1
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Sun B, Liu Z, Liu J, Zhao S, Wang L, Wang F. The utility of proteases in proteomics, from sequence profiling to structure and function analysis. Proteomics 2023; 23:e2200132. [PMID: 36382392 DOI: 10.1002/pmic.202200132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
In mass spectrometry (MS)-based bottom-up proteomics, protease digestion plays an essential role in profiling both proteome sequences and post-translational modifications (PTMs). Trypsin is the gold standard in digesting intact proteins into small-size peptides, which are more suitable for high-performance liquid chromatography (HPLC) separation and tandem MS (MS/MS) characterization. However, protein sequences lacking Lys and Arg cannot be cleaved by trypsin and may be missed in conventional proteomic analysis. Proteases with cleavage sites complementary to trypsin are widely applied in proteomic analysis to greatly improve the coverage of proteome sequences and PTM sites. In this review, we survey the common and newly emerging proteases used in proteomics analysis mainly in the last 5 years, focusing on their unique cleavage features and specific proteomics applications such as missing protein characterization, new PTM discovery, and de novo sequencing. In addition, we summarize the applications of proteases in structural proteomics and protein function analysis in recent years. Finally, we discuss the future development directions of new proteases and applications in proteomics.
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Affiliation(s)
- Binwen Sun
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
- Engineering Technology Research Center for Translational Medicine, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
| | - Jin Liu
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Engineering Technology Research Center for Translational Medicine, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
| | - Liming Wang
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Engineering Technology Research Center for Translational Medicine, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
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2
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Luenenschloss A, Ter Veld F, Albaum SP, Neddermann TM, Wendisch VF, Poetsch A. Functional Genomics Uncovers Pleiotropic Role of Rhomboids in Corynebacterium glutamicum. Front Microbiol 2022; 13:771968. [PMID: 35265054 PMCID: PMC8899591 DOI: 10.3389/fmicb.2022.771968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
The physiological role of ubiquitous rhomboid proteases, membrane-integral proteins that cleave their substrates inside the lipid bilayer, is still ill-defined in many prokaryotes. The two rhomboid genes cg0049 and cg2767 of Corynebacterium glutamicum were mutated and it was the aim of this study to investigate consequences in respect to growth phenotype, stress resistance, transcriptome, proteome, and lipidome composition. Albeit increased amount of Cg2767 upon heat stress, its absence did not change the growth behavior of C. glutamicum during exponential and stationary phase. Quantitative shotgun mass spectrometry was used to compare the rhomboid mutant with wild type strain and revealed that proteins covering diverse cellular functions were differentially abundant with more proteins affected in the stationary than in the exponential growth phase. An observation common to both growth phases was a decrease in ribosomal subunits and RNA polymerase, differences in iron uptake proteins, and abundance changes in lipid and mycolic acid biosynthesis enzymes that suggested a functional link of rhomboids to cell envelope lipid biosynthesis. The latter was substantiated by shotgun lipidomics in the stationary growth phase, where in a strain-dependent manner phosphatidylglycerol, phosphatidic acid, diacylglycerol and phosphatidylinositol increased irrespective of cultivation temperature.
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Affiliation(s)
| | - Frank Ter Veld
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefan P Albaum
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias M Neddermann
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany.,Department of Marine Biology, Ocean University of China, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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3
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Sala V, Cnudde SJ, Murabito A, Massarotti A, Hirsch E, Ghigo A. Therapeutic peptides for the treatment of cystic fibrosis: Challenges and perspectives. Eur J Med Chem 2021; 213:113191. [PMID: 33493828 DOI: 10.1016/j.ejmech.2021.113191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/21/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
Cystic fibrosis (CF) is the most common amongst rare genetic diseases, affecting more than 70.000 people worldwide. CF is characterized by a dysfunctional chloride channel, termed cystic fibrosis conductance regulator (CFTR), which leads to the production of a thick and viscous mucus layer that clogs the lungs of CF patients and traps pathogens, leading to chronic infections and inflammation and, ultimately, lung damage. In recent years, the use of peptides for the treatment of respiratory diseases, including CF, has gained growing interest. Therapeutic peptides for CF include antimicrobial peptides, inhibitors of proteases, and modulators of ion channels, among others. Peptides display unique features that make them appealing candidates for clinical translation, like specificity of action, high efficacy, and low toxicity. Nevertheless, the intrinsic properties of peptides, together with the need of delivering these compounds locally, e.g. by inhalation, raise a number of concerns in the development of peptide therapeutics for CF lung disease. In this review, we discuss the challenges related to the use of peptides for the treatment of CF lung disease through inhalation, which include retention within mucus, proteolysis, immunogenicity and aggregation. Strategies for overcoming major shortcomings of peptide therapeutics will be presented, together with recent developments in peptide design and optimization, including computational analysis and high-throughput screening.
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Affiliation(s)
- Valentina Sala
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Sophie Julie Cnudde
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Alessandra Murabito
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy
| | - Alberto Massarotti
- Department of Pharmaceutical Science, University of Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100, Novara, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy; Kither Biotech S.r.l., Via Nizza 52, 10126, Torino, Italy
| | - Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126, Torino, Italy; Kither Biotech S.r.l., Via Nizza 52, 10126, Torino, Italy.
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4
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Sun B, Liu Z, Fang Z, Dong W, Yu Y, Ye M, Liu L, Wang H, Wang F. Probing the Proteomics Dark Regions by VAILase Cleavage at Aliphatic Amino Acids. Anal Chem 2020; 92:2770-2777. [PMID: 31903742 DOI: 10.1021/acs.analchem.9b05048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteomics emerges from the protein identification to protein functional elucidation, which depends to a large extent on the characterization of protein sequences. However, a large part of proteome sequences remains unannotated due to the limitation in proteolytic digestion by golden standard protease trypsin. Herein, we demonstrated that a cyanobacterial protease VAILase could specifically cleave at the short-chain aliphatic amino acids valine, alanine, leucine, isoleucine and threonine with cleavage specificity about 92% in total for proteomic analysis. The unique features of VAILase cleavage facilitate the characterization of most proteins and exhibit high complementarity to trypsin, and 22% of the covered sequences by VAILase are unique. VAILase can greatly improve the coverages of sequences with abundant aliphatic residues that are usually dark regions in conventional proteomic analysis, such as the transmembrane regions within anion exchanger 1 and photosystem II.
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Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China
| | - Zheng Fang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Wei Dong
- CAS Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , Beijing , 100049 , China
| | - Yang Yu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , 130022 , China.,University of Science and Technology of China , Hefei , 230026 , China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China
| | - Lin Liu
- CAS Key Laboratory of Photobiology , Institute of Botany, Chinese Academy of Sciences , Beijing , 100049 , China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun , 130022 , China.,University of Science and Technology of China , Hefei , 230026 , China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , 116023 , China.,University of Chinese Academy of Sciences , Beijing , 100049 , China
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5
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Dau T, Gupta K, Berger I, Rappsilber J. Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry. Anal Chem 2019; 91:4472-4478. [PMID: 30817130 PMCID: PMC6458965 DOI: 10.1021/acs.analchem.8b05222] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cross-linking mass spectrometry has become an important approach for studying protein structures and protein-protein interactions. The amino acid compositions of some protein regions impede the detection of cross-linked residues, although it would yield invaluable information for protein modeling. Here, we report on a sequential-digestion strategy with trypsin and elastase to penetrate regions with a low density of trypsin-cleavage sites. We exploited intrinsic substrate-recognition properties of elastase to specifically target larger tryptic peptides. Our application of this protocol to the TAF4-12 complex allowed us to identify cross-links in previously inaccessible regions.
