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Srzentić K, Zhurov KO, Lobas AA, Nikitin G, Fornelli L, Gorshkov MV, Tsybin YO. Chemical-Mediated Digestion: An Alternative Realm for Middle-down Proteomics? J Proteome Res 2018; 17:2005-2016. [PMID: 29722266 DOI: 10.1021/acs.jproteome.7b00834] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein digestion in mass spectrometry (MS)-based bottom-up proteomics targets mainly lysine and arginine residues, yielding primarily 0.6-3 kDa peptides for the proteomes of organisms of all major kingdoms. Recent advances in MS technology enable analysis of complex mixtures of increasingly longer (>3 kDa) peptides in a high-throughput manner supporting the development of a middle-down proteomics (MDP) approach. Generating longer peptides is a paramount step in launching an MDP pipeline, but the quest for the selection of a cleaving agent that would provide the desired 3-15 kDa peptides remains open. Recent bioinformatics studies have shown that cleavage at the rarely occurring amino acid residues such as methionine (Met), tryptophan (Trp), or cysteine (Cys) would be suitable for MDP approach. Interestingly, chemical-mediated proteolytic cleavages uniquely allow targeting these rare amino acids, for which no specific proteolytic enzymes are known. Herein, as potential candidates for MDP-grade proteolysis, we have investigated the performance of chemical agents previously reported to target primarily Met, Trp, and Cys residues: CNBr, BNPS-Skatole (3-bromo-3-methyl-2-(2-nitrophenyl)sulfanylindole), and NTCB (2-nitro-5-thiobenzoic acid), respectively. Figures of merit such as digestion reproducibility, peptide size distribution, and occurrence of side reactions are discussed. The NTCB-based MDP workflow has demonstrated particularly attractive performance, and NTCB is put forward here as a potential cleaving agent for further MDP development.
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Affiliation(s)
- Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | | | - Anna A Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia
| | - Gennady Nikitin
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Luca Fornelli
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. , Dolgoprudny, Moscow 141707 , Russia
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park , Lausanne 1015 , Switzerland
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2
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Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
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Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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3
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Fang X, Zhao J, Zhang K, Yang P, Qiao L, Liu B. Polydopamine Grafted Porous Graphene as Biocompatible Nanoreactor for Efficient Identification of Membrane Proteins. ACS APPLIED MATERIALS & INTERFACES 2016; 8:6363-6370. [PMID: 26913964 DOI: 10.1021/acsami.6b00407] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Functional nanomaterials, used as nanoreactors, have shown great advantages in a variety of applications in biomedical fields. Herein, we designed a novel nanoreactor system toward the application in membrane proteomics by using polydopamine-coated nanoporous graphene foams (NGFs-PD) prepared by a facile in situ oxidative polymerization. Taking advantage of the unique 3-D structure and surface functionalization, NGFs-PD can quickly adsorb a large amount of hydrophobic membrane proteins dissolved in sodium dodecyl sulfonate (SDS)/methanol and hydrophilic trypsin in aqueous solution, and then confine the proteolysis in the nanoscale domains to fasten the reaction rate. Therefore, the current nanoreactor system combines the multifunctions of highly efficient solubilization, immobilization, and proteolysis of membrane proteins. With the nanoreactor, digestion of standard membrane proteins can be finished in 10 min. 893 membrane proteins were identified from human glioma cells (U251). All these superiorities indicate that the biocompatible NGFs-PD nanoreactor system is of great promise to facilitate high-throughput membrane proteomic analysis.
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Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Jingjing Zhao
- Department of Chemistry, Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Kun Zhang
- Department of Chemistry, Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry, Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Liang Qiao
- Department of Chemistry, Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Institute of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
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4
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Abstract
The blood serum proteome may be an ideal source of disease biomarkers, although its complexity necessitates novel strategies to enrich and quantify lower-abundance proteins with biomarker utility. Herein, serum samples from pre-diagnosis pancreatic cancer cases and controls were compared using a workflow of immunodepletion, multi-lectin fractionation, and peptide tandem mass tag (TMT) labeling. Samples were then subjected to SCX and high pH reversed-phase fractionation and analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). The aim was the discovery of candidate serum biomarkers of pancreatic cancer, although the method is applicable to any comparative proteomic analysis of serum samples.
