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Fu Q, Murray CI, Karpov OA, Van Eyk JE. Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis. MASS SPECTROMETRY REVIEWS 2023; 42:873-886. [PMID: 34786750 DOI: 10.1002/mas.21750] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/11/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Sample preparation for mass spectrometry-based proteomics has many tedious and time-consuming steps that can introduce analytical errors. In particular, the steps around the proteolytic digestion of protein samples are prone to inconsistency. One route for reliable sample processing is the development and optimization of a workflow utilizing an automated liquid handling workstation. Diligent assessment of the sample type, protocol design, reagents, and incubation conditions can significantly improve the speed and consistency of preparation. When combining robust liquid chromatography-mass spectrometry with either discovery or targeted methods, automated sample preparation facilitates increased throughput and reproducible quantitation of biomarker candidates. These improvements in analysis are also essential to process the large patient cohorts necessary to validate a candidate biomarker for potential clinical use. This article reviews the steps in the workflow, optimization strategies, and known applications in clinical, pharmaceutical, and research fields that demonstrate the broad utility for improved automation of sample preparation in the proteomic field.
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Affiliation(s)
- Qin Fu
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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2
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The aminopeptidase B (Ap-B) is phosphorylated in HEK293 cells. Biochimie 2022; 201:204-212. [PMID: 35952945 DOI: 10.1016/j.biochi.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/22/2022]
Abstract
Proteolysis is a post-translational modification (PTM) that affects the whole proteome. First regarded as only destructive, it is more precise than expected. It is finely regulated by other PTMs like phosphorylation. Aminopeptidase B (Ap-B), a M1 metallopeptidase, hydrolyses the peptide bond on the carbonyl side of basic residues at the NH2-terminus of peptides. 2D electrophoresis (2DE) was used to show that Ap-B is modified by phosphorylation. Detection of Ap-B by western blot after 2DE reveals several isoforms with different isoelectric points. Using alkaline phosphatase, Pro-Q Diamond phosphorylation-specific dye and kinase-specific inhibitors, we confirmed that Ap-B is phosphorylated. Phosphorylation can alter the structure of proteins leading to changes in their activity, localization, stability and association with other interacting molecules. We showed that Ap-B phosphorylation might delay its turnover. Our study illustrates the central role of the crosstalk between kinases and proteases in the regulation of many biological processes.
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3
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Altenbach SB, Chang HC, Simon-Buss A, Mohr T, Huo N, Gu YQ. Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring. Funct Integr Genomics 2019; 20:1-16. [PMID: 31250230 PMCID: PMC6954139 DOI: 10.1007/s10142-019-00694-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/12/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022]
Abstract
Although the economic value of wheat flour is determined by the complement of gluten proteins, these proteins have been challenging to study because of the complexity of the major protein groups and the tremendous sequence diversity among wheat cultivars. The completion of a high-quality wheat genome sequence from the reference wheat Chinese Spring recently facilitated the assembly and annotation of a complete set of gluten protein genes from a single cultivar, making it possible to link individual proteins in the flour to specific gene sequences. In a proteomic analysis of total wheat flour protein from Chinese Spring using quantitative two-dimensional gel electrophoresis combined with tandem mass spectrometry, gliadins or low-molecular-weight glutenin subunits were identified as the predominant proteins in 72 protein spots. Individual spots were associated with 40 of 56 Chinese Spring gene sequences, including 16 of 26 alpha gliadins, 10 of 11 gamma gliadins, six of seven omega gliadins, one of two delta gliadins, and nine of ten LMW-GS. Most genes that were not associated with protein spots were either expressed at low levels in endosperm or encoded proteins with high similarity to other proteins. A wide range of protein accumulation levels were observed and discrepancies between transcript levels and protein levels were noted. This work together with similar studies using other commercial cultivars should provide new insight into the molecular basis of wheat flour quality and allergenic potential.
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Affiliation(s)
- Susan B Altenbach
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Han-Chang Chang
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Annamaria Simon-Buss
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Toni Mohr
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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4
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Mouchahoir T, Schiel JE. Development of an LC-MS/MS peptide mapping protocol for the NISTmAb. Anal Bioanal Chem 2018; 410:2111-2126. [PMID: 29411091 PMCID: PMC5830484 DOI: 10.1007/s00216-018-0848-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/04/2017] [Accepted: 01/03/2018] [Indexed: 11/12/2022]
Abstract
Peptide mapping is a component of the analytical toolbox used within the biopharmaceutical industry to aid in the identity confirmation of a protein therapeutic and to monitor degradative events such as oxidation or deamidation. These methods offer the advantage of providing site-specific information regarding post-translational and chemical modifications that may arise during production, processing or storage. A number of such variations may also be induced by the sample preparation methods themselves which may confound the ability to accurately evaluate the true modification levels. One important focus when developing a peptide mapping method should therefore be the use of sample preparation conditions that will minimize the degree of artificial modifications induced. Unfortunately, the conditions that are amenable to effective reduction, alkylation and digestion are often the same conditions that promote unwanted modifications. Here we describe the optimization of a tryptic digestion protocol used for peptide mapping of the NISTmAb IgG1κ which addresses the challenge of balancing maximum digestion efficiency with minimum artificial modifications. The parameters on which we focused include buffer concentration, digestion time and temperature, as well as the source and type of trypsin (recombinant vs. pancreatic; bovine vs porcine) used. Using the optimized protocol we generated a peptide map of the NISTmAb which allowed us to confirm its identity at the level of primary structure. Graphical abstract Peptide map of the NISTmAb RM 8671 monoclonal antibody. Tryptic digestion was performed using an optimized protocol and followed by LC-UV-MS analysis. The trace represents the total ion chromatogram. Each peak was mapped to peptides identified using mass spectrometry data.
