosphatase Dephosphorylation. Molecules 2020; 25:molecules25225316. [PMID: 33202651 PMCID: PMC7697701 DOI: 10.3390/molecules25225316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Protein phosphorylation is a crucial post-translational modification that plays an important role in the regulation of cellular signaling processes. Site-specific quantitation of phosphorylation levels can help decipher the physiological functions of phosphorylation modifications under diverse physiological statuses. However, quantitative analysis of protein phosphorylation degrees is still a challenging task due to its dynamic nature and the lack of an internal standard simultaneously available for the samples differently prepared for various phosphorylation extents. In this study, stable-isotope dimethyl labeling coupled with phosphatase dephosphorylation (DM + deP) was tried to determine the site-specific degrees of phosphorylation in proteins. Firstly, quantitation accuracy of the (DM + deP) approach was confirmed using synthetic peptides of various simulated phosphorylation degrees. Afterwards, it was applied to evaluate the phosphorylation stoichiometry of milk caseins. The phosphorylation degree of Ser130 on α-S1-casein was also validated by absolute quantification with the corresponding synthetic phosphorylated and nonphosphorylated peptides under a selected reaction monitoring (SRM) mode. Moreover, this (DM + deP) method was used to detect the phosphorylation degree change of Ser82 on the Hsp27 protein of HepG2 cells caused by tert-butyl hydroperoxide (t-BHP) treatment. The results showed that the absolute phosphorylation degree obtained from the (DM + deP) approach was comparable with the relative quantitation resulting from stable-isotope dimethyl labeling coupled with TiO2 enrichment. This study suggested that the (DM + deP) approach is promising for absolute quantification of site-specific degrees of phosphorylation in proteins, and it may provide more convincing information than the relative quantification method.
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Affiliation(s)
- Sin-Hong Chen
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Ya-Chi Lin
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Ming-Kuei Shih
- Graduate Institute of Food Culture and Innovation, National Kaohsiung University of Hospitality and Tourism, Kaohsiung 81271, Taiwan;
| | - Li-Fei Wang
- Hospitality and Tourism Research Center, National Kaohsiung University of Hospitality and Tourism, Kaohsiung 81271, Taiwan;
| | - Shyh-Shyan Liu
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Correspondence: (S.-S.L.); (J.-L.H.); Tel.: +886-8-7703202 (ext. 5075) (S.-S.L.); +886-8-7703202 (ext. 5197) (J.-L.H.); Fax: +886-8-7740178 (S.-S.L.); +886-8-7740550 (J.-L.H.)
| | - Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Research Center for Tropic Agriculture, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Correspondence: (S.-S.L.); (J.-L.H.); Tel.: +886-8-7703202 (ext. 5075) (S.-S.L.); +886-8-7703202 (ext. 5197) (J.-L.H.); Fax: +886-8-7740178 (S.-S.L.); +886-8-7740550 (J.-L.H.)