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5
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Shahinian H, Tholen S, Schilling O. Proteomic identification of protease cleavage sites: cell-biological and biomedical applications. Expert Rev Proteomics 2014; 10:421-33. [DOI: 10.1586/14789450.2013.841547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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6
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Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates. Nat Protoc 2011; 6:1578-611. [PMID: 21959240 DOI: 10.1038/nprot.2011.382] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we describe the step-by-step procedures for performing terminal amine isotopic labeling of substrates (TAILS), a 2- to 3-d (depending on method of labeling) high-throughput method to identify and distinguish protease-generated neo-N termini from mature protein N termini with all natural modifications with high confidence. TAILS uses negative selection to enrich for all N-terminal peptides and uses primary amine labeling-based quantification as the discriminating factor. Labeling is versatile and suited to many applications, including biochemical and cell culture analyses in vitro; in vivo analyses using tissue samples from animal and human sources can also be readily performed. At the protein level, N-terminal and lysine amines are blocked by dimethylation (formaldehyde/sodium cyanoborohydride) and isotopically labeled by incorporating heavy and light dimethylation reagents or stable isotope labeling with amino acids in cell culture labels. Alternatively, easy multiplex sample analysis can be achieved using amine blocking and labeling with isobaric tags for relative and absolute quantification, also known as iTRAQ. After tryptic digestion, N-terminal peptide separation is achieved using a high-molecular-weight dendritic polyglycerol aldehyde polymer that binds internal tryptic and C-terminal peptides that now have N-terminal alpha amines. The unbound naturally blocked (acetylation, cyclization, methylation and so on) or labeled mature N-terminal and neo-N-terminal peptides are recovered by ultrafiltration and analyzed by tandem mass spectrometry (MS/MS). Hierarchical substrate winnowing discriminates substrates from the background proteolysis products and non-cleaved proteins by peptide isotope quantification and bioinformatics search criteria.
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7
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Lee JE, Kwon J, Baek MC. A combination method of chemical with enzyme reactions for identification of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:397-404. [PMID: 21146638 DOI: 10.1016/j.bbapap.2010.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 11/30/2010] [Accepted: 12/02/2010] [Indexed: 11/29/2022]
Abstract
A simple method for effective analysis of various proteins has been developed, including membrane proteins, with LC-MS/MS, using CNBr and acetic acid cleavage in one reaction for the digestion of both the M/ and /D/ positions within the target proteins. This dual chemical reaction has been compared with traditional CNBr or an acid cleavage method using a rat kidney membrane fraction and it showed an advantage of the dual reaction with respect to a high number of peptides detected and a high protein recovery. Furthermore, when this dual chemical reaction was combined with trypsin digestion, the number of proteins surprisingly increased approximately 3.0 times more than in the cases with the trypsin digestion only. It was also 1.9 times more than in cases dealing with Tube-Gel trypsin digestion, which is one of the most efficient digestion methods. In addition, it was shown that this dual chemical reaction could be applied to an in-gel digestion. Using the combination of the chemical and enzyme reaction, 172 proteins including 95 membrane proteins were identified. This indicated that this method is one of the efficient systems in single MS/MS analysis. In particular, many membrane proteins identified in this study were detected by a new combination, but not by a traditional trypsin digestion method.
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Affiliation(s)
- Jeong-Eun Lee
- Dept. of Molecular Medicine, Kyungpook National University, Daegu, 700-422, Republic of Korea.
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8
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García-Murria MJ, Valero ML, Sánchez del Pino MM. Simple chemical tools to expand the range of proteomics applications. J Proteomics 2010; 74:137-50. [PMID: 21074642 DOI: 10.1016/j.jprot.2010.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Revised: 10/08/2010] [Accepted: 11/03/2010] [Indexed: 12/26/2022]
Abstract
Proteomics is an expanding technology with potential applications in many research fields. Even though many research groups do not have direct access to its main analytical technique, mass spectrometry, they can interact with proteomics core facilities to incorporate this technology into their projects. Protein identification is the analysis most frequently performed in core facilities and is, probably, the most robust procedure. Here we discuss a few chemical reactions that are easily implemented within the conventional protein identification workflow. Chemical modification of proteins with N-hydroxysuccinimide esters, 4-sulfophenyl isothiocyanate, O-methylisourea or through β-elimination/Michael addition can be easily performed in any laboratory. The reactions are quite specific with almost no side reactions. These chemical tools increase considerably the number of applications and have been applied to characterize protein-protein interactions, to determine the N-terminal residues of proteins, to identify proteins with non-sequenced genomes or to locate phosphorylated and O-glycosylated.