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Affiliation(s)
- Trina Mouchahoir
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
| | - John E Schiel
- Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
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5
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Suttapitugsakul S, Xiao H, Smeekens J, Wu R. Evaluation and optimization of reduction and alkylation methods to maximize peptide identification with MS-based proteomics. MOLECULAR BIOSYSTEMS 2017; 13:2574-2582. [PMID: 29019370 PMCID: PMC5698164 DOI: 10.1039/c7mb00393e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass spectrometry (MS) has become an increasingly important technique to analyze proteins. In popular bottom-up MS-based proteomics, reduction and alkylation are routine steps to facilitate peptide identification. However, incomplete reactions and side reactions may occur, which compromise the experimental results. In this work, we systematically evaluated the reduction step with commonly used reagents, i.e., dithiothreitol, 2-mercaptoethanol, tris(2-carboxyethyl)phosphine, or tris(3-hydroxypropyl)phosphine, and alkylation with iodoacetamide, acrylamide, N-ethylmaleimide, or 4-vinylpyridine. By using digested peptides from a yeast whole-cell lysate, the number of proteins and peptides identified were very similar using four different reducing reagents. The results from four alkylating reagents, however, were dramatically different with iodoacetamide giving the highest number of peptides with alkylated cysteine and the lowest number of peptides with incomplete cysteine alkylation and side reactions. Alkylation conditions with iodoacetamide were further optimized. To identify more peptides with cysteine, thiopropyl-sepharose 6B resins were used to enrich them, and the optimal conditions were employed for the reduction and alkylation. The enrichment resulted in over three times more cysteine-containing peptides than without enrichment. Systematic evaluation of the reduction and alkylation with different reagents can aid in a better design of bottom-up proteomic experiments.
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Affiliation(s)
- Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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6
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Erde J, Loo RRO, Loo JA. Improving Proteome Coverage and Sample Recovery with Enhanced FASP (eFASP) for Quantitative Proteomic Experiments. Methods Mol Biol 2017; 1550:11-18. [PMID: 28188519 DOI: 10.1007/978-1-4939-6747-6_2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Enhanced Filter Aided Sample Preparation (eFASP) incorporates plastics passivation and digestion-enhancing surfactants into the traditional FASP workflow to reduce sample loss and increase hydrophobic protein representation in qualitative and quantitative proteomics experiments. Resulting protein digests are free of contaminants and can be analyzed directly by LC-MS.
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Affiliation(s)
- Jonathan Erde
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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7
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Brown S, Norris G. Improved consistency in 2D gel electrophoresis: Sheep plasma as a test case. Electrophoresis 2016; 38:906-913. [PMID: 27925263 DOI: 10.1002/elps.201600433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/09/2022]
Abstract
Two-dimensional (2D) gel electrophoresis is a well-proven proteomic technique; however, sample-specific optimisation can often be necessary in order to get consistent quantitation. In particular, plasma samples are often smeared on 2D gels making spot matching difficult. A variety of different sample preparation and 2D methods were tested by using sheep plasma, and it was found that lowering sample pH prior to precipitation, using a long voltage gradient for isoelectric focusing and the inclusion of carrier ampholytes in the electrode wicks, improved both the quality and consistency of spot resolution. Analysis of the internal standards from two different DIGE experiments, one with conventional methodology and one with the improved method, showed that along with substantially improving the number of spots resolved, the average CV (coefficient of variation) of matched standards was lower with the new method. 428 matched spots were found using the improved method compared to 208 matched spots using conventional methodology. For the 174 spots that were matched between the two DIGE experiments, the average CV's of spot volumes were also significantly lower, at 0.20 for the new method compared to 0.24 for the conventional method (p < 0.001).
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Affiliation(s)
- Stuart Brown
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Gillian Norris
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Giuliani MM, Palermo C, De Santis MA, Mentana A, Pompa M, Giuzio L, Masci S, Centonze D, Flagella Z. Differential Expression of Durum Wheat Gluten Proteome under Water Stress during Grain Filling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:6501-12. [PMID: 26138860 DOI: 10.1021/acs.jafc.5b01635] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Environmental stress during grain filling may affect wheat protein composition, thus influencing its final quality. A proteomic approach was used to evaluate changes in storage protein composition under water stress of two Italian durum wheat (Triticum turgidum ssp. durum) cultivars, Ciccio and Svevo. The high-molecular-weight glutenin region increased progressively in both cultivars and under two water regimens. The L48-35 region, corresponding to low-molecular-weight (LMW) glutenin subunits, increased slightly during grain development and decreased under water stress in both cultivars. In particular, an s-type LMW related to superior technological quality was down-expressed in the early-mid period in Svevo and in the mid-late period in Ciccio. Finally, the L<35 region, corresponding to gliadin-like proteins, decreased slightly during grain development and increased under stress in both cultivars. Several α-gliadins, associated with immunological potential, increased their expression under water stress, especially in Svevo in the early-mid stage of grain filling.