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Affiliation(s)
- Therese Dau
- Wellcome
Centre for Cell Biology, Institute of Cell Biology, School of Biological
Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Kapil Gupta
- BrisSynBio
Centre, The School of Biochemistry, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Imre Berger
- BrisSynBio
Centre, The School of Biochemistry, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Juri Rappsilber
- Wellcome
Centre for Cell Biology, Institute of Cell Biology, School of Biological
Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom,Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany,E-mail: or
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6
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Schräder CU, Heinz A, Majovsky P, Karaman Mayack B, Brinckmann J, Sippl W, Schmelzer CEH. Elastin is heterogeneously cross-linked. J Biol Chem 2018; 293:15107-15119. [PMID: 30108173 DOI: 10.1074/jbc.ra118.004322] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/12/2018] [Indexed: 01/30/2023] Open
Abstract
Elastin is an essential vertebrate protein responsible for the elasticity of force-bearing tissues such as those of the lungs, blood vessels, and skin. One of the key features required for the exceptional properties of this durable biopolymer is the extensive covalent cross-linking between domains of its monomer molecule tropoelastin. To date, elastin's exact molecular assembly and mechanical properties are poorly understood. Here, using bovine elastin, we investigated the different types of cross-links in mature elastin to gain insight into its structure. We purified and proteolytically cleaved elastin from a single tissue sample into soluble cross-linked and noncross-linked peptides that we studied by high-resolution MS. This analysis enabled the elucidation of cross-links and other elastin modifications. We found that the lysine residues within the tropoelastin sequence were simultaneously unmodified and involved in various types of cross-links with different other domains. The Lys-Pro domains were almost exclusively linked via lysinonorleucine, whereas Lys-Ala domains were found to be cross-linked via lysinonorleucine, allysine aldol, and desmosine. Unexpectedly, we identified a high number of intramolecular cross-links between lysine residues in close proximity. In summary, we show on the molecular level that elastin formation involves random cross-linking of tropoelastin monomers resulting in an unordered network, an unexpected finding compared with previous assumptions of an overall beaded structure.
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Affiliation(s)
- Christoph U Schräder
- From the Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Andrea Heinz
- From the Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany.,the Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
| | - Petra Majovsky
- the Proteome Analytics Research Group, Leibniz Institute for Plant Biochemistry, Halle (Saale) 06120, Germany
| | - Berin Karaman Mayack
- From the Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Jürgen Brinckmann
- the Institute of Virology and Cell Biology, Department of Dermatology, University of Lübeck, Lübeck 23538, Germany, and
| | - Wolfgang Sippl
- From the Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Christian E H Schmelzer
- From the Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany, .,the Fraunhofer Institute for Microstructure of Materials and Systems IMWS, Halle (Saale) 06120, Germany
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7
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Witzel K, Matros A, Møller ALB, Ramireddy E, Finnie C, Peukert M, Rutten T, Herzog A, Kunze G, Melzer M, Kaspar-Schoenefeld S, Schmülling T, Svensson B, Mock HP. Plasma membrane proteome analysis identifies a role of barley membrane steroid binding protein in root architecture response to salinity. PLANT, CELL & ENVIRONMENT 2018; 41:1311-1330. [PMID: 29385242 DOI: 10.1111/pce.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
Although the physiological consequences of plant growth under saline conditions have been well described, understanding the core mechanisms conferring plant salt adaptation has only started. We target the root plasma membrane proteomes of two barley varieties, cvs. Steptoe and Morex, with contrasting salinity tolerance. In total, 588 plasma membrane proteins were identified by mass spectrometry, of which 182 were either cultivar or salinity stress responsive. Three candidate proteins with increased abundance in the tolerant cv. Morex were involved either in sterol binding (a GTPase-activating protein for the adenosine diphosphate ribosylation factor [ZIGA2], and a membrane steroid binding protein [MSBP]) or in phospholipid synthesis (phosphoethanolamine methyltransferase [PEAMT]). Overexpression of barley MSBP conferred salinity tolerance to yeast cells, whereas the knock-out of the heterologous AtMSBP1 increased salt sensitivity in Arabidopsis. Atmsbp1 plants showed a reduced number of lateral roots under salinity, and root-tip-specific expression of barley MSBP in Atmsbp1 complemented this phenotype. In barley, an increased abundance of MSBP correlates with reduced root length and lateral root formation as well as increased levels of auxin under salinity being stronger in the tolerant cv. Morex. Hence, we concluded the involvement of MSBP in phytohormone-directed adaptation of root architecture in response to salinity.
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Affiliation(s)
- Katja Witzel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
| | - Andrea Matros
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Anders L B Møller
- Technical University of Denmark, Søltofts Plads, Building 224, 2800, Kongens Lyngby, Denmark
| | - Eswarayya Ramireddy
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Free University of Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Christine Finnie
- Technical University of Denmark, Søltofts Plads, Building 224, 2800, Kongens Lyngby, Denmark
| | - Manuela Peukert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Andreas Herzog
- Biosystems Engineering, Fraunhofer Institute for Factory Operation and Automation, Joseph-von-Fraunhofer-Straße 1, 39106, Magdeburg, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Stephanie Kaspar-Schoenefeld
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Sciences, Free University of Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Birte Svensson
- Technical University of Denmark, Søltofts Plads, Building 224, 2800, Kongens Lyngby, Denmark
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Stadt Seeland, Gatersleben, Germany
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8
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Eckersley A, Mellody KT, Pilkington S, Griffiths CEM, Watson REB, O'Cualain R, Baldock C, Knight D, Sherratt MJ. Structural and compositional diversity of fibrillin microfibrils in human tissues. J Biol Chem 2018; 293:5117-5133. [PMID: 29453284 PMCID: PMC5892578 DOI: 10.1074/jbc.ra117.001483] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/07/2018] [Indexed: 12/11/2022] Open
Abstract
Elastic fibers comprising fibrillin microfibrils and elastin are present in many tissues, including the skin, lungs, and arteries, where they confer elasticity and resilience. Although fibrillin microfibrils play distinct and tissue-specific functional roles, it is unclear whether their ultrastructure and composition differ between elastin-rich (skin) and elastin-poor (ciliary body and zonule) organs or after in vitro synthesis by cultured cells. Here, we used atomic force microscopy, which revealed that the bead morphology of fibrillin microfibrils isolated from the human eye differs from those isolated from the skin. Using newly developed pre-MS preparation methods and LC-MS/MS, we detected tissue-specific regions of the fibrillin-1 primary structure that were differentially susceptible to proteolytic extraction. Comparing tissue- and culture-derived microfibrils, we found that dermis- and dermal fibroblast–derived fibrillin microfibrils differ in both bead morphology and periodicity and also exhibit regional differences in fibrillin-1 proteolytic susceptibility. In contrast, collagen VI microfibrils from the same dermal or fibroblast samples were invariant in ultrastructure (periodicity) and protease susceptibility. Finally, we observed that skin- and eye-derived microfibril suspensions were enriched in elastic fiber– and basement membrane–associated proteins, respectively. LC-MS/MS also identified proteins (such as calreticulin and protein-disulfide isomerase) that are potentially fundamental to fibrillin microfibril biology, regardless of their tissue source. Fibrillin microfibrils synthesized in cell culture lacked some of these key proteins (MFAP2 and -4 and fibrillin-2). These results showcase the structural diversity of these key extracellular matrix assemblies, which may relate to their distinct roles in the tissues where they reside.