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Affiliation(s)
- María Jesús García-Murria
- Laboratorio de Proteómica, Centro de Investigación Príncipe Felipe, Avda, Autopista del Saler 16, 46012 Valencia, Spain
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9
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Nakajima C, Kuyama H, Nakazawa T, Nishimura O, Tsunasawa S. A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry. Analyst 2010; 136:113-9. [PMID: 20936200 DOI: 10.1039/c0an00384k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A method for de novo sequencing of N(α)-blocked proteins by mass spectrometry (MS) is presented. The approach consists of enzymatic digestion of N(α)-blocked protein, recovery of N-terminal peptide by depletion of non-N-terminal peptides from the digest pool, and selective derivatization of a C-terminal α-carboxyl group of isolated N-terminal peptide. The C-terminal α-carboxyl group of the N-terminal peptide was selectively derivatized with 3-aminopropyl-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-propylamine), according to oxazolone chemistry. The reagent TMPP-propylamine was designed to facilitate sequence analysis with MALDI-MS by mass- and charge-tagging. All of the identities and N-terminal sequences of two N(α)-acetylated proteins (rabbit phosphorylase b and bovine calmodulin) and human orexin A, which has pyroglutamic acid at the N-terminus, were successfully analyzed by allowing for the y-type ions almost exclusively.
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Affiliation(s)
- Chihiro Nakajima
- Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
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10
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Impens F, Colaert N, Helsens K, Plasman K, Van Damme P, Vandekerckhove J, Gevaert K. MS-driven protease substrate degradomics. Proteomics 2010; 10:1284-96. [PMID: 20058249 DOI: 10.1002/pmic.200900418] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteolytic processing has recently received increased attention in the field of signal propagation and cellular differentiation. Because of its irreversible nature, protein cleavage has been associated with committed steps in cell function. One aspect of protease biology that boomed the past few years is the detailed characterization of protease substrates by both shotgun as well as targeted MS-driven proteomics techniques. The most promising techniques are discussed in this review and we further elaborate on the bioinformatics challenges that accompany mainly qualitative, MS-driven protease substrate degradome studies.
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Affiliation(s)
- Francis Impens
- Department of Medical Protein Research, VIB, Ghent, Belgium
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11
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auf dem Keller U, Schilling O. Proteomic techniques and activity-based probes for the system-wide study of proteolysis. Biochimie 2010; 92:1705-14. [PMID: 20493233 DOI: 10.1016/j.biochi.2010.04.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/29/2010] [Indexed: 11/17/2022]
Abstract
Proteolysis constitutes a major post-translational modification but specificity and substrate selectivity of numerous proteases have remained elusive. In this review, we highlight how advanced techniques in the areas of proteomics and activity-based probes can be used to investigate i) protease active site specificity; ii) protease in vivo substrates; iii) protease contribution to proteome homeostasis and composition; and iv) detection and localization of active proteases. Peptide libraries together with genetical or biochemical selection have traditionally been used for active site profiling of proteases. These are now complemented by proteome-derived peptide libraries that simultaneously determine prime and non-prime specificity and characterize subsite cooperativity. Cell-contextual discovery of protease substrates is rendered possible by techniques that isolate and quantitate protein termini. Here, a novel approach termed Terminal Amine Isotopic Labeling of Substrates (TAILS) provides an integrated platform for substrate discovery and appropriate statistical evaluation of terminal peptide identification and quantification. Proteolytically generated carboxy-termini can now also be analyzed on a proteome-wide level. Proteolytic regulation of proteome composition is monitored by quantitative proteomic approaches employing stable isotope coding or label free quantification. Activity-based probes specifically recognize active proteases. In proteomic screens, they can be used to detect and quantitate proteolytic activity while their application in cellular histology allows to locate proteolytic activity in situ. Activity-based probes - especially in conjunction with positron emission tomography - are also promising tools to monitor proteolytic activities on an organism-wide basis with a focus on in vivo tumor imaging. Together, this array of methodological possibilities enables unveiling physiological protease substrate repertoires and defining protease function in the cellular- and organism-wide context.