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Affiliation(s)
- Marcella Michela Giuliani
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Carmen Palermo
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Michele Andrea De Santis
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Annalisa Mentana
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Marianna Pompa
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Luigia Giuzio
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Stefania Masci
- §Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia (DAFNE), Università degli Studi della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Diego Centonze
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Zina Flagella
- †Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente (SAFE), Università degli Studi di Foggia, Via Napoli 25, 71122 Foggia, Italy
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9
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Gorr TA, Vogel J. Western blotting revisited: Critical perusal of underappreciated technical issues. Proteomics Clin Appl 2015; 9:396-405. [DOI: 10.1002/prca.201400118] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/19/2014] [Accepted: 01/14/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Thomas A. Gorr
- Institute of Veterinary Physiology; Vetsuisse Faculty; University of Zürich; Zürich Switzerland
- Center for Pediatrics and Adolescent Medicine; Clinic IV: Division of Pediatric Hematology and Oncology; University Medical Center Freiburg; Freiburg Germany
| | - Johannes Vogel
- Institute of Veterinary Physiology; Vetsuisse Faculty; University of Zürich; Zürich Switzerland
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10
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Fasoli E, Righetti PG, Moltrasio D, D'Amato A. Extensive heterogeneity of human urokinase, as detected by two-dimensional mapping. Anal Chem 2015; 87:1509-13. [PMID: 25525926 DOI: 10.1021/ac5037796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urokinase (uPA, urinary plasminogen activator) is a serine protease belonging to the peptidase S1 family. Specifically, uPA cleaves the zymogen plasminogen into the active form (plasmin), which then degrades the fibrin clots. It is widely used as a fibrinolytic agent in thrombolytic therapy and it is also used clinically as a thrombolytic agent. It can be administered to improve the drainage of complicated pleural effusions and empyemas and it is the most effective drug in myocardial infarction. The enzyme was originally identified in human urine for its ability to catalyze the transformation of plasminogen into its active form (plasmin), which degrades fibrin and extracellular matrix components. The present report deals with the analysis and characterization of this preparation.
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Affiliation(s)
- Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano , Via Mancinelli 7, Milano 20131, Italy
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11
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Correia S, Nunes-Miranda JD, Pinto L, Santos HM, de Toro M, Sáenz Y, Torres C, Capelo JL, Poeta P, Igrejas G. Complete proteome of a quinolone-resistant Salmonella Typhimurium phage type DT104B clinical strain. Int J Mol Sci 2014; 15:14191-219. [PMID: 25196519 PMCID: PMC4159846 DOI: 10.3390/ijms150814191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 06/27/2014] [Accepted: 07/25/2014] [Indexed: 11/26/2022] Open
Abstract
Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one of these emerging epidemic multidrug resistant strains. Here we collate information from the diverse and comprehensive range of experiments on Salmonella proteomes that have been published. We then present a new study of the proteome of the quinolone-resistant Se20 strain (phage type DT104B), recovered after ciprofloxacin treatment and compared it to the proteome of reference strain SL1344. A total of 186 and 219 protein spots were recovered from Se20 and SL1344 protein extracts, respectively, after two-dimensional gel electrophoresis. The signatures of 94% of the protein spots were successfully identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). Three antimicrobial resistance related proteins, whose genes were previously detected by polymerase chain reaction (PCR), were identified in the clinical strain. The presence of these proteins, dihydropteroate synthase type-2 (sul2 gene), aminoglycoside resistance protein A (strA gene) and aminoglycoside 6'-N-acetyltransferase type Ib-cr4 (aac(6')-Ib-cr4 gene), was confirmed in the DT104B clinical strain. The aac(6')-Ib-cr4 gene is responsible for plasmid-mediated aminoglycoside and quinolone resistance. This is a preliminary analysis of the proteome of these two S. Typhimurium strains and further work is being developed to better understand how antimicrobial resistance is developing in this pathogen.
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Affiliation(s)
- Susana Correia
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Júlio D Nunes-Miranda
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Luís Pinto
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Hugo M Santos
- BIOSCOPE group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Monte de Caparica, Portugal.
| | - María de Toro
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander 39011, Spain.
| | - Yolanda Sáenz
- Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, C/Piqueras 98, 26006 Logroño, La Rioja, Spain.
| | - Carmen Torres
- Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, C/Piqueras 98, 26006 Logroño, La Rioja, Spain.
| | - José Luis Capelo
- BIOSCOPE group, REQUIMTE-CQFB, Chemistry Department, Faculty of Science and Technology, University NOVA of Lisbon, 2829-516 Monte de Caparica, Portugal.
| | - Patrícia Poeta
- Centre of Studies of Animal and Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
| | - Gilberto Igrejas
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal.