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Affiliation(s)
| | - Kieran T Mellody
- From the Division of Cell Matrix Biology and Regenerative Medicine
| | | | - Christopher E M Griffiths
- the Division of Musculoskeletal and Dermatological Sciences.,the NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PT, United Kingdom
| | - Rachel E B Watson
- the Division of Musculoskeletal and Dermatological Sciences.,the NIHR Manchester Biomedical Research Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9PT, United Kingdom
| | | | - Clair Baldock
- From the Division of Cell Matrix Biology and Regenerative Medicine.,the Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom and
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9
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Maus A, Mignon R, Basile F. Enhanced protein identification using graphite-modified MALDI plates for offline LC-MALDI-MS/MS bottom-up proteomics. Anal Biochem 2018; 545:31-37. [PMID: 29326070 DOI: 10.1016/j.ab.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
The use of offline liquid chromatography-matrix assisted laser desorption/ionization (LC-MALDI) tandem mass spectrometry (MS/MS) for bottom-up proteomics offers advantages in terms of cost, ease of use, and the time-decoupled nature of the separation step and the mass analysis. A method was developed to improve the capabilities of LC-MALDI-MS/MS in terms of protein identification in a bottom-up proteomic workflow. Enhanced protein identification is achieved by an increase in the MALDI signal intensity of the precursor peptides brought about by coating the MALDI plate with a thin film of graphite powder. Using the Escherichia coli proteome, it is demonstrated that the graphite-modified MALDI plates used in an offline LC-MALDI-MS/MS bottom-up protocol led to a 50-135% increase in the number of peptide identifications, and a concomitant 21%-105% increase in the number of proteins inferred. We identify factors that lead to improvements in peptide sequence identifications and in the number of unique proteins identified when compared to using an unmodified MALDI plate. These improvements are achieved using a low cost approach that it is easy to implement, requires no hardware/protocol modification, it is compatible with LC and adds no additional analysis time.
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Affiliation(s)
- Anthony Maus
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States
| | - Rudolph Mignon
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States
| | - Franco Basile
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82072, United States.
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10
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Gonczarowska-Jorge H, Loroch S, Dell'Aica M, Sickmann A, Roos A, Zahedi RP. Quantifying Missing (Phospho)Proteome Regions with the Broad-Specificity Protease Subtilisin. Anal Chem 2017; 89:13137-13145. [PMID: 29136377 DOI: 10.1021/acs.analchem.7b02395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Despite huge efforts to map the human proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%. Reasons for missing areas of the proteome comprise protease-resistant domains including the lack/excess of enzymatic cleavage sites, nonunique peptide sequences, impaired peptide ionization/separation and low expression levels. To access novel areas of the proteome the beneficial use of enzymes complementary to trypsin, such as Glu-C, Asp-N, Lys-N, Arg-C, LysargiNase has been reported. Here, we present how the broad-specificity protease subtilisin enables mapping of previously hidden areas of the proteome. We systematically evaluated its digestion efficiency and reproducibility and compared it to the gold standard in the field, trypsin. Notably, subtilisin allows reproducible near-complete digestion of cells lysates in 1-5 min. As expected from its broad specificity the generation of overlapping peptide sequences reduces the number of identified proteins compared to trypsin (8363 vs 6807; 1% protein FDR). However, subtilisin considerably improved the coverage of missing and particularly proline-rich areas of the proteome. Along 14 628 high confidence phosphorylation sites identified in total, only 33% were shared between both enzymes, while 37% were exclusive to subtilisin. Notably, 926 of these were not even accessible by additional in silico digestion with either Asp-N, Arg-C, Glu-C, Lys-C, or Lys-N. Thus, subtilisin might be particularly beneficial for system-wide profiling of post-translational modification sites. Finally, we demonstrate that subtilisin can be used for reporter-ion based in-depth quantification, providing a precision comparable to trypsin-despite broad specificity and fast digestion that may increase technical variance.
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Affiliation(s)
- Humberto Gonczarowska-Jorge
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,CAPES Foundation, Ministry of Education of Brazil, Brasília Distrito Federal 70040-020, Brazil
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany
| | - Margherita Dell'Aica
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen , Aberdeen, AB24 3FX, United Kingdom
| | - Andreas Roos
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Newcastle University , Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University , Montreal, Quebec H4A 3T2, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal, Quebec H3T 1E2, Canada
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11
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Schräder CU, Lee L, Rey M, Sarpe V, Man P, Sharma S, Zabrouskov V, Larsen B, Schriemer DC. Neprosin, a Selective Prolyl Endoprotease for Bottom-up Proteomics and Histone Mapping. Mol Cell Proteomics 2017; 16:1162-1171. [PMID: 28404794 DOI: 10.1074/mcp.m116.066803] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/07/2017] [Indexed: 01/10/2023] Open
Abstract
Trypsin dominates bottom-up proteomics, but there are reasons to consider alternative enzymes. Improving sequence coverage, exposing proteomic "dark matter," and clustering post-translational modifications in different ways and with higher-order drive the pursuit of reagents complementary to trypsin. Additionally, enzymes that are easy to use and generate larger peptides that capitalize upon newer fragmentation technologies should have a place in proteomics. We expressed and characterized recombinant neprosin, a novel prolyl endoprotease of the DUF239 family, which preferentially cleaves C-terminal to proline residues under highly acidic conditions. Cleavage also occurs C-terminal to alanine with some frequency, but with an intriguingly high "skipping rate." Digestion proceeds to a stable end point, resulting in an average peptide mass of 2521 units and a higher dependence upon electron-transfer dissociation for peptide-spectrum matches. In contrast to most proline-cleaving enzymes, neprosin effectively degrades proteins of any size. For 1251 HeLa cell proteins identified in common using trypsin, Lys-C, and neprosin, almost 50% of the neprosin sequence contribution is unique. The high average peptide mass coupled with cleavage at residues not usually modified provide new opportunities for profiling clusters of post-translational modifications. We show that neprosin is a useful reagent for reading epigenetic marks on histones. It generates peptide 1-38 of histone H3 and peptide 1-32 of histone H4 in a single digest, permitting the analysis of co-occurring post-translational modifications in these important N-terminal tails.
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Affiliation(s)
- Christoph U Schräder
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Linda Lee
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Martial Rey
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Vladimir Sarpe
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Petr Man
- §BioCev-Institute of Microbiology, Czech Academy of Sciences, Vestec, Czech Republic 117 20.,¶Department of Biochemistry, Faculty of Science, Charles University in Prague, Prague, Czech Republic 116 36
| | - Seema Sharma
- ‖Thermo Fisher Scientific, San Jose, California 95134
| | | | - Brett Larsen
- **Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada M5G 1X5; and
| | - David C Schriemer
- From the ‡Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N4N1, Canada; .,‡‡Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N 4N1
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12
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Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R. Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis. J Proteome Res 2017; 16:1288-1299. [PMID: 28164708 PMCID: PMC5363888 DOI: 10.1021/acs.jproteome.6b00915] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ∼8000-10 000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multienzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth by employing a workflow that addresses current limitations in deep proteome analysis in multiple stages: We used (i) gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, (ii) concatenated high-pH prefractionation, and (iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion (Lumos) mass spectrometer, to achieve 57% median protein sequence coverage in 13 728 protein groups (8949 Unigene IDs) in a single cell line. CHOPIN allows the use of both detectors in the Orbitrap on predefined precursor types that optimizes parallel ion processing, leading to the identification of a total of 179 549 unique peptides covering the deep proteome in unprecedented detail.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Lin He
- Bioinformatics Solutions, Inc. , 470 Weber Street North Suite 204, Waterloo, Ontario N2L 6J2, Canada
| | - Peter Mowlds
- Thermo Fisher, Inc. , Stafford House, 1 Boundary Park, Hemel Hampstead HP2 7GE, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, United Kingdom
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13
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Issa H, Huc-Claustre E, Reddad T, Bonadé Bottino N, Tropis M, Houssin C, Daffé M, Bayan N, Dautin N. Click-chemistry approach to study mycoloylated proteins: Evidence for PorB and PorC porins mycoloylation in Corynebacterium glutamicum. PLoS One 2017; 12:e0171955. [PMID: 28199365 PMCID: PMC5310785 DOI: 10.1371/journal.pone.0171955] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/27/2017] [Indexed: 01/23/2023] Open
Abstract
Protein mycoloylation is a recently identified, new form of protein acylation. This post-translational modification consists in the covalent attachment of mycolic acids residues to serine. Mycolic acids are long chain, α-branched, β-hydroxylated fatty acids that are exclusively found in the cell envelope of Corynebacteriales, a bacterial order that includes important genera such as Mycobacterium, Nocardia or Corynebacterium. So far, only 3 mycoloylated proteins have been identified: PorA, PorH and ProtX from C. glutamicum. Whereas the identity and function of ProtX is unknown, PorH and PorA associate to form a membrane channel, the activity of which is dependent upon PorA mycoloylation. However, the exact role of mycoloylation and the generality of this phenomenon are still unknown. In particular, the identity of other mycoloylated proteins, if any, needs to be determined together with establishing whether such modification occurs in Corynebacteriales genera other than Corynebacterium. Here, we tested whether a metabolic labeling and click-chemistry approach could be used to detect mycoloylated proteins. Using a fatty acid alkyne analogue, we could indeed label PorA, PorH and ProtX and determine ProtX mycoloylation site. Importantly, we also show that two other porins from C. glutamicum, PorB and PorC are mycoloylated.