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Affiliation(s)
- Ulrich auf dem Keller
- ETH Zürich Institute of Cell Biology, Schafmattstrasse 18, CH-8093 Zurich, Switzerland
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12
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Kleifeld O, Doucet A, auf dem Keller U, Prudova A, Schilling O, Kainthan RK, Starr AE, Foster LJ, Kizhakkedathu JN, Overall CM. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat Biotechnol 2010; 28:281-8. [PMID: 20208520 DOI: 10.1038/nbt.1611] [Citation(s) in RCA: 423] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 01/28/2010] [Indexed: 11/09/2022]
Abstract
Effective proteome-wide strategies that distinguish the N-termini of proteins from the N-termini of their protease cleavage products would accelerate identification of the substrates of proteases with broad or unknown specificity. Our approach, named terminal amine isotopic labeling of substrates (TAILS), addresses this challenge by using dendritic polyglycerol aldehyde polymers that remove tryptic and C-terminal peptides. We analyze unbound naturally acetylated, cyclized or labeled N-termini from proteins and their protease cleavage products by tandem mass spectrometry, and use peptide isotope quantification to discriminate between the substrates of the protease of interest and the products of background proteolysis. We identify 731 acetylated and 132 cyclized N-termini, and 288 matrix metalloproteinase (MMP)-2 cleavage sites in mouse fibroblast secretomes. We further demonstrate the potential of our strategy to link proteases with defined biological pathways in complex samples by analyzing mouse inflammatory bronchoalveolar fluid and showing that expression of the poorly defined breast cancer protease MMP-11 in MCF-7 human breast cancer cells cleaves both endoplasmin and the immunomodulator and apoptosis inducer galectin-1.
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Affiliation(s)
- Oded Kleifeld
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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13
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Abstract
We describe a method for the specific isolation of representative N-terminal peptides of proteins and their proteolytic fragments. Their isolation is based on a gel-free, peptide-centric proteomics approach using the principle of diagonal chromatography. We will indicate that the introduction of an altered chemical property to internal peptides holding a free alpha-N-terminus results in altered column retention of these peptides, thereby enabling the isolation and further characterization by mass spectrometry of N-terminal peptides. Besides pointing to changes in protein expression levels when performing such proteome surveys in a differential modus, protease specificity and substrate repertoires can be allocated since both are specified by neo-N-termini generated after a protease cleavage event. As such, our gel-free proteomics technology is widely applicable and amenable for a variety of proteome-driven protease degradomics research.
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14
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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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15
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Yamaguchi M, Nakayama D, Shima K, Kuyama H, Ando E, Okamura TA, Ueyama N, Nakazawa T, Norioka S, Nishimura O, Tsunasawa S. Selective isolation of N-terminal peptides from proteins and their de novo sequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without regard to unblocking or blocking of N-terminal amino acids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3313-3319. [PMID: 18821723 DOI: 10.1002/rcm.3735] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have developed a new method to determine the N-terminal amino acid sequences of proteins, regardless of whether their N-termini are modified. This method consists of the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling of sulfo-NHS-SS-biotin to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease followed by oxidation with performic acid; (4) specific isolation of N-terminal peptides from digests using DITC resins; (5) de novo sequence analysis of the N-terminal peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using the CAF (chemically assisted fragmentation) method or tandem mass spectrometric (MS/MS) analysis according to unblocked or blocked peptides, respectively. By employing DITC resins instead of avidin resins used in our previous method (Yamaguchi et al., Rapid Commun. Mass Spectrom. 2007; 21: 3329), it has been possible to isolate selectively N-terminal peptides from proteins regardless of modification of N-terminal amino acids. Here we propose a universal method for N-terminal sequence analysis of proteins.
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Affiliation(s)
- Minoru Yamaguchi
- Life Science Business Department, Shimadzu Corporation, Kyoto 604-8511, Japan.