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12
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Saraygord-Afshari N, Naderi-Manesh H, Naderi M. Enhanced reproducibility of the human gel-based tear proteome maps in the presence of di-(2-hydroxyethyl) disulfide. Biotechnol Appl Biochem 2014; 61:660-7. [PMID: 24575874 DOI: 10.1002/bab.1221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/21/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Neda Saraygord-Afshari
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics; Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Mostafa Naderi
- Bina Eye Hospital; Tehran Iran
- Department of Ophthalmology; Baqiyatallah University of Medical Sciences; Tehran Iran
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13
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Erde J, Loo RRO, Loo JA. Enhanced FASP (eFASP) to increase proteome coverage and sample recovery for quantitative proteomic experiments. J Proteome Res 2014; 13:1885-95. [PMID: 24552128 PMCID: PMC3993969 DOI: 10.1021/pr4010019] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The integrity of quantitative proteomic experiments depends on the reliability and the robustness of the protein extraction, solubilization, and digestion methods utilized. Combinations of detergents, chaotropes, and mechanical disruption can yield successful protein preparations; however, the methods subsequently required to eliminate these added contaminants, in addition to the salts, nucleic acids, and lipids already in the sample, can result in significant sample losses and incomplete contaminant removal. A recently introduced method for proteomic sample preparation, filter-aided sample preparation (FASP), cleverly circumvents many of the challenges associated with traditional protein purification methods but is associated with significant sample loss. Presented here is an enhanced FASP (eFASP) approach that incorporates alternative reagents to those of traditional FASP, improving sensitivity, recovery, and proteomic coverage for processed samples. The substitution of 0.2% deoxycholic acid for urea during eFASP digestion increases tryptic digestion efficiency for both cytosolic and membrane proteins yet obviates needed cleanup steps associated with use of the deoxycholate sodium salt. For classic FASP, prepassivating Microcon filter surfaces with 5% TWEEN-20 reduces peptide loss by 300%. An express eFASP method uses tris(2-carboxyethyl)phosphine and 4-vinylpyridine to alkylate proteins prior to deposition on the Microcon filter, increasing alkylation specificity and speeding processing.
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Affiliation(s)
- Jonathan Erde
- Department of Chemistry and Biochemistry and ‡Department of Biological Chemistry, University of California-Los Angeles , Los Angeles, California 90095, United States
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14
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Di Michele M, Van Geet C, Freson K. Recent advances in platelet proteomics. Expert Rev Proteomics 2014; 9:451-66. [DOI: 10.1586/epr.12.31] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Raymond BBA, Tacchi JL, Jarocki VM, Minion FC, Padula MP, Djordjevic SP. P159 from Mycoplasma hyopneumoniae Binds Porcine Cilia and Heparin and Is Cleaved in a Manner Akin to Ectodomain Shedding. J Proteome Res 2013; 12:5891-903. [DOI: 10.1021/pr400903s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Benjamin B. A. Raymond
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Jessica L. Tacchi
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Veronica M. Jarocki
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - F. Chris Minion
- Department
of Preventive and Veterinary Medicine, Iowa State University, 2180
Veterinary Medicine, Ames, Iowa 50011, United States
| | - Matthew P. Padula
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Steven P. Djordjevic
- The
ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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16
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Mikkat S, Kischstein T, Kreutzer M, Glocker MO. Mass spectrometric peptide analysis of 2DE-separated mouse spinal cord and rat hippocampus proteins suggests an NGxG motif of importance for in vivo deamidation. Electrophoresis 2013; 34:1610-8. [DOI: 10.1002/elps.201200682] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 02/11/2013] [Accepted: 02/20/2013] [Indexed: 12/16/2022]
Affiliation(s)
| | - Timo Kischstein
- Oscar Langendorff Institute of Physiology; University Medicine Rostock; Rostock; Germany
| | - Michael Kreutzer
- Proteome Center Rostock; University Medicine Rostock; Rostock; Germany
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17
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Pompa M, Giuliani MM, Palermo C, Agriesti F, Centonze D, Flagella Z. Comparative analysis of gluten proteins in three durum wheat cultivars by a proteomic approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:2606-2617. [PMID: 23414385 DOI: 10.1021/jf304566d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The gluten protein composition and expression level influence dough properties and are cultivar and environment dependent. To broaden the knowledge of the durum wheat gluten proteome, three cultivars were compared in two different growing seasons by a proteomic approach. Cultivar-specific and differentially expressed spots in the two years were identified by mass spectrometry. Significant differences were observed among the cultivars: Ofanto showed the lowest protein spot volumes in the high molecular weight (HMW) and low molecular weight (LMW) <35,000 regions and the highest in the LMW 48,000-35,000 region, Latino the lowest in the LMW 48,000-35,000 region, and Simeto an intermediate expression level in both LMW regions. In the warmer year the up-regulation of HMW glutenins, α-gliadins, and a globulin 3 protein and the down-expression of LMW glutenins and γ-gliadins were observed. Among the cultivars, Simeto showed the highest stability across the environments.
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Affiliation(s)
- Marianna Pompa
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università degli Studi di Foggia , Via Napoli 25- 71122, Foggia, Italy
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18
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Kollipara L, Zahedi RP. Protein carbamylation: In vivo modification or in vitro artefact? Proteomics 2013; 13:941-4. [DOI: 10.1002/pmic.201200452] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 10/31/2012] [Accepted: 11/14/2012] [Indexed: 11/08/2022]
Affiliation(s)
| | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V.; Dortmund Germany
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19
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Sylvestersen KB, Young C, Nielsen ML. Advances in characterizing ubiquitylation sites by mass spectrometry. Curr Opin Chem Biol 2013; 17:49-58. [PMID: 23298953 DOI: 10.1016/j.cbpa.2012.12.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/07/2012] [Accepted: 12/02/2012] [Indexed: 01/01/2023]
Abstract
The attachment of one or more ubiquitin moieties to proteins plays a central regulatory mechanism in eukaryotic cells. Protein ubiquitylation regulates numerous cellular processes, including protein degradation, signal transduction, DNA repair and cell division. The characterization of ubiquitylation is a two-fold challenge that involves the mapping of ubiquitylation sites and the determination of ubiquitin chain topology. This review focuses on the technical advances in the mass spectrometry-based characterization of ubiquitylation sites, which have recently involved the large-scale identification of ubiquitylation sites by peptide-level enrichment strategies. The discovery that ubiquitylation is a widespread modification similar to phosphorylation and acetylation suggests cross-talk may also occur at the post translational modification level.