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20
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Önal B, Odabaşı M. Design and application of a newly generated bio/synthetic cryogel column for DNA capturing. Polym Bull (Berl) 2020. [DOI: 10.1007/s00289-020-03387-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Armutcu C, Tartan Ç, Özgür E, Nemutlu E, Uzun L. Phosphate Anion Imprinted Cryogel Cartridges for Selective Preconcentration of Phosphorylated Amino Acids from Protein Lysate: An Alternative Sorbent for Proteome Analyses. ChemistrySelect 2020. [DOI: 10.1002/slct.202001959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Canan Armutcu
- Hacettepe University Faculty of Science Department of Chemistry Ankara Turkey
| | - Çağrı Tartan
- Hacettepe University Faculty of Science Department of Chemistry Ankara Turkey
| | - Erdoğan Özgür
- Hacettepe University Faculty of Science Department of Chemistry Ankara Turkey
- Hacettepe University Advanced Technologies Application and Research Center Ankara Turkey
| | - Emirhan Nemutlu
- Hacettepe University Faculty of Pharmacy Analytical Chemistry Division Ankara Turkey
| | - Lokman Uzun
- Hacettepe University Faculty of Science Department of Chemistry Ankara Turkey
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22
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Marcus K, Lelong C, Rabilloud T. What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World? Proteomes 2020; 8:proteomes8030017. [PMID: 32781532 PMCID: PMC7563651 DOI: 10.3390/proteomes8030017] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
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Affiliation(s)
- Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty & Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum Gesundheitscampus, 4 44801 Bochum, Germany;
| | - Cécile Lelong
- CBM UMR CNRS5249, Université Grenoble Alpes, CEA, CNRS, 17 rue des Martyrs, CEDEX 9, 38054 Grenoble, France;
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Université Grenoble Alpes, CNRS, 38054 Grenoble, France
- Correspondence: ; Tel.: +33-438-783-212
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23
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Dual metal cations coated magnetic mesoporous silica probe for highly selective capture of endogenous phosphopeptides in biological samples. Mikrochim Acta 2020; 187:400. [DOI: 10.1007/s00604-020-04323-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/14/2020] [Indexed: 11/25/2022]
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24
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Serinbaş A, Önal B, Acet Ö, Özdemir N, Dzmitruk V, Halets-Bui I, Shcharbin D, Odabaşı M. A new application of inorganic sorbent for biomolecules: IMAC practice of Fe 3+-nano flowers for DNA separation. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 113:111020. [PMID: 32487418 DOI: 10.1016/j.msec.2020.111020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 12/12/2022]
Abstract
Selection of purification method and type of adsorbent has high significance for separation of a biomolecule like deoxyribonucleic acid (DNA). Nanoflowers are a newly improved class of adsorbent. Due to showing very structural similarity to plant flowers, they are named as nanoflowers. Herein, after synthesize of copper phosphate three hydrate nanoflowers [(Cu3(PO4)2.3H2O), CP-NFs], Fe3+ ions were attached to their surfaces. Obtained Fe3+-CP-NFs, before investigation of some adsorption parameters for DNA, they were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). Some attained data from the results of adsorption experiments as follows: While maximum DNA adsorption on Fe3+-CP-NFs was found as an excellent value of 845.8 mg/g, nanoflowers without Fe3+ ions adsorbed DNA as only 25.3 mg/g. Optimum media conditions for DNA adsorption were observed at pH 7 and 25 °C with an initial concentration of 1.5 mg/mL DNA. Langmuir and Freundlich adsorption equations were applied to determine which adsorption model was appropriate, and it was seen that Langmuir model was fit with a R2 of 0.9885.
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Affiliation(s)
- Ayça Serinbaş
- Chemistry Dept. Biochemistry Division, Faculty of Arts and Science, Aksaray University, Aksaray, Turkey
| | - Burcu Önal
- Chemistry Dept. Biochemistry Division, Faculty of Arts and Science, Aksaray University, Aksaray, Turkey
| | - Ömür Acet
- Chemistry Dept. Biochemistry Division, Faculty of Arts and Science, Aksaray University, Aksaray, Turkey
| | - Nalan Özdemir
- Chemistry Dept. Biochemistry Division, Faculty of Science, Erciyes University, Kayseri, Turkey
| | - Volha Dzmitruk
- Institute of Biophysics and Cell Engineering of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - Inessa Halets-Bui
- Institute of Biophysics and Cell Engineering of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - Dzmitry Shcharbin
- Institute of Biophysics and Cell Engineering of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - Mehmet Odabaşı
- Chemistry Dept. Biochemistry Division, Faculty of Arts and Science, Aksaray University, Aksaray, Turkey.