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16
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Kuyama H, Sonomura K, Nishimura O, Tsunasawa S. A method for N-terminal de novo sequence analysis of proteins by matrix-assisted laser desorption/ionization mass spectrometry. Anal Biochem 2008; 380:291-6. [PMID: 18577371 DOI: 10.1016/j.ab.2008.05.053] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 05/30/2008] [Accepted: 05/30/2008] [Indexed: 11/16/2022]
Abstract
A novel method for isolation and de novo sequencing of N-terminal peptides from proteins is described. The method presented here combines selective chemical tagging using succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) at the N(alpha)-amino group of peptides after digestion by metalloendopeptidase (from Grifola frondosa) and selective capture procedures using p-phenylenediisothiocyanate resin, by which the N-terminal peptide can be isolated, whether or not it is N-terminally blocked. The isolated N-terminal peptide modified N-terminally with TMPP-Ac-OSu reagent produces a simple fragmentation pattern under tandem mass spectrometric analysis to significantly facilitate sequencing.
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Affiliation(s)
- Hiroki Kuyama
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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17
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Nakazawa T, Yamaguchi M, Okamura TA, Ando E, Nishimura O, Tsunasawa S. Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS. Proteomics 2008; 8:673-85. [PMID: 18214847 DOI: 10.1002/pmic.200700084] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In proteomics, MS plays an essential role in identifying and quantifying proteins. To characterize mature target proteins from living cells, candidate proteins are often analyzed with PMF and MS/MS ion search methods in combination with computational search routines based on bioinformatics. In contrast to shotgun proteomics, which is widely used to identify proteins, proteomics based on the analysis of N- and C-terminal amino acid sequences (terminal proteomics) should render higher fidelity results because of the high information content of terminal sequence and potentially high throughput of the method not requiring very high sequence coverage to be achieved by extensive sequencing. In line with this expectation, we review recent advances in methods for N- and C-terminal amino acid sequencing of proteins. This review focuses mainly on the methods of N- and C-terminal analyses based on MALDI-TOF MS for its easy accessibility, with several complementary approaches using LC/MS/MS. We also describe problems associated with MS and possible remedies, including chemical and enzymatic procedures to enhance the fidelity of these methods.
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18
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Jiang X, Ye M, Zou H. Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis. Proteomics 2008; 8:686-705. [DOI: 10.1002/pmic.200700617] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Gevaert K, Impens F, Van Damme P, Ghesquière B, Hanoulle X, Vandekerckhove J. Applications of diagonal chromatography for proteome-wide characterization of protein modifications and activity-based analyses. FEBS J 2007; 274:6277-89. [PMID: 18021238 DOI: 10.1111/j.1742-4658.2007.06149.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous gel-free proteomics techniques have been reported over the past few years, introducing a move from proteins to peptides as bits of information in qualitative and quantitative proteome studies. Many shotgun proteomics techniques randomly sample thousands of peptides in a qualitative and quantitative manner but overlook the vast majority of protein modifications that are often crucial for proper protein structure and function. Peptide-based proteomic approaches have thus been developed to profile a diverse set of modifications including, but not at all limited, to phosphorylation, glycosylation and ubiquitination. Typical here is that each modification needs a specific, tailor-made analytical procedure. In this minireview, we discuss how one technique - diagonal reverse-phase chromatography - is applied to study two different types of protein modification: protein processing and protein N-glycosylation. Additionally, we discuss an activity-based proteome study in which purine-binding proteins were profiled by diagonal chromatography.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
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Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007; 7:2698-718. [PMID: 17640001 DOI: 10.1002/pmic.200700114] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel-free proteomics techniques. In this review, we discuss several of these gel-free techniques both for monitoring protein concentration changes and protein modifications, in particular protein phosphorylation, glycosylation, and protein processing. Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
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21
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Abstract
Alzheimer's disease (AD) is a horribly debilitating disease that will increase in prevalence as the populations of the USA and Europe continue to age. It is expected that the USA alone will see some 16 million cases by 2050. At present, there is no cure for the disease and early diagnosis is all but impossible. The onset of disease is not manifested clinically and little is known regarding the cause of nonfamiliar AD. There is a need for biomarkers associated with AD to aid the diagnosis of this disease and to detect progression. Especially needed are biomarkers to monitor the effect of new drugs and therapeutic strategies as they are developed. A biomarker may be a genetic trait, a biochemical change, such as a protein, peptide or metabolite, or a change in a structural or functional feature detected using imaging technology. This review aims to cover the important field of biomarker research in association with AD.