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Affiliation(s)
- Hanane Issa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
- Holy Spirit University of Kaslik (USEK), Jounieh, Mount Lebanon, Lebanon
| | | | - Thamila Reddad
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nolwenn Bonadé Bottino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maryelle Tropis
- Institute of Pharmacology and Structural Biology (IPBS), UMR 5089, France
| | - Christine Houssin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mamadou Daffé
- Institute of Pharmacology and Structural Biology (IPBS), UMR 5089, France
| | - Nicolas Bayan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nathalie Dautin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
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14
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Seligmann H. Natural mitochondrial proteolysis confirms transcription systematically exchanging/deleting nucleotides, peptides coded by expanded codons. J Theor Biol 2016; 414:76-90. [PMID: 27899286 DOI: 10.1016/j.jtbi.2016.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022]
Abstract
Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-, tetra- and pentacodons, and (b) deleting mono-, dinucleotides after each trinucleotide (delRNAs). Here analyses of two independent proteomic datasets considering natural proteolysis confirm independently translation of these non-canonical RNAs, also along tetra- and pentacodons, increasing coverage of putative, cryptically encoded proteins. Analyses assuming endoproteinase GluC and elastase digestions (cleavages after residues D, E, and A, L, I, V, respectively) detect additional peptides colocalizing with detected non-canonical RNAs. Analyses detect fewer peptides matching GluC-, elastase- than trypsin-digestions: artificial trypsin-digestion outweighs natural proteolysis. Results suggest occurrences of complete proteins entirely matching non-canonical, superimposed encoding(s). Protein-coding after bijective transformations could explain genetic code symmetries, such as along Rumer's transformation.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, IHU (Institut Hospitalo-Universitaire), Aix-Marseille University, Marseille, France.
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15
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Losensky G, Jung K, Urlaub H, Pfeifer F, Fröls S, Lenz C. Shedding light on biofilm formation ofHalobacterium salinarumR1 by SWATH-LC/MS/MS analysis of planktonic and sessile cells. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/30/2016] [Accepted: 09/05/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Gerald Losensky
- Microbiology and Archaea; Department of Biology; Technische Universität Darmstadt; Darmstadt Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics; University of Veterinary Medicine Foundation; Hannover Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group; Max Planck Institute for Biophysical Chemistry; Göttingen Germany
- Institute of Clinical Chemistry; Bioanalytics; University Medical Center Göttingen; Göttingen Germany
| | - Felicitas Pfeifer
- Microbiology and Archaea; Department of Biology; Technische Universität Darmstadt; Darmstadt Germany
| | - Sabrina Fröls
- Microbiology and Archaea; Department of Biology; Technische Universität Darmstadt; Darmstadt Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group; Max Planck Institute for Biophysical Chemistry; Göttingen Germany
- Institute of Clinical Chemistry; Bioanalytics; University Medical Center Göttingen; Göttingen Germany
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16
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Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations. Comput Struct Biotechnol J 2016; 14:391-403. [PMID: 27830053 PMCID: PMC5094600 DOI: 10.1016/j.csbj.2016.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 01/14/2023] Open
Abstract
Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.
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17
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Li S, Dabir A, Misal SA, Tang H, Radivojac P, Reilly JP. Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics. J Proteome Res 2016; 15:3656-3665. [PMID: 27615690 DOI: 10.1021/acs.jproteome.6b00468] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Peptide amidination labeling using S-methyl thioacetimidate (SMTA) is investigated in an attempt to increase the number and types of peptides that can be detected in a bottom-up proteomics experiment. This derivatization method affects the basicity of lysine residues and is shown here to significantly impact the idiosyncracies of peptide fragmentation and peptide detectability. The unique and highly reproducible fragmentation properties of SMTA-labeled peptides, such as the strong propensity for forming b1 fragment ions, can be further exploited to modify the scoring of peptide-spectrum pairs and improve peptide identification. To this end, we have developed a supervised postprocessing algorithm to exploit these characteristics of peptides labeled by SMTA. Our experiments show that although the overall number of identifications are similar, the SMTA modification enabled the detection of 16-26% peptides not previously observed in comparable CID/HCD tandem mass spectrometry experiments without SMTA labeling.
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Affiliation(s)
- Sujun Li
- School of Informatics and Computing, Indiana University , Bloomington, Indiana 47405, United States
| | - Aditi Dabir
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Santosh A Misal
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Haixu Tang
- School of Informatics and Computing, Indiana University , Bloomington, Indiana 47405, United States
| | - Predrag Radivojac
- School of Informatics and Computing, Indiana University , Bloomington, Indiana 47405, United States
| | - James P Reilly
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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18
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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19
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Seligmann H. Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations. Biosystems 2016; 147:78-93. [PMID: 27477600 DOI: 10.1016/j.biosystems.2016.07.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 07/15/2016] [Accepted: 07/26/2016] [Indexed: 12/22/2022]
Abstract
Mass spectra of human mitochondrial peptides match non-canonical transcripts systematically (a) deleting mono/dinucleotides after trinucleotides (delRNA), (b) exchanging nucleotides (swinger RNA), translated according to tri, (c) tetra- and pentacodons (codons expanded by a 4th (and 5th) silent nucleotide(s)). Swinger transcriptions are 23 bijective transformations, nine symmetric (X<->Y, e.g. A<->C) and fourteen asymmetric exchanges (X->Y->Z->X, e.g. A->C->G->A). Here, proteomic analyses assuming cleavage after W,Y, F (chymotrypsin-like, for trypsinized samples) detect fewer chymotrypsinized than trypsinized peptides. Detected non-canonical peptides map preferentially on detected non-canonical RNAs for chymotrypsinized peptides, as previously found for trypsinized peptides. This suggests residual natural chymotrypsin-like digestion detectable within experimentally trypsinized peptide data. Some trypsinized peptides are detected twice, by analyses assuming trypsin, and those assuming chymotrypsin cleavages. They have higher spectra counts than peptides detected only once, meaning that abundant peptides are more frequently detected, but detection certainties resemble those for peptides detected only once. Analyses assuming 'incorrect' digestions are inadequate negative controls for digestion enzymes naturally active in biological samples. Chymotrypsin-analyses confirm non-canonical transcriptions/translations independently of results obtained assuming trypsinization, increase non-canonical peptidome coverage, indicating mitogenome-encoding of yet undetected proteins.
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, Université d'Aix-Marseille, URMITE CNRS-IRD 198 UMER 6236, Marseille, France.
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20
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Liu Y, Yan G, Gao M, Deng C, Zhang X. Membrane protein isolation and identification by covalent binding for proteome research. Proteomics 2015; 15:3892-900. [DOI: 10.1002/pmic.201400572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 08/21/2015] [Accepted: 09/11/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Yiying Liu
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Mingxia Gao
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Chunhui Deng
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Xiangmin Zhang
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
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21
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Tsiatsiani L, Heck AJR. Proteomics beyond trypsin. FEBS J 2015; 282:2612-26. [PMID: 25823410 DOI: 10.1111/febs.13287] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/13/2022]
Abstract
Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome.