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25
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26
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Kupcik R, Macak JM, Rehulkova H, Sopha H, Fabrik I, Anitha VC, Klimentova J, Murasova P, Bilkova Z, Rehulka P. Amorphous TiO 2 Nanotubes as a Platform for Highly Selective Phosphopeptide Enrichment. ACS OMEGA 2019; 4:12156-12166. [PMID: 31460330 PMCID: PMC6682070 DOI: 10.1021/acsomega.9b00571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
This work reports highly selective phosphopeptide enrichment using amorphous TiO2 nanotubes (TiO2NTs) and the same material decorated with superparamagnetic Fe3O4 nanoparticles (TiO2NTs@Fe3O4NPs). TiO2NTs and TiO2NTs@Fe3O4NPs materials were applied for phosphopeptide enrichment both from a simple peptide mixture (tryptic digest of bovine serum albumin and α-casein) and from a complex peptide mixture (tryptic digest of Jurkat T cell lysate). The obtained enrichment efficiency and selectivity for phosphopeptides of TiO2NTs and TiO2NTs@Fe3O4NPs were increased to 28.7 and 25.3%, respectively, as compared to those of the well-established TiO2 microspheres. The enrichment protocol was extended for a second elution step facilitating the identification of additional phosphopeptides. It further turned out that both types of amorphous TiO2 nanotubes provide qualitatively new physicochemical features that are clearly advantageous for highly selective phosphopeptide enrichment. This has been confirmed experimentally resulting in substantial reduction of non-phosphorylated peptides in the enriched samples. In addition, TiO2NTs@Fe3O4NPs combine high selectivity and ease of handling due to the superparamagnetic character of the material. The presented materials and performances are further promising for applications toward a whole range of other types of biomolecules to be treated in a similar fashion.
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Affiliation(s)
- Rudolf Kupcik
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Jan M. Macak
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Helena Rehulkova
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - Hanna Sopha
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
- Central
European Institute of Technology, Brno University
of Technology, Purkynova
123, 612 00 Brno, Czech Republic
| | - Ivo Fabrik
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - V. C. Anitha
- Center
of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice, Nam. Cs. Legii 565, 530 02 Pardubice, Czech Republic
| | - Jana Klimentova
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
| | - Pavla Murasova
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Zuzana Bilkova
- Department
of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532
10 Pardubice, Czech Republic
| | - Pavel Rehulka
- Department
of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500
01 Hradec Kralove, Czech Republic
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Morsa D, Baiwir D, La Rocca R, Zimmerman TA, Hanozin E, Grifnée E, Longuespée R, Meuwis MA, Smargiasso N, Pauw ED, Mazzucchelli G. Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics? J Proteome Res 2019; 18:2501-2513. [DOI: 10.1021/acs.jproteome.9b00044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Denis Morsa
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Tyler A. Zimmerman
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Elodie Grifnée
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Rémi Longuespée
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Marie-Alice Meuwis
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU, Liege 4000, Belgium
- Laboratory of Translational Gastroenterology, GIGA, Liege 4000, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
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28
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Gao Y, Lee H, Kwon OK, Cheng Z, Tan M, Kim K, Lee S. Profiling of Histidine Phosphoproteome in
Danio rerio
by TiO
2
Enrichment. Proteomics 2019; 19:e1800471. [DOI: 10.1002/pmic.201800471] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/25/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Yan Gao
- BK21 Plus KNU Multi‐Omics based Creative Drug Research TeamCollege of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National University Daegu 41566 Republic of Korea
| | - Hyojin Lee
- Department of Energy and Environmental Engineering and Department of Environmental EngineeringSeoul National University of Science and Technology Seoul 01811 Republic of Korea
| | - Oh Kwang Kwon
- BK21 Plus KNU Multi‐Omics based Creative Drug Research TeamCollege of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National University Daegu 41566 Republic of Korea
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd. Hangzhou 310018 China
| | - Minjia Tan
- Shanghai Institute of Materia MedicaChinese Academy of Sciences Shanghai 201203 China
| | - Ki‐Tae Kim
- Department of Energy and Environmental Engineering and Department of Environmental EngineeringSeoul National University of Science and Technology Seoul 01811 Republic of Korea
- Jingjie PTM BioLab (Hangzhou) Co. Ltd. Hangzhou 310018 China
| | - Sangkyu Lee