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Affiliation(s)
- Kathrine B Sylvestersen
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark
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20
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Wetie AGN, Sokolowska I, Woods AG, Darie CC. Identification of Post-Translational Modifications by Mass Spectrometry. Aust J Chem 2013. [DOI: 10.1071/ch13144] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are the effector molecules of many cellular and biological processes and are thus very dynamic and flexible. Regulation of protein activity, structure, stability, and turnover is in part controlled by their post-translational modifications (PTMs). Common PTMs of proteins include phosphorylation, glycosylation, methylation, ubiquitination, acetylation, and oxidation. Understanding the biology of protein PTMs can help elucidate the mechanisms of many pathological conditions and provide opportunities for prevention, diagnostics, and treatment of these disorders. Prior to the era of proteomics, it was standard to use chemistry methods for the identification of protein modifications. With advancements in proteomic technologies, mass spectrometry has become the method of choice for the analysis of protein PTMs. In this brief review, we will highlight the biochemistry of PTMs with an emphasis on mass spectrometry.
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21
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Heukeshoven J, März A, Warnecke G, Deppert W, Tolstonog GV. Recombinant p53 displays heterogeneity during isoelectric focusing. Electrophoresis 2012; 33:2818-27. [DOI: 10.1002/elps.201200205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jochen Heukeshoven
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Annette März
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Gabriele Warnecke
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Wolfgang Deppert
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Genrich V. Tolstonog
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
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22
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Quantitative proteomics to decipher ubiquitin signaling. Amino Acids 2012; 43:1049-60. [PMID: 22821265 DOI: 10.1007/s00726-012-1286-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/03/2012] [Indexed: 12/21/2022]
Abstract
Ubiquitin signaling plays an essential role in controlling cellular processes in eukaryotes, and the impairment of ubiquitin regulation contributes to the pathogenesis of a wide range of human diseases. During the last decade, mass spectrometry-based proteomics has emerged as an indispensable approach for identifying the ubiquitinated proteome (ubiquitinome), ubiquitin modification sites, the linkages of complex ubiquitin chains, as well as the interactome of ubiquitin enzymes. In particular, implementation of quantitative strategies allows the detection of dynamic changes in the ubiquitinome, enhancing the ability to differentiate between function-relevant protein targets and false positives arising from biological and experimental variations. The profiling of total cell lysate and the ubiquitinated proteome in the same sets of samples has become a powerful tool, revealing a subset of substrates that are modulated by specific physiological and pathological conditions, such as gene mutations in ubiquitin signaling. This strategy is equally useful for dissecting the pathways of ubiquitin-like proteins.
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23
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Reed PW, Densmore A, Bloch RJ. Optimization of large gel 2D electrophoresis for proteomic studies of skeletal muscle. Electrophoresis 2012; 33:1263-70. [PMID: 22589104 DOI: 10.1002/elps.201100642] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We describe improved methods for large format, two-dimensional gel electrophoresis (2DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7 M urea and 2 M thiourea, instead of 9 M urea, in sample preparation and in the tops of the gel tubes; (ii) standardized deionization of all solutions containing urea with a mixed bed ion exchange resin and removal of urea from the electrode solutions; and (iii) use of a new gel tank and cooling device that eliminate the need to run two separating gels in the SDS dimension. These changes make 2DE analysis more reproducible and sensitive, with minimal artifacts. Application of this method to the soluble fraction of muscle tissues reliably resolves ~1800 protein spots in adult human skeletal muscle and over 2800 spots in myotubes.
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Affiliation(s)
- Patrick W Reed
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, Department of Physiology, University of Maryland School of Medicine University of Maryland, Baltimore, MD 21201, USA.
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24
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Bae N, Lödl M, Pollak A, Lubec G. Mass spectrometrical analysis of bilin-binding protein from the wing of Hebomoia glaucippe (Linnaeus, 1758) (Lepidoptera: Pieridae). Electrophoresis 2012; 33:1787-94. [DOI: 10.1002/elps.201100569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Narkhyun Bae
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Martin Lödl
- Naturhistorisches Museum Wien; Vienna; Austria
| | - Arnold Pollak
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
| | - Gert Lubec
- Department of Pediatrics; Medical University of Vienna; Vienna; Austria
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25
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Deng X, Hahne T, Schröder S, Redweik S, Nebija D, Schmidt H, Janssen O, Lachmann B, Wätzig H. The challenge to quantify proteins with charge trains due to isoforms or conformers. Electrophoresis 2011; 33:263-9. [DOI: 10.1002/elps.201100321] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/30/2011] [Accepted: 08/05/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Xi Deng
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thomas Hahne
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simone Schröder
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sabine Redweik
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dashnor Nebija
- Department of Medicinal and Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Hendrik Schmidt
- Laboratory for Molecular Immunology, Institute for Immunology, University Hospital Schleswig‐Holstein, Kiel, Germany
| | - Ottmar Janssen
- Laboratory for Molecular Immunology, Institute for Immunology, University Hospital Schleswig‐Holstein, Kiel, Germany
| | - Bodo Lachmann
- Department of Medicinal and Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Hermann Wätzig
- Institute of Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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26
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Bae N, Lödl M, Pollak A, Lubec G. Mass spectrometrical analysis of cuticular proteins from the wing of Hebemoia glaucippe (Linnaeus, 1758) (Lepidoptera: Pieridae). J Proteomics 2011; 75:517-31. [DOI: 10.1016/j.jprot.2011.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/02/2011] [Accepted: 08/22/2011] [Indexed: 12/29/2022]
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27
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Two-dimensional gel electrophoresis in proteomics: a tutorial. J Proteomics 2011; 74:1829-41. [PMID: 21669304 DOI: 10.1016/j.jprot.2011.05.040] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 05/23/2011] [Accepted: 05/26/2011] [Indexed: 12/12/2022]
Abstract
Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose of this tutorial paper is to guide the reader through the history of the field, then through the main steps of the process, from sample preparation to in-gel detection of proteins, commenting the constraints and caveats of the technique. Then the limitations and positive features of two-dimensional electrophoresis are discussed (e.g. its unique ability to separate complete proteins and its easy interfacing with immunoblotting techniques), so that the optimal type of applications of this technique in current and future proteomics can be perceived. This is illustrated by a detailed example taken from the literature and commented in detail. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 2).