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Affiliation(s)
- Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
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22
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Heijs B, Carreira RJ, Tolner EA, de Ru AH, van den Maagdenberg AMJM, van Veelen PA, McDonnell LA. Comprehensive Analysis of the Mouse Brain Proteome Sampled in Mass Spectrometry Imaging. Anal Chem 2015; 87:1867-75. [DOI: 10.1021/ac503952q] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Ricardo J. Carreira
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Else A. Tolner
- Department
of Neurology, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Arnoud H. de Ru
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Arn M. J. M. van den Maagdenberg
- Department
of Neurology, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
- Department
of Human Genetics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Peter A. van Veelen
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
| | - Liam A. McDonnell
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, 2333ZA The Netherlands
- Fondazione Pisana
per la Scienza ONLUS, Pisa, 56121 Italy
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23
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Long Y, Wood TD. Immobilized pepsin microreactor for rapid peptide mapping with nanoelectrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:194-197. [PMID: 25374334 DOI: 10.1007/s13361-014-1015-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 06/04/2023]
Abstract
Most enzymatic microreactors for protein digestion are based on trypsin, but proteins with hydrophobic segments may be difficult to digest because of the paucity of Arg and Lys residues. Microreactors based on pepsin, which is less specific than trypsin, can overcome this challenge. Here, an integrated immobilized pepsin microreactor (IPMR)/nanoelectrospray emitter is examined for its potential for peptide mapping. For myoglobin, equivalent sequence coverage is obtained in a thousandth the time of solution digestion with better sequence coverage. While sequence coverage of cytochrome c is lesser than solution in this short duration, more highly-charged peptic peptides are produced and a number of peaks are unidentified at low-resolution, suggesting that high-resolution mass spectrometry is needed to take full advantage of integrated IPMR/nanoelectrospray devices.
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Affiliation(s)
- Ying Long
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA
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24
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Laßek M, Weingarten J, Volknandt W. The synaptic proteome. Cell Tissue Res 2014; 359:255-65. [PMID: 25038742 DOI: 10.1007/s00441-014-1943-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/04/2014] [Indexed: 11/29/2022]
Abstract
Synapses are focal hot spots for signal transduction and plasticity in the brain. A synapse comprises an axon terminus, the presynapse, the synaptic cleft containing extracellular matrix proteins as well as adhesion molecules, and the postsynaptic density as target structure for chemical signaling. The proteomes of the presynaptic and postsynaptic active zones control neurotransmitter release and perception. These tasks demand short- and long-term structural and functional dynamics of the synapse mediated by its proteinaceous inventory. This review addresses subcellular fractionation protocols and the related proteomic approaches to the various synaptic subcompartments with an emphasis on the presynaptic active zone (PAZ). Furthermore, it discusses major constituents of the PAZ including the amyloid precursor protein family members. Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the pre- and postsynapse. The identification of protein candidates of the synapse provides the basis for further analyzing the interaction of synaptic proteins with their targets, and the effect of their deletion opens novel insights into the functional role of these proteins in neuronal communication. The knowledge of the molecular interactome is also a prerequisite for understanding numerous neurodegenerative diseases.
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Affiliation(s)
- Melanie Laßek
- Molecular and Cellular Neurobiology, Goethe University, Frankfurt, Germany
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Laßek M, Weingarten J, Volknandt W. The Proteome of the Murine Presynaptic Active Zone. Proteomes 2014; 2:243-257. [PMID: 28250380 PMCID: PMC5302740 DOI: 10.3390/proteomes2020243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/09/2014] [Accepted: 04/21/2014] [Indexed: 01/09/2023] Open
Abstract
The proteome of the presynaptic active zone controls neurotransmitter release and the short- and long-term structural and functional dynamics of the nerve terminal. The proteinaceous inventory of the presynaptic active zone has recently been reported. This review will evaluate the subcellular fractionation protocols and the proteomic approaches employed. A breakthrough for the identification of the proteome of the presynaptic active zone was the successful employment of antibodies directed against a cytosolic epitope of membrane integral synaptic vesicle proteins for the immunopurification of synaptic vesicles docked to the presynaptic plasma membrane. Combining immunopurification and subsequent analytical mass spectrometry, hundreds of proteins, including synaptic vesicle proteins, components of the presynaptic fusion and retrieval machinery, proteins involved in intracellular and extracellular signaling and a large variety of adhesion molecules, were identified. Numerous proteins regulating the rearrangement of the cytoskeleton are indicative of the functional and structural dynamics of the presynapse. This review will critically discuss both the experimental approaches and prominent protein candidates identified. Many proteins have not previously been assigned to the presynaptic release sites and may be directly involved in the short- and long-term structural modulation of the presynaptic compartment. The identification of proteinaceous constituents of the presynaptic active zone provides the basis for further analyzing the interaction of presynaptic proteins with their targets and opens novel insights into the functional role of these proteins in neuronal communication.
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Affiliation(s)
- Melanie Laßek
- Institute for Cell Biology and Neuroscience, Department Molecular and Cellular Neurobiology, Max von Laue Str. 13, 60438 Frankfurt am Main, Germany.
| | - Jens Weingarten
- Institute for Cell Biology and Neuroscience, Department Molecular and Cellular Neurobiology, Max von Laue Str. 13, 60438 Frankfurt am Main, Germany.
| | - Walter Volknandt
- Institute for Cell Biology and Neuroscience, Department Molecular and Cellular Neurobiology, Max von Laue Str. 13, 60438 Frankfurt am Main, Germany.
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Meyer JG. In Silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage. ISRN COMPUTATIONAL BIOLOGY 2014; 2014:960902. [PMID: 30687733 PMCID: PMC6347401 DOI: 10.1155/2014/960902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the postgenome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome is digested into peptides that are identified followed by protein inference. Despite continuous improvements to all steps of the shotgun proteomics workflow, observed proteome coverage is often low; some proteins are identified by a single peptide sequence. Complete proteome sequence coverage would allow comprehensive characterization of RNA splicing variants and all posttranslational modifications, which would drastically improve the accuracy of biological models. There are many reasons for the sequence coverage deficit, but ultimately peptide length determines sequence observability. Peptides that are too short are lost because they match many protein sequences and their true origin is ambiguous. The maximum observable peptide length is determined by several analytical challenges. This paper explores computationally how peptide lengths produced from several common proteome digestion methods limit observable proteome coverage. Iterative proteome cleavage strategies are also explored. These simulations reveal that maximized proteome coverage can be achieved by use of an iterative digestion protocol involving multiple proteases and chemical cleavages that theoretically allow 92.9% proteome coverage.
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Affiliation(s)
- Jesse G Meyer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
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27
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Guo X, Trudgian DC, Lemoff A, Yadavalli S, Mirzaei H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Mol Cell Proteomics 2014; 13:1573-84. [PMID: 24696503 DOI: 10.1074/mcp.m113.035170] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bottom-up proteomics largely relies on tryptic peptides for protein identification and quantification. Tryptic digestion often provides limited coverage of protein sequence because of issues such as peptide length, ionization efficiency, and post-translational modification colocalization. Unfortunately, a region of interest in a protein, for example, because of proximity to an active site or the presence of important post-translational modifications, may not be covered by tryptic peptides. Detection limits, quantification accuracy, and isoform differentiation can also be improved with greater sequence coverage. Selected reaction monitoring (SRM) would also greatly benefit from being able to identify additional targetable sequences. In an attempt to improve protein sequence coverage and to target regions of proteins that do not generate useful tryptic peptides, we deployed a multiprotease strategy on the HeLa proteome. First, we used seven commercially available enzymes in single, double, and triple enzyme combinations. A total of 48 digests were performed. 5223 proteins were detected by analyzing the unfractionated cell lysate digest directly; with 42% mean sequence coverage. Additional strong-anion exchange fractionation of the most complementary digests permitted identification of over 3000 more proteins, with improved mean sequence coverage. We then constructed a web application (https://proteomics.swmed.edu/confetti) that allows the community to examine a target protein or protein isoform in order to discover the enzyme or combination of enzymes that would yield peptides spanning a certain region of interest in the sequence. Finally, we examined the use of nontryptic digests for SRM. From our strong-anion exchange fractionation data, we were able to identify three or more proteotypic SRM candidates within a single digest for 6056 genes. Surprisingly, in 25% of these cases the digest producing the most observable proteotypic peptides was neither trypsin nor Lys-C. SRM analysis of Asp-N versus tryptic peptides for eight proteins determined that Asp-N yielded higher signal in five of eight cases.