- BK21 Plus KNU Multi‐Omics based Creative Drug Research TeamCollege of Pharmacy and Research Institute of Pharmaceutical SciencesKyungpook National University Daegu 41566 Republic of Korea
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Woods AG, Sokolowska I, Ngounou Wetie AG, Channaveerappa D, Dupree EJ, Jayathirtha M, Aslebagh R, Wormwood KL, Darie CC. Mass Spectrometry for Proteomics-Based Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:1-26. [DOI: 10.1007/978-3-030-15950-4_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Kanshin E, Pascariu M, Tyers M, D’Amours D, Thibault P. Combined Enrichment/Enzymatic Approach To Study Tightly Clustered Multisite Phosphorylation on Ser-Rich Domains. J Proteome Res 2018; 17:3050-3060. [DOI: 10.1021/acs.jproteome.8b00205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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32
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Adam K, Hunter T. Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. J Transl Med 2018; 98:233-247. [PMID: 29058706 PMCID: PMC5815933 DOI: 10.1038/labinvest.2017.118] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
Protein phosphorylation is the most common type of post-translational modification in eukaryotes. The phosphoproteome is defined as the complete set of experimentally detectable phosphorylation sites present in a cell's proteome under various conditions. However, we are still far from identifying all the phosphorylation sites in a cell mainly due to the lack of information about phosphorylation events involving residues other than Ser, Thr and Tyr. Four types of phosphate-protein linkage exist and these generate nine different phosphoresidues-pSer, pThr, pTyr, pHis, pLys, pArg, pAsp, pGlu and pCys. Most of the effort in studying protein phosphorylation has been focused on Ser, Thr and Tyr phosphorylation. The recent development of 1- and 3-pHis monoclonal antibodies promises to increase our understanding of His phosphorylation and the kinases and phosphatases involved. Several His kinases are well defined in prokaryotes, especially those involved in two-component system (TCS) signaling. However, in higher eukaryotes, NM23, a protein originally characterized as a nucleoside diphosphate kinase, is the only characterized protein-histidine kinase. This ubiquitous and conserved His kinase autophosphorylates its active site His, and transfers this phosphate either onto a nucleoside diphosphate or onto a protein His residue. Studies of NM23 protein targets using newly developed anti-pHis antibodies will surely help illuminate the elusive His phosphorylation-based signaling pathways. This review discusses the role that the NM23/NME/NDPK phosphotransferase has, how the addition of the pHis phosphoproteome will expand the phosphoproteome and make His phosphorylation part of the global phosphorylation world. It also summarizes why our understanding of phosphorylation is still largely restricted to the acid stable phosphoproteome, and highlights the study of NM23 histidine kinase as an entrée into the world of histidine phosphorylation.
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Affiliation(s)
- Kevin Adam
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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Houyoux N, Wattiez R, Ris L. A proteomic analysis of contextual fear conditioned rats reveals dynamic modifications in neuron and oligodendrocyte protein expression in the dentate gyrus. Eur J Neurosci 2017; 46:2177-2189. [PMID: 28833751 DOI: 10.1111/ejn.13664] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/30/2022]
Abstract
Contextual memory is an intricate process involving synaptic plasticity and network rearrangement. Both are governed by many molecular processes including phosphorylation and modulation of protein expression. However, little is known about the molecules involved in it. Here, we exploited the advantages of a quantitative proteomic approach to identify a great number of molecules in the rat dentate gyrus after a contextual fear conditioning session. Our results allowed us to highlight protein expression patterns, not only related to neuroplasticity, but also to myelin structure, such as myelin basic protein and myelin proteolipid protein showing a decrease in expression. Validation of the modification in protein expression reveals a dynamic profile during the 48 h following the fear conditioning session. The expression of proteins involved in neurite outgrowth, such as BASP-1 and calcineurin B1, and in synaptic structure and function, VAMP2 and RAB3C, was increased in the dentate gyrus of rats submitted to fear conditioning compared to controls. We showed that the increase in BASP-1 protein was specific to fear conditioning learning as it was not present in immediate-shock rats, neither in rats exposed to a novel environment without being shocked. As myelin is known to stabilise synaptic network, the decrease in myelin proteins suggests a neuroglia interactive process taking place in the dentate gyrus in the 24 h following contextual fear learning, which has never been demonstrated before. These results therefore open the way to the study of new plasticity mechanisms underlying learning and memory.