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28
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Sixt BS, Heinz C, Pichler P, Heinz E, Montanaro J, Op den Camp HJM, Ammerer G, Mechtler K, Wagner M, Horn M. Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila. Proteomics 2011; 11:1868-92. [PMID: 21500343 DOI: 10.1002/pmic.201000510] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 01/19/2011] [Accepted: 01/24/2011] [Indexed: 12/16/2022]
Abstract
Chlamydiae belong to the most successful intracellular bacterial pathogens. They display a complex developmental cycle and an extremely broad host spectrum ranging from vertebrates to protozoa. The family Chlamydiaceae comprises exclusively well-known pathogens of humans and animals, whereas the members of its sister group, the Parachlamydiaceae, naturally occur as symbionts of free-living amoebae. Comparative analysis of these two groups provides valuable insights into chlamydial evolution and mechanisms for microbe-host interaction. Based on the complete genome sequence of the Acanthamoeba spp. symbiont Protochlamydia amoebophila UWE25, we performed the first detailed proteome analysis of the infectious stage of a symbiotic chlamydia. A 2-D reference proteome map was established and the analysis was extensively complemented by shotgun proteomics. In total, 472 proteins were identified, which represent 23.2% of all encoded proteins. These cover a wide range of functional categories, including typical house-keeping proteins, but also putative virulence-associated proteins. A number of proteins that are not encoded in genomes of Chlamydiaceae were observed and the expression of 162 proteins classified as hypothetical or unknown proteins could be demonstrated. Our findings indicate that P. amoebophila exploits its additional genetic repertoire (compared with the Chlamydiaceae), and that its elementary bodies are remarkably well equipped with proteins involved in transcription, translation, and energy generation.
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Affiliation(s)
- Barbara S Sixt
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
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29
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Zhang E, Chen X, Liang X. Resolubilization of TCA precipitated plant proteins for 2-D electrophoresis. Electrophoresis 2011; 32:696-8. [DOI: 10.1002/elps.201000557] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 11/09/2022]
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30
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Dupont FM, Vensel WH, Tanaka CK, Hurkman WJ, Altenbach SB. Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry. Proteome Sci 2011; 9:10. [PMID: 21314956 PMCID: PMC3238214 DOI: 10.1186/1477-5956-9-10] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 02/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat flour is one of the world's major food ingredients, in part because of the unique end-use qualities conferred by the abundant glutamine- and proline-rich gluten proteins. Many wheat flour proteins also present dietary problems for consumers with celiac disease or wheat allergies. Despite the importance of these proteins it has been particularly challenging to use MS/MS to distinguish the many proteins in a flour sample and relate them to gene sequences. RESULTS Grain from the extensively characterized spring wheat cultivar Triticum aestivum 'Butte 86' was milled to white flour from which proteins were extracted, then separated and quantified by 2-DE. Protein spots were identified by separate digestions with three proteases, followed by tandem mass spectrometry analysis of the peptides. The spectra were used to interrogate an improved protein sequence database and results were integrated using the Scaffold program. Inclusion of cultivar specific sequences in the database greatly improved the results, and 233 spots were identified, accounting for 93.1% of normalized spot volume. Identified proteins were assigned to 157 wheat sequences, many for proteins unique to wheat and nearly 40% from Butte 86. Alpha-gliadins accounted for 20.4% of flour protein, low molecular weight glutenin subunits 18.0%, high molecular weight glutenin subunits 17.1%, gamma-gliadins 12.2%, omega-gliadins 10.5%, amylase/protease inhibitors 4.1%, triticins 1.6%, serpins 1.6%, purinins 0.9%, farinins 0.8%, beta-amylase 0.5%, globulins 0.4%, other enzymes and factors 1.9%, and all other 3%. CONCLUSIONS This is the first successful effort to identify the majority of abundant flour proteins for a single wheat cultivar, relate them to individual gene sequences and estimate their relative levels. Many genes for wheat flour proteins are not expressed, so this study represents further progress in describing the expressed wheat genome. Use of cultivar-specific contigs helped to overcome the difficulties of matching peptides to gene sequences for members of highly similar, rapidly evolving storage protein families. Prospects for simplifying this process for routine analyses are discussed. The ability to measure expression levels for individual flour protein genes complements information gained from efforts to sequence the wheat genome and is essential for studies of effects of environment on gene expression.