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Affiliation(s)
- Xiaofeng Guo
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
| | - David C Trudgian
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Andrew Lemoff
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
| | | | - Hamid Mirzaei
- From the ‡Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390
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28
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Meyer JG, Kim S, Maltby DA, Ghassemian M, Bandeira N, Komives EA. Expanding proteome coverage with orthogonal-specificity α-lytic proteases. Mol Cell Proteomics 2014; 13:823-35. [PMID: 24425750 DOI: 10.1074/mcp.m113.034710] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bottom-up proteomics studies traditionally involve proteome digestion with a single protease, trypsin. However, trypsin alone does not generate peptides that encompass the entire proteome. Alternative proteases have been explored, but most have specificity for charged amino acid side chains. Therefore, additional proteases that improve proteome coverage through cleavage at sequences complementary to trypsin's may increase proteome coverage. We demonstrate the novel application of two proteases for bottom-up proteomics: wild type α-lytic protease (WaLP) and an active site mutant of WaLP, M190A α-lytic protease (MaLP). We assess several relevant factors, including MS/MS fragmentation, peptide length, peptide yield, and protease specificity. When data from separate digestions with trypsin, LysC, WaLP, and MaLP were combined, proteome coverage was increased by 101% relative to that achieved with trypsin digestion alone. To demonstrate how the gained sequence coverage can yield additional post-translational modification information, we show the identification of a number of novel phosphorylation sites in the Schizosaccharomyces pombe proteome and include an illustrative example from the protein MPD2 wherein two novel sites are identified, one in a tryptic peptide too short to identify and the other in a sequence devoid of tryptic sites. The specificity of WaLP and MaLP for aliphatic amino acid side chains was particularly valuable for coverage of membrane protein sequences, which increased 350% when the data from trypsin, LysC, WaLP, and MaLP were combined.
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Affiliation(s)
- Jesse G Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr., La Jolla, California 92093-0378
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29
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Silva AMN, Vitorino R, Domingues MRM, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med 2013; 65:925-941. [PMID: 24002012 DOI: 10.1016/j.freeradbiomed.2013.08.184] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 12/14/2022]
Abstract
In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.
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Affiliation(s)
- André M N Silva
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7 ET, United Kingdom
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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30
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Optimized proteomic analysis of rat liver microsomes using dual enzyme digestion with 2D-LC–MS/MS. J Proteomics 2013; 82:166-78. [DOI: 10.1016/j.jprot.2013.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/24/2013] [Accepted: 02/08/2013] [Indexed: 12/23/2022]
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31
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Simm S, Papasotiriou DG, Ibrahim M, Leisegang MS, Müller B, Schorge T, Karas M, Mirus O, Sommer MS, Schleiff E. Defining the core proteome of the chloroplast envelope membranes. FRONTIERS IN PLANT SCIENCE 2013; 4:11. [PMID: 23390424 PMCID: PMC3565376 DOI: 10.3389/fpls.2013.00011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/15/2013] [Indexed: 05/20/2023]
Abstract
High-throughput protein localization studies require multiple strategies. Mass spectrometric analysis of defined cellular fractions is one of the complementary approaches to a diverse array of cell biological methods. In recent years, the protein content of different cellular (sub-)compartments was approached. Despite of all the efforts made, the analysis of membrane fractions remains difficult, in that the dissection of the proteomes of the envelope membranes of chloroplasts or mitochondria is often not reliable because sample purity is not always warranted. Moreover, proteomic studies are often restricted to single (model) species, and therefore limited in respect to differential individual evolution. In this study we analyzed the chloroplast envelope proteomes of different plant species, namely, the individual proteomes of inner and outer envelope (OE) membrane of Pisum sativum and the mixed envelope proteomes of Arabidopsis thaliana and Medicago sativa. The analysis of all three species yielded 341 identified proteins in total, 247 of them being unique. 39 proteins were genuine envelope proteins found in at least two species. Based on this and previous envelope studies we defined the core envelope proteome of chloroplasts. Comparing the general overlap of the available six independent studies (including ours) revealed only a number of 27 envelope proteins. Depending on the stringency of applied selection criteria we found 231 envelope proteins, while less stringent criteria increases this number to 649 putative envelope proteins. Based on the latter we provide a map of the outer and inner envelope core proteome, which includes many yet uncharacterized proteins predicted to be involved in transport, signaling, and response. Furthermore, a foundation for the functional characterization of yet unidentified functions of the inner and OE for further analyses is provided.
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Affiliation(s)
- Stefan Simm
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | | | - Mohamed Ibrahim
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | | | - Bernd Müller
- Department of Biology I, Ludwig-Maximilians-UniversityMunich, Germany
| | - Tobias Schorge
- Institute of Pharmaceutical Chemistry, Goethe UniversityFrankfurt, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Goethe UniversityFrankfurt, Germany
- Center of Membrane Proteomics, Goethe UniversityFrankfurt, Germany
- Cluster of Excellence ‘Macromolecular Complexes’, Goethe UniversityFrankfurt, Germany
| | - Oliver Mirus
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | - Maik S. Sommer
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
| | - Enrico Schleiff
- Institute of Molecular Cell Biology of Plants, Goethe UniversityFrankfurt, Germany
- Center of Membrane Proteomics, Goethe UniversityFrankfurt, Germany
- Cluster of Excellence ‘Macromolecular Complexes’, Goethe UniversityFrankfurt, Germany
- *Correspondence: Enrico Schleiff, Center of Membrane Proteomics, Cluster of Excellence ’Macromolecular Complexes’, Institute of Molecular Cell Biology of Plants, Goethe University, Max-von-Laue Strasse 9, Frankfurt 60438, Germany. e-mail:
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32
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Maupin-Furlow JA, Humbard MA, Kirkland PA. Extreme challenges and advances in archaeal proteomics. Curr Opin Microbiol 2012; 15:351-6. [PMID: 22386447 DOI: 10.1016/j.mib.2012.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/06/2012] [Accepted: 02/10/2012] [Indexed: 12/14/2022]
Abstract
Archaea display amazing physiological properties that are of interest to understand at the molecular level including the ability to thrive at extreme environmental conditions, the presence of novel metabolic pathways (e.g. methanogenesis, methylaspartate cycle) and the use of eukaryotic-like protein machineries for basic cellular functions. Coupling traditional genetic and biochemical approaches with advanced technologies, such as genomics and proteomics, provides an avenue for scientists to discover new aspects related to the molecular physiology of archaea. This review emphasizes the unusual properties of archaeal proteomes and how high-throughput and specialized mass spectrometry-based proteomic studies have provided insight into the molecular properties of archaeal cells.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA.
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33
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Volknandt W, Karas M. Proteomic analysis of the presynaptic active zone. Exp Brain Res 2012; 217:449-61. [DOI: 10.1007/s00221-012-3031-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 02/04/2012] [Indexed: 02/06/2023]
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34
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Quantitative and integrative proteome analysis of peripheral nerve myelin identifies novel myelin proteins and candidate neuropathy loci. J Neurosci 2012; 31:16369-86. [PMID: 22072688 DOI: 10.1523/jneurosci.4016-11.2011] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Peripheral nerve myelin facilitates rapid impulse conduction and normal motor and sensory functions. Many aspects of myelin biogenesis, glia-axonal interactions, and nerve homeostasis are poorly understood at the molecular level. We therefore hypothesized that only a fraction of all relevant myelin proteins has been identified so far. Combining gel-based and gel-free proteomic approaches, we identified 545 proteins in purified mouse sciatic nerve myelin, including 36 previously known myelin constituents. By mass spectrometric quantification, the predominant P0, periaxin, and myelin basic protein constitute 21, 16, and 8% of the total myelin protein, respectively, suggesting that their relative abundance was previously misestimated due to technical limitations regarding protein separation and visualization. Focusing on tetraspan-transmembrane proteins, we validated novel myelin constituents using immuno-based methods. Bioinformatic comparison with mRNA-abundance profiles allowed the categorization in functional groups coregulated during myelin biogenesis and maturation. By differential myelin proteome analysis, we found that the abundance of septin 9, the protein affected in hereditary neuralgic amyotrophy, is strongly increased in a novel mouse model of demyelinating neuropathy caused by the loss of prion protein. Finally, the systematic comparison of our compendium with the positions of human disease loci allowed us to identify several candidate genes for hereditary demyelinating neuropathies. These results illustrate how the integration of unbiased proteome, transcriptome, and genome data can contribute to a molecular dissection of the biogenesis, cell biology, metabolism, and pathology of myelin.