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Affiliation(s)
- Nicolas Houyoux
- Proteomics and Microbiology Department, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laurence Ris
- Department of Neuroscience, Research Institute for Biosciences, University of Mons, 20 Place du Parc, 7000, Mons, Belgium
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34
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Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NC, Verheul HM, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics 2017; 162:99-107. [DOI: 10.1016/j.jprot.2017.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
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Dai J, Wang M, Liu H. Highly selective enrichment of phosphopeptides using Zr4+-immobilized Titania nanoparticles. Talanta 2017; 164:222-227. [DOI: 10.1016/j.talanta.2016.11.058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/24/2016] [Accepted: 11/26/2016] [Indexed: 10/20/2022]
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He Y, Liu W, Chen L, Lin G, Xiao Q, Gao C, Jianlin W, Lin Z. Facile synthesis of Ti4+-immobilized affinity silica nanoparticles for the highly selective enrichment of intact phosphoproteins. J Sep Sci 2017; 40:1516-1523. [DOI: 10.1002/jssc.201601048] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/12/2017] [Accepted: 01/15/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Yanting He
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Wei Liu
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Lei Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Guo Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Qi Xiao
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Chenling Gao
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
| | - Wu Jianlin
- State Key Laboratory for Quality Research in Chinese Medicines; Macau University of Science and Technology; Macau China
| | - Zian Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety; Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry; Fuzhou University; Fuzhou Fujian China
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von Stechow L, Olsen JV. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies. Proteomics 2017; 17:1600018. [PMID: 27682984 PMCID: PMC5333460 DOI: 10.1002/pmic.201600018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/07/2016] [Accepted: 09/26/2016] [Indexed: 12/31/2022]
Abstract
Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways, collectively known as the DNA damage response (DDR). Deciphering DDR signalling pathways with high-throughput technologies could provide insights into oncogenic transformation, metastasis formation and therapy responses, and could build a basis for better therapeutic interventions in cancer treatment. Mass spectrometry (MS)-based proteomics emerged as a method of choice for global studies of proteins and their posttranslational modifications (PTMs). MS-based studies of the DDR have aided in delineating DNA damage-induced signalling responses. Those studies identified changes in abundance, interactions and modification of proteins in the context of genotoxic stress. Here we review ground-breaking MS-based proteomics studies, which analysed changes in protein abundance, protein-protein and protein-DNA interactions, phosphorylation, acetylation, ubiquitylation, SUMOylation and Poly(ADP-ribose)ylation (PARylation) in the DDR. Finally, we provide an outlook on how proteomics studies of the DDR could aid clinical developments on multiple levels.
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Affiliation(s)
- Louise von Stechow
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jesper V. Olsen
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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38
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The Use of Omic Technologies Applied to Traditional Chinese Medicine Research. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:6359730. [PMID: 28250795 PMCID: PMC5307000 DOI: 10.1155/2017/6359730] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 12/28/2022]
Abstract
Natural products represent one of the most important reservoirs of structural and chemical diversity for the generation of leads in the drug development process. A growing number of researchers have shown interest in the development of drugs based on Chinese herbs. In this review, the use and potential of omic technologies as powerful tools in the modernization of traditional Chinese medicine are discussed. The analytical combination from each omic approach is crucial for understanding the working mechanisms of cells, tissues, organs, and organisms as well as the mechanisms of disease. Gradually, omic approaches have been introduced in every stage of the drug development process to generate high-quality Chinese medicine-based drugs. Finally, the future picture of the use of omic technologies is a promising tool and arena for further improvement in the modernization of traditional Chinese medicine.