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Affiliation(s)
- Frances M Dupont
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - William H Vensel
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - Charlene K Tanaka
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - William J Hurkman
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
| | - Susan B Altenbach
- USDA Agricultural Research Service, Western Regional Research Center, Albany CA 94710, USA
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31
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Taouatas N, Mohammed S, Heck AJR. Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics. Methods Mol Biol 2011; 753:157-167. [PMID: 21604122 DOI: 10.1007/978-1-61779-148-2_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The current advances in mass spectrometry technology have led to the possibility of analyzing more complex biological samples such as entire proteomes. Here, we describe a new and powerful methodology that combines the use of the metalloendopeptidase Lys-N and strong cation exchange with mass spectrometric analysis. The approach described here allows one to separate peptides with different functional groups. The peptides we are able to isolate are N-terminal peptides, phosphorylated peptides with a single lysine, peptides with a single basic residue (lysine), and peptides with multiply basic residues. When this separation strategy is combined with tandem mass spectrometry that involves both collision-induced dissociation and electron transfer dissociation, one can achieve an optimal targeted strategy for proteome analysis.
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Affiliation(s)
- Nadia Taouatas
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands
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Muñoz J, Heck AJR. Quantitative proteome and phosphoproteome analysis of human pluripotent stem cells. Methods Mol Biol 2011; 767:297-312. [PMID: 21822884 DOI: 10.1007/978-1-61779-201-4_22] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding the signaling pathways governing pluripotency and self-renewal is a prerequisite for better controlling stem cell differentiation to specific fates. Reversible protein phosphorylation is one of the most important posttranslational modifications regulating signaling pathways in biological processes. Global analysis of dynamic changes in protein phosphorylation is, therefore, key to understanding signaling at the system level. Here, we describe a generic mass spectrometry (MS)-based phosphoproteomics strategy applied to monitor phosphorylation dynamics after bone morphogenetic protein 4 (BMP4)-induced differentiation of human embryonic stem cells (hESCs). Our method combines the use of strong cation exchange (SCX) and titanium dioxide (TiO(2)) for phosphopeptide enrichment, high-resolution MS for peptide and protein identification, and stable isotope labeling by amino acids in cell culture (SILAC) for quantification. This approach allows us to identify thousands of phosphorylation sites and profile their relative abundance during differentiation. This systems-biology-based approach provides new insights into how human pluripotent stem cells exit the pluripotent state.
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Affiliation(s)
- Javier Muñoz
- Bijvoet Center for Biomolecular Research, Biomolecular Mass Spectrometry and Proteomics Group, Utrecht, The Netherlands
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33
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Lee DY, Chang GD. Electrolytic reduction: modification of proteins occurring in isoelectric focusing electrophoresis and in electrolytic reactions in the presence of high salts. Anal Chem 2009; 81:3957-64. [PMID: 19438264 PMCID: PMC2682429 DOI: 10.1021/ac900281n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artifacts in two-dimensional electrophoresis (2-DE) caused by the presence of salts in isoelectric focusing (IEF) have been previously described as a result of increasing conductivity and inducing electroosmosis. However, electrolysis induced by the presence of salts should not be disregarded. In this study, electrolytic reduction−oxidation reaction (redox) was found to be enhanced in the presence of salts in IEF. The consequence of the electrolytic redox leads to acidification of the low-pH region and alkalization of the high-pH region within the immobilized pH gradient (IPG) strip. As a result, a breakdown of immobilized pH buffer near the high pH region of IPG strips along with reduction of basic proteins resulted in uncharacterized artifacts in 2-DE. Electrolytic reduction in the presence of alkali and alkaline metal ions was demonstrated to reduce 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), protein disulfide bonds, and protein carboxylic acids. Importantly, semipreparative electrolytic reduction of proteins can be carried out in the presence of sodium ions in a homemade electrolytic apparatus. These findings give additional explanations to the observed artifacts in 2-DE and reveal the unknown effects of salts in IEF. Moreover, we have provided a method with the potential to convert proteins or peptides to corresponding modified products containing aldehyde groups that can be used for conjugation with amine-containing compounds.
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Affiliation(s)
- Der-Yen Lee
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, P.O. Box 23-106, Taipei 106, Taiwan
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34
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Etheridge N, Lewohl JM, Mayfield RD, Harris RA, Dodd PR. Synaptic proteome changes in the superior frontal gyrus and occipital cortex of the alcoholic brain. Proteomics Clin Appl 2009; 3:730-742. [PMID: 19924264 DOI: 10.1002/prca.200800202] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cognitive deficits and behavioral changes that result from chronic alcohol abuse are a consequence of neuropathological changes which alter signal transmission through the neural network. To focus on the changes that occur at the point of connection between the neural network cells, synaptosomal preparations from post-mortem human brain of six chronic alcoholics and six non-alcoholic controls were compared using 2D-DIGE. Functionally affected and spared regions (superior frontal gyrus, SFG, and occipital cortex, OC, respectively) were analyzed from both groups to further investigate the specific pathological response that alcoholism has on the brain. Forty-nine proteins were differentially regulated between the SFG of alcoholics and the SFG of controls and 94 proteins were regulated in the OC with an overlap of 23 proteins. Additionally, the SFG was compared to the OC within each group (alcoholics or controls) to identify region specific differences. A selection were identified by MALDI-TOF mass spectrometry revealing proteins involved in vesicle transport, metabolism, folding and trafficking, and signal transduction, all of which have the potential to influence synaptic activity. A number of proteins identified in this study have been previously related to alcoholism; however, the focus on synaptic proteins has also uncovered novel alcoholism-affected proteins. Further exploration of these proteins will illuminate the mechanisms altering synaptic plasticity, and thus neuronal signaling and response, in the alcoholic brain.