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35
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Prefractionation and separation by C8 stationary phase: Effective strategies for integral membrane proteins analysis. Talanta 2012; 88:567-72. [DOI: 10.1016/j.talanta.2011.11.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 11/10/2011] [Accepted: 11/13/2011] [Indexed: 11/18/2022]
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36
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Poetsch A, Haussmann U, Burkovski A. Proteomics of corynebacteria: From biotechnology workhorses to pathogens. Proteomics 2011; 11:3244-55. [PMID: 21674800 DOI: 10.1002/pmic.201000786] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 11/09/2022]
Abstract
Corynebacteria belong to the high G+C Gram-positive bacteria (Actinobacteria) and are closely related to Mycobacterium and Nocardia species. The best investigated member of this group of almost seventy species is Corynebacterium glutamicum, a soil bacterium isolated in 1957, which is used for the industrial production of more than two million tons of amino acids per year. This review focuses on the technical advances made in proteomics approaches during the last years and summarizes applications of these techniques with respect to C. glutamicum metabolic pathways and stress response. Additionally, selected proteome applications for other biotechnologically important or pathogenic corynebacteria are described.
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Affiliation(s)
- Ansgar Poetsch
- Lehrstuhl Biochemie der Pflanzen, Ruhr-Universität Bochum, Germany
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37
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Baeumlisberger D, Rohmer M, Arrey TN, Mueller BF, Beckhaus T, Bahr U, Barka G, Karas M. Simple Dual-Spotting Procedure Enhances nLC–MALDI MS/MS Analysis of Digests with Less Specific Enzymes. J Proteome Res 2011; 10:2889-94. [DOI: 10.1021/pr2001644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dominic Baeumlisberger
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Marion Rohmer
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Tabiwang N. Arrey
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Benjamin F. Mueller
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Tobias Beckhaus
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Ute Bahr
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
| | - Guenes Barka
- SunChrom Wissenschaftliche Geräte GmbH, Max-Planck-Strasse 22, 61381 Friedrichsdorf, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry, Cluster of Excellence “Macromolecular Complexes”, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt a. M., Germany
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38
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Neue K, Mormann M, Peter-Katalinić J, Pohlentz G. Elucidation of Glycoprotein Structures by Unspecific Proteolysis and Direct nanoESI Mass Spectrometric Analysis of ZIC-HILIC-Enriched Glycopeptides. J Proteome Res 2011; 10:2248-60. [DOI: 10.1021/pr101082c] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristina Neue
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Michael Mormann
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Jasna Peter-Katalinić
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Gottfried Pohlentz
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
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39
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Baeumlisberger D, Arrey TN, Rietschel B, Rohmer M, Papasotiriou DG, Mueller B, Beckhaus T, Karas M. Labeling elastase digests with TMT: informational gain by identification of poorly detectable peptides with MALDI-TOF/TOF mass spectrometry. Proteomics 2011; 10:3905-9. [PMID: 20925058 DOI: 10.1002/pmic.201000288] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The applicability of the less specific protease elastase for the identification of membrane and cytosolic proteins has already been demonstrated. MALDI as ionization technique particularly favors the detection of basic and to a lesser extent of weakly acidic peptides, whereas neutral peptides often remain undetected. Moreover, peptides below 700 Da are routinely excluded. In the following study, the advantage of additional information gained from tandem mass tag zero labeled peptides and the resultant increase in sequence coverage was evaluated. Through derivatization with tandem mass tag reagents, peptide measurement within the standard mass range of the MALDI reflector mode is achievable due to the mass increase. Compared to the unlabeled sample, peptides exhibiting relatively low molecular masses, pI values or higher hydrophobicity could be identified.
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Affiliation(s)
- Dominic Baeumlisberger
- Cluster of Excellence Macromolecular Complexes, Institute for Pharmaceutical Chemistry, Goethe-University, Frankfurt/Main, Germany.
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40
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Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms. Appl Microbiol Biotechnol 2011; 90:407-16. [DOI: 10.1007/s00253-011-3172-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
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41
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Vertommen A, Panis B, Swennen R, Carpentier SC. Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 2011; 74:1165-81. [PMID: 21354347 DOI: 10.1016/j.jprot.2011.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/04/2011] [Accepted: 02/16/2011] [Indexed: 01/27/2023]
Abstract
The workhorse for proteomics in non-model plants is classical two-dimensional electrophoresis, a combination of iso-electric focusing and SDS-PAGE. However, membrane proteins with multiple membrane spanning domains are hardly detected on classical 2-DE gels because of their low abundance and poor solubility in aqueous media. In the current review, solutions that have been proposed to handle these two problems in non-model plants are discussed. An overview of alternative techniques developed for membrane proteomics is provided together with a comparison of their strong and weak points. Subsequently, strengths and weaknesses of the different techniques and methods to evaluate the identification of membrane proteins are discussed. Finally, an overview of recent plant membrane proteome studies is provided with the used separation technique and the number of identified membrane proteins listed.
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Affiliation(s)
- A Vertommen
- Laboratory of Tropical Crop Improvement, Department of Biosystems, K.U. Leuven, Kasteelpark Arenberg 13, B-3001 Heverlee, Belgium
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42
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Zhou Y, Yi T, Park SS, Chadwick W, Shen RF, Wu WW, Martin B, Maudsley S. Rapid and enhanced proteolytic digestion using electric-field-oriented enzyme reactor. J Proteomics 2011; 74:1030-5. [PMID: 21338726 DOI: 10.1016/j.jprot.2011.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 01/25/2011] [Accepted: 02/06/2011] [Indexed: 01/26/2023]
Abstract
We have created a novel enzyme reactor using electric field-mediated orientation and immobilization of proteolytic enzymes (trypsin/chymotrypsin) on biocompatible PVDF membranes in a continuous flow-through chamber. Using less than 5min, this reactor in various enzyme combinations can produce enhanced rapid digestion for standardized prototypic proteins, hydrophilic proteins and hydrophobic transmembrane proteins when compared to in-solution techniques. With improved digestive efficiency, our reactor improved the overall functional analysis of lipid raft proteomes by identifying more closely functionally linked proteins and elucidated a richer set of biological processes and pathways linked to the proteins than traditional in-solution methods.