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39
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Araya-Farias M, Dziomba S, Carbonnier B, Guerrouache M, Ayed I, Aboud N, Taverna M, Tran NT. A lab-on-a-chip for monolith-based preconcentration and electrophoresis separation of phosphopeptides. Analyst 2017; 142:485-494. [DOI: 10.1039/c6an02324j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A real μTAS integrating monolith-based IMAC enrichment, electrophoresis separation and fluorescence detection of phosphopeptides is reported for the first time.
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Affiliation(s)
- Monica Araya-Farias
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - Szymon Dziomba
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | | | | | - Ichraf Ayed
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - Nacera Aboud
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - Myriam Taverna
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
| | - N. Thuy Tran
- Institut Galien Paris Sud
- UMR 8612
- Protein and Nanotechnology in Analytical Science (PNAS)
- CNRS
- Univ. Paris-Sud
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40
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Bai B, Tan H, Pagala VR, High AA, Ichhaporia VP, Hendershot L, Peng J. Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry. Methods Enzymol 2016; 585:377-395. [PMID: 28109439 DOI: 10.1016/bs.mie.2016.10.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry-based proteomics has experienced an unprecedented advance in comprehensive analysis of proteins and posttranslational modifications, with particular technical progress in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an optimized LC-MS/MS platform to quantitate whole proteome and phosphoproteome. The major steps include protein extraction and digestion, TMT labeling, two-dimensional liquid chromatography, TiO2-mediated phosphopeptide enrichment, high-resolution mass spectrometry, and computational data processing. This protocol routinely leads to confident quantification of more than 10,000 proteins and approximately 30,000 phosphosites in mammalian samples. Quality control steps are implemented for troubleshooting and evaluating experimental variation. Such a multiplexed robust method provides a powerful tool for dissecting proteomic signatures at the systems level in a variety of complex samples, ranging from cell culture, animal tissues to human clinical specimens.
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Affiliation(s)
- B Bai
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - H Tan
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - V R Pagala
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - A A High
- St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - V P Ichhaporia
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - L Hendershot
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | - J Peng
- St. Jude Children's Research Hospital, Memphis, TN, United States; St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, TN, United States.
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41
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Angeleri M, Muth-Pawlak D, Aro EM, Battchikova N. Study of O-Phosphorylation Sites in Proteins Involved in Photosynthesis-Related Processes in Synechocystis sp. Strain PCC 6803: Application of the SRM Approach. J Proteome Res 2016; 15:4638-4652. [DOI: 10.1021/acs.jproteome.6b00732] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Martina Angeleri
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Dorota Muth-Pawlak
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Molecular Plant Biology,
Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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42
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Cutillas PR. Targeted In-Depth Quantification of Signaling Using Label-Free Mass Spectrometry. Methods Enzymol 2016; 585:245-268. [PMID: 28109432 DOI: 10.1016/bs.mie.2016.09.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein phosphorylation encodes information on the activity of kinase-driven signaling pathways that regulate cell biology. This chapter discusses an approach, named TIQUAS (targeted in-depth quantification of signaling), to quantify cell signaling comprehensively and without bias. The workflow-based on mass spectrometry (MS) and computational science-consists of targeting the analysis of phosphopeptides previously identified by shotgun liquid chromatography tandem MS (LC-MS/MS) across the samples that are being compared. TIQUAS therefore takes advantage of concepts derived from both targeted (data-independent) and data-dependent acquisition methods; phosphorylation sites are quantified in all experimental samples regardless of whether or not these phosphopeptides were identified by MS/MS in all runs. As a result, datasets are obtained containing quantitative information on several thousand phosphorylation sites in as many samples and replicates as required in the experimental design, and these rich datasets are devoid of a significant number of missing data points. This chapter discussed the biochemical, analytical, and computational procedures required to apply the approach and for obtaining a biological interpretation of the data in the context of our understanding of cell signaling regulation and kinase-substrate relationships.