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Affiliation(s)
- Naomi Etheridge
- School of Molecular and Microbial Sciences, University of Queensland, St Lucia, Queensland, 4072, Australia
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35
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Dormeyer W, van Hoof D, Mummery CL, Krijgsveld J, Heck AJR. A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. Proteomics 2008; 8:4036-53. [DOI: 10.1002/pmic.200800143] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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36
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Martinez A, Traverso JA, Valot B, Ferro M, Espagne C, Ephritikhine G, Zivy M, Giglione C, Meinnel T. Extent of N-terminal modifications in cytosolic proteins from eukaryotes. Proteomics 2008; 8:2809-31. [PMID: 18655050 DOI: 10.1002/pmic.200701191] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Most proteins in all organisms undergo crucial N-terminal modifications involving N-terminal methionine excision, N-alpha-acetylation or N-myristoylation (N-Myr), or S-palmitoylation. We investigated the occurrence of these poorly annotated but essential modifications in proteomes, focusing on eukaryotes. Experimental data for the N-terminal sequences of animal, fungi, and archaeal proteins, were used to build dedicated predictive modules in a new software. In vitro N-Myr experiments were performed with both plant and animal N-myristoyltransferases, for accurate prediction of the modification. N-terminal modifications from the fully sequenced genome of Arabidopsis thaliana were determined by MS. We identified 105 new modified protein N-termini, which were used to check the accuracy of predictive data. An accuracy of more than 95% was achieved, demonstrating (i) overall conservation of the specificity of the modification machinery in higher eukaryotes and (ii) robustness of the prediction tool. Predictions were made for various proteomes. Proteins that had undergone both N-terminal methionine (Met) cleavage and N-acetylation were found to be strongly overrepresented among the most abundant proteins, in contrast to those retaining their genuine unblocked Met. Here we propose that the nature of the second residue of an ORF is a key marker of the abundance of the mature protein in eukaryotes.
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Affiliation(s)
- Aude Martinez
- Institut des Sciences du Végétal, UPR2355, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
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Hellman J. Stabilization of thin-layer agarose gels after isoelectric focusing with polyacrylamide enables reverse imidazole-zinc staining and facilitates two-dimensional gel electrophoresis. Anal Bioanal Chem 2008; 392:239-45. [DOI: 10.1007/s00216-008-2247-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 05/21/2008] [Accepted: 06/12/2008] [Indexed: 11/29/2022]
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38
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Navare A, Zhou M, McDonald J, Noriega FG, Sullards MC, Fernandez FM. Serum biomarker profiling by solid-phase extraction with particle-embedded micro tips and matrix-assisted laser desorption/ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:997-1008. [PMID: 18320548 PMCID: PMC2665883 DOI: 10.1002/rcm.3462] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
One of the main challenges in high-throughput serum profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is the development of proteome fractionation approaches that allow the acquisition of reproducible profiles with a maximum number of spectral features and minimum interferences from biological matrices. This study evaluates a new class of solid-phase extraction (SPE) pipette tips embedded with different chromatographic media for fractionation of model protein digests and serum samples. The materials embedded include strong anion exchange (SAX), weak cation exchange (WCX), C18, C8, C4, immobilized metal affinity chromatography (IMAC) and zirconium dioxide particles. Simple and rapid serum proteome profiling protocols based on these SPE micro tips are described and tested using a variety of MALDI matrices. We show that different types of particle-embedded SPE micro tips provide complementary information in terms of the spectral features detected for beta-casein digests and control human serum samples. The effect of different sample pretreatments, such as serum dilution and ultrafiltration using molecular weight cut-off membranes, and the reproducibility observed for replicate experiments, are also evaluated. The results demonstrate the usefulness of these simple SPE tips combined with offline MALDI-TOF MS for obtaining information-rich serum profiles, resulting in a robust, versatile and reproducible open-source platform for serum biomarker discovery.
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Affiliation(s)
- Arti Navare
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Manshui Zhou
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - John McDonald
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Fernando G. Noriega
- Department of Biology, Florida International University, Miami, FL 33199, USA
| | - M. Cameron Sullards
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Facundo M. Fernandez
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Tran B, Pepaj M, Lundanes E, Greibrokk T. The Behaviour of Reduced, Alkylated and Native Proteins in a pH-Gradient LC System. Chromatographia 2007. [DOI: 10.1365/s10337-007-0390-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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40
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Barelli S, Crettaz D, Thadikkaran L, Rubin O, Tissot JD. Plasma/serum proteomics: pre-analytical issues. Expert Rev Proteomics 2007; 4:363-70. [PMID: 17552920 DOI: 10.1586/14789450.4.3.363] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High-throughput proteomics technologies tend to provide highly sensitive information about living tissues and biological fluids. Analytes are characterized by intrinsic and extrinsic properties, the latter depending on each phase of their preparation, sometimes adding artifacts with crucial repercussions in result reliability and interpretation. This review aims to address some issues that can be encountered when handling plasma and serum in experimental and clinical proteomic settings.
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Affiliation(s)
- Stefano Barelli
- Service Régional Vaudois de Transfusion Sanguine, Lausanne, Switzerland.
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