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Affiliation(s)
- Yu Zhou
- Receptor Pharmacology Unit, Laboratory of Neuroscience, National Institute on Aging, Biomedical Research Center, Baltimore, MD, USA
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43
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Ma J, Hou C, Sun L, Tao D, Zhang Y, Shan Y, Liang Z, Zhang L, Yang L, Zhang Y. Coupling Formic Acid Assisted Solubilization and Online Immobilized Pepsin Digestion with Strong Cation Exchange and Microflow Reversed-Phase Liquid Chromatography with Electrospray Ionization Tandem Mass Spectrometry for Integral Membrane Proteome Analysis. Anal Chem 2010; 82:9622-5. [DOI: 10.1021/ac1023099] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Junfeng Ma
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Chunyan Hou
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Liangliang Sun
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Dingyin Tao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yanyan Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yichu Shan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Ling Yang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center and Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
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44
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Benedikt A, Baltruschat S, Scholz B, Bursen A, Arrey TN, Meyer B, Varagnolo L, Müller AM, Karas M, Dingermann T, Marschalek R. The leukemogenic AF4-MLL fusion protein causes P-TEFb kinase activation and altered epigenetic signatures. Leukemia 2010; 25:135-44. [PMID: 21030982 DOI: 10.1038/leu.2010.249] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Expression of the AF4-MLL fusion protein in murine hematopoietic progenitor/stem cells results in the development of proB acute lymphoblastic leukemia. In this study, we affinity purified the AF4-MLL and AF4 protein complexes to elucidate their function. We observed that the AF4 complex consists of 11 binding partners and exhibits positive transcription elongation factor b (P-TEFb)-mediated activation of promoter-arrested RNA polymerase (pol) II in conjunction with several chromatin-modifying activities. In contrast, the AF4-MLL complex consists of at least 16 constituents including P-TEFb kinase, H3K4(me3) and H3K79(me3) histone methyltransferases (HMT), a protein arginine N-methyltransferase and a histone acetyltransferase. These findings suggest that the AF4-MLL protein disturbs the fine-tuned activation cycle of promoter-arrested RNA Pol II and causes altered histone methylation signatures. Thus, we propose that these two processes are key to trigger cellular reprogramming that leads to the onset of acute leukemia.
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Affiliation(s)
- A Benedikt
- Institute of Pharmaceutical Biology/ZAFES, Goethe-University of Frankfurt, Biocenter, Frankfurt/Main, Germany
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45
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Gilmore JM, Washburn MP. Advances in shotgun proteomics and the analysis of membrane proteomes. J Proteomics 2010; 73:2078-91. [PMID: 20797458 DOI: 10.1016/j.jprot.2010.08.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 08/16/2010] [Accepted: 08/18/2010] [Indexed: 12/24/2022]
Abstract
The emergence of shotgun proteomics has facilitated the numerous biological discoveries made by proteomic studies. However, comprehensive proteomic analysis remains challenging and shotgun proteomics is a continually changing field. This review details the recent developments in shotgun proteomics and describes emerging technologies that will influence shotgun proteomics going forward. In addition, proteomic studies of integral membrane proteins remain challenging due to the hydrophobic nature in integral membrane proteins and their general low abundance levels. However, there have been many strategies developed for enriching, isolating and separating membrane proteins for proteomic analysis that have moved this field forward. In summary, while shotgun proteomics is a widely used and mature technology, the continued pace of improvements in mass spectrometry and proteomic technology and methods indicate that future studies will have an even greater impact on biological discovery.
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Affiliation(s)
- Joshua M Gilmore
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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46
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Cao R, Liu Y, Chen P, Lv R, Song Q, Sheng T, He Q, Wang Y, Wang X, Liang S. Improvement of hydrophobic integral membrane protein identification by mild performic acid oxidation-assisted digestion. Anal Biochem 2010; 407:196-204. [PMID: 20732293 DOI: 10.1016/j.ab.2010.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 08/11/2010] [Accepted: 08/17/2010] [Indexed: 10/19/2022]
Abstract
Integral membrane proteins (IMPs) are critical for the maintenance of biological systems and represent important targets for the treatment of disease. The hydrophobicity and low abundance of IMPs make them difficult to analyze. In proteomic analyses, hydrophobic peptides including transmembrane domains are often underrepresented, and this reduces the sequence coverage and reliability of the identified IMPs. Here we report a new strategy, mild performic acid oxidation treatment (mPAOT), for improvement of IMP identification. In the mPAOT strategy, the hydrophobicity of IMPs is significantly decreased by oxidizing their methionine and cysteine residues with performic acid, thereby improving the solubility and enzymolysis of these proteins. The application of the mPAOT strategy to the analysis of IMPs from human nasopharyngeal carcinoma CNE1 cell line demonstrated that many IMPs, including those with high hydrophobicity, could be reliably identified.
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Affiliation(s)
- Rui Cao
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, People's Republic of China
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47
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Meyer B, Papasotiriou DG, Karas M. 100% protein sequence coverage: a modern form of surrealism in proteomics. Amino Acids 2010; 41:291-310. [DOI: 10.1007/s00726-010-0680-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/25/2010] [Indexed: 01/11/2023]
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48
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López-Ferrer D, Petritis K, Robinson EW, Hixson KK, Tian Z, Lee JH, Lee SW, Tolić N, Weitz KK, Belov ME, Smith RD, Pasa-Tolić L. Pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics. Mol Cell Proteomics 2010; 10:M110.001479. [PMID: 20627868 PMCID: PMC3033671 DOI: 10.1074/mcp.m110.001479] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. Bottom-up proteomics ultimately provides the peptide sequences derived from the tandem MS analyses of peptides after the proteome has been digested. Top-down proteomics conversely entails the MS analyses of intact proteins for more effective characterization of genetic variations and/or post-translational modifications. Herein, we describe recent efforts toward efficient integration of bottom-up and top-down LC-MS-based proteomics strategies. Since most proteomics separations utilize acidic conditions, we exploited the compatibility of pepsin (where the optimal digestion conditions are at low pH) for integration into bottom-up and top-down proteomics work flows. Pressure-enhanced pepsin digestions were successfully performed and characterized with several standard proteins in either an off-line mode using a Barocycler or an on-line mode using a modified high pressure LC system referred to as a fast on-line digestion system (FOLDS). FOLDS was tested using pepsin and a whole microbial proteome, and the results were compared against traditional trypsin digestions on the same platform. Additionally, FOLDS was integrated with a RePlay configuration to demonstrate an ultrarapid integrated bottom-up top-down proteomics strategy using a standard mixture of proteins and a monkey pox virus proteome.
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Affiliation(s)
- Daniel López-Ferrer
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.
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49
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Taouatas N, Heck AJR, Mohammed S. Evaluation of Metalloendopeptidase Lys-N Protease Performance under Different Sample Handling Conditions. J Proteome Res 2010; 9:4282-8. [DOI: 10.1021/pr100341e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nadia Taouatas
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and The Netherlands Proteomics Center
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and The Netherlands Proteomics Center
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands, and The Netherlands Proteomics Center
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50
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Griffin NM, Schnitzer JE. Overcoming key technological challenges in using mass spectrometry for mapping cell surfaces in tissues. Mol Cell Proteomics 2010; 10:R110.000935. [PMID: 20548103 DOI: 10.1074/mcp.r110.000935] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Plasma membranes form a critical biological interface between the inside of every cell and its external environment. Their roles in multiple key cellular functions make them important drug targets. However the protein composition of plasma membranes in general is poorly defined as the inherent properties of lipid embedded proteins, such as their hydrophobicity, low abundance, poor solubility and resistance to digestion and extraction makes them difficult to isolate, solubilize, and identify on a large scale by traditional mass spectrometry methods. Here we describe some of the significant advances that have occurred over the past ten years to address these challenges including: i) the development of new and improved membrane isolation techniques via either subfractionation or direct labeling and isolation of plasma membranes from cells and tissues; ii) modification of mass spectrometry methods to adapt to the hydrophobic nature of membrane proteins and peptides; iii) improvements to digestion protocols to compensate for the shortage of trypsin cleavage sites in lipid-embedded proteins, particularly multi-spanning proteins, and iv) the development of numerous bioinformatics tools which allow not only the identification and quantification of proteins, but also the prediction of membrane protein topology, membrane post-translational modifications and subcellular localization. This review emphasis the importance and difficulty of defining cells in proper patho- and physiological context to maintain the in vivo reality. We focus on how key technological challenges associated with the isolation and identification of cell surface proteins in tissues using mass spectrometry are being addressed in order to identify and quantify a comprehensive plasma membrane for drug and target discovery efforts.
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Affiliation(s)
- Noelle M Griffin
- Proteogenomics Research Institute for Systems Medicine, San Diego, California 92121, USA
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