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Affiliation(s)
- P R Cutillas
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, United Kingdom.
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43
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Kruse R, Højlund K. Mitochondrial phosphoproteomics of mammalian tissues. Mitochondrion 2016; 33:45-57. [PMID: 27521611 DOI: 10.1016/j.mito.2016.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 12/31/2022]
Abstract
Mitochondria are essential for several biological processes including energy metabolism and cell survival. Accordingly, impaired mitochondrial function is involved in a wide range of human pathologies including diabetes, cancer, cardiovascular, and neurodegenerative diseases. Within the past decade a growing body of evidence indicates that reversible phosphorylation plays an important role in the regulation of a variety of mitochondrial processes as well as tissue-specific mitochondrial functions in mammals. The rapidly increasing number of mitochondrial phosphorylation sites and phosphoproteins identified is largely ascribed to recent advances in phosphoproteomic technologies such as fractionation, phosphopeptide enrichment, and high-sensitivity mass spectrometry. However, the functional importance and the specific kinases and phosphatases involved have yet to be determined for the majority of these mitochondrial phosphorylation sites. This review summarizes the progress in establishing the mammalian mitochondrial phosphoproteome and the technical challenges encountered while characterizing it, with a particular focus on large-scale phosphoproteomic studies of mitochondria from human skeletal muscle.
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Affiliation(s)
- Rikke Kruse
- Department of Endocrinology, Odense University Hospital, DK-5000, Odense, Denmark; The Section of Molecular Diabetes & Metabolism, Department of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Kurt Højlund
- Department of Endocrinology, Odense University Hospital, DK-5000, Odense, Denmark; The Section of Molecular Diabetes & Metabolism, Department of Clinical Research and Institute of Molecular Medicine, University of Southern Denmark, DK-5000 Odense, Denmark.
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44
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von Stechow L, Francavilla C, Olsen JV. Recent findings and technological advances in phosphoproteomics for cells and tissues. Expert Rev Proteomics 2016; 12:469-87. [PMID: 26400465 PMCID: PMC4819829 DOI: 10.1586/14789450.2015.1078730] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.
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Affiliation(s)
- Louise von Stechow
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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45
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Leroy B, Gillet L, Vanderplasschen A, Wattiez R. Structural Proteomics of Herpesviruses. Viruses 2016; 8:v8020050. [PMID: 26907323 PMCID: PMC4776205 DOI: 10.3390/v8020050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/15/2016] [Accepted: 02/04/2016] [Indexed: 12/27/2022] Open
Abstract
Herpesviruses are highly prevalent viruses associated with numerous pathologies both in animal and human populations. Until now, most of the strategies used to prevent or to cure these infections have been unsuccessful because these viruses have developed numerous immune evasion mechanisms. Therefore, a better understanding of their complex lifecycle is needed. In particular, while the genome of numerous herpesviruses has been sequenced, the exact composition of virions remains unknown for most of them. Mass spectrometry has recently emerged as a central method and has permitted fundamental discoveries in virology. Here, we review mass spectrometry-based approaches that have recently allowed a better understanding of the composition of the herpesvirus virion. In particular, we describe strategies commonly used for proper sample preparation and fractionation to allow protein localization inside the particle but also to avoid contamination by nonstructural proteins. A collection of other important data regarding post-translational modifications or the relative abundance of structural proteins is also described. This review also discusses the poorly studied importance of host proteins in herpesvirus structural proteins and the necessity to develop a quantitative workflow to better understand the dynamics of the structural proteome. In the future, we hope that this collaborative effort will assist in the development of new strategies to fight these infections.
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Affiliation(s)
- Baptiste Leroy
- Laboratory of Proteomic and Microbiology, Research Institute of Biosciences, University of MONS, 4000 Mons, Belgium.
| | - Laurent Gillet
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium.
| | - Alain Vanderplasschen
- Immunology-Vaccinology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liege, 4000 Liege, Belgium.
| | - Ruddy Wattiez
- Laboratory of Proteomic and Microbiology, Research Institute of Biosciences, University of MONS, 4000 Mons, Belgium.
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46
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Phosphopeptide enrichment: Development of magnetic solid phase extraction method based on polydopamine coating and Ti4+-IMAC. Anal Chim Acta 2016; 909:67-74. [DOI: 10.1016/j.aca.2016.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/18/2015] [Accepted: 01/02/2016] [Indexed: 11/19/2022]
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47
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Champleboux M, Govin J. Bromodomains shake the hegemony of pan-acetyl antibodies. Proteomics 2016; 15:1457-8. [PMID: 25825234 PMCID: PMC4440388 DOI: 10.1002/pmic.201500116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 11/12/2022]
Abstract
Acetylation signaling pathways are involved in numerous cellular processes and are used as therapeutic targets in several disease contexts. However, acetylated proteins only represent a minor fraction of the full proteome, and the identification and quantification of acetylated sites remain a technological challenge. Currently, pan-acetyl antibodies are used to increase the abundance of acetylated peptides through affinity purification before MS analysis. These antibodies are powerful reagents, but they are hampered by a lack of specificity, affinity, and batch-to-batch reproducibility. In this issue, Bryson et al. (Proteomics 2015 15, 1470-1475) present an interesting alternative to these antibodies, in the form of bromodomains. These domains specifically recognize acetylated lysines, and were successfully used in this study to enrich for acetylated peptides before MS analysis. Future development of this pioneering approach could help overcome this limiting step in the characterization of acetylproteomes.
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Affiliation(s)
- Morgane Champleboux
- Institut National de la Recherche Médicale (Inserm), iRTSV-BGE, Grenoble, France; Université de Grenoble Alpes, iRTSV-BGE, Grenoble, France; Commissariat à l'Energie Atomique (CEA), iRTSV-BGE, Grenoble, France
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Abstract
The comprehensive study of the phosphoproteome is heavily dependent on appropriate enrichment strategies that are most often, but not exclusively, carried out on the peptide level. In this chapter, I give an overview of the most widely used techniques. In addition to dedicated antibodies, phosphopeptides are enriched by their selective interaction with metals in the form of chelated metal ions or metal oxides. The negative charge of the phosphate group is also exploited in a variety of chromatographic fractionation methods that include different types of ion exchange chromatography, hydrophilic interaction chromatography (HILIC), and electrostatic repulsion HILIC (ERLIC) chromatography. Selected examples from the literature will demonstrate how a combination of these techniques with current high-performance mass spectrometry enables the identification of thousands of phosphorylation sites from various sample types.
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Affiliation(s)
- Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Aasebø E, Forthun RB, Berven F, Selheim F, Hernandez-Valladares M. Global Cell Proteome Profiling, Phospho-signaling and Quantitative Proteomics for Identification of New Biomarkers in Acute Myeloid Leukemia Patients. Curr Pharm Biotechnol 2016; 17:52-70. [PMID: 26306748 PMCID: PMC5388801 DOI: 10.2174/1389201016666150826115626] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/29/2015] [Accepted: 07/23/2015] [Indexed: 12/31/2022]
Abstract
The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low resolution mass spectrometers. However, most of the studies did not follow up, confirm or validate their candidates with more patient samples. Current proteomics methods, new high resolution and fast mass spectrometers allow the identification and quantification of several thousands of proteins obtained from few tens of μg of AML cell lysate. Enrichment methods for posttranslational modifications (PTM), such as phosphorylation, can isolate several thousands of site-specific phosphorylated peptides from AML patient samples, which subsequently can be quantified with high confidence in new mass spectrometers. While recent reports aiming to propose proteomic or phosphoproteomic biomarkers on the studied AML patient samples have taken advantage of the technological progress, the access to large cohorts of AML patients to sample from and the availability of appropriate control samples still remain challenging.
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Affiliation(s)
| | | | | | | | - Maria Hernandez-Valladares
- Department of Biomedicine, Faculty of Medicine, Building for Basic Biology, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.
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