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Affiliation(s)
- Malcolm Ward
- Proteome Sciences plc, South Wing Laboratory (PO 045), Institute of Psychiatry, London, SE5 8AF, UK.
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22
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Desrivières S, Kuhn K, Müller J, Gläser M, Laria NCP, Korder J, Sonnentag M, Neumann T, Schwarz J, Schäfer J, Hamon C, Groner B, Prinz T. Comparison of the nuclear proteomes of mammary epithelial cells at different stages of functional differentiation. Proteomics 2007; 7:2019-37. [PMID: 17514683 DOI: 10.1002/pmic.200600994] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The progression of stem cells to proliferating progenitor cells and finally to a quiescent differentiated state is a hallmark of organ development. This process proceeds through distinct steps and is regulated through cell-cell interactions and by systemically and locally acting factors. We have established a cell culture system which recapitulates features of mammary gland development in vitro and allows the comparison of three characteristic differentiation stages. Cell fate decisions relating to proliferation and differentiation are dependent on the function of proteins in the nucleus. Therefore, we have applied proteomic approaches, including 1- and 2-DE coupled with MS and a gel-free system, called protein sequence tag technology (PST), to assess the changes in the nuclear protein composition during differentiation of mammary epithelial cells. We identified about 250 individual proteins which are present in the nucleus of proliferating and functionally differentiated mammary epithelial cells. We functionally categorised the differentially expressed proteins and identified a multitude of proteins that regulate gene expression at the transcriptional or post-transcriptional level. This analysis greatly enriches our global view of the dynamic changes of nuclear proteins during the development of mammary epithelial cells and suggests models for the control of differentiation-specific protein expression.
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23
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Abstract
We developed a method for selective isolation of N-blocked peptides from a complex mixture such as an enzymatic digest of a protein. The approach is based on a newly designed isocyanate-resin (resin-NCO), which specifically reacts with alpha-amino or imino groups. This method, then, permits the isolation of N-blocked peptides, even those containing Lys, from a peptide mixture as intact forms by trapping N-free peptides via covalent bonding to the resin-NCO. The present study demonstrates the performance of this method for the selective isolation of N-blocked peptides by applying it to several peptide mixtures, including proteolytic digests.
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Affiliation(s)
- Toshiyuki Mikami
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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24
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Affiliation(s)
- Anna E Speers
- Department of Pharmacology, University of Colorado School of Medicine, P.O. Box 6511, MS 8303, Aurora, Colorado 80045, USA
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25
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Lovestone S, Güntert A, Hye A, Lynham S, Thambisetty M, Ward M. Proteomics of Alzheimer's disease: understanding mechanisms and seeking biomarkers. Expert Rev Proteomics 2007; 4:227-38. [PMID: 17425458 DOI: 10.1586/14789450.4.2.227] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Alzheimer's disease is the scourge of the modern, aging world: a costly, damaging disease that robs the elderly of their ability to function as well as their memories. Three decades of progress have resulted in a deep understanding of the pathological processes and a range of targets for therapy, many of which have advanced to late-stage clinical trials. Proteomics has contributed greatly to these advances and will continue to have a growing role in determining the nature of the pathological lesions in the brain. In addition, proteomics (both gel based and gel free, mass spectrometry based), is likely to play an increasing role in identifying biomarkers that may assist in early diagnosis and in monitoring progression and, most importantly, response to therapy.
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Affiliation(s)
- Simon Lovestone
- Institute of Psychiatry, MRC Centre for Neurodegeneration Research and NIHR Biomedical Research Centre, KCL, London, UK.
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26
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Jones BJ, Vergne MJ, Bunk DM, Locascio LE, Hayes MA. Cleavage of Peptides and Proteins Using Light-Generated Radicals from Titanium Dioxide. Anal Chem 2007; 79:1327-32. [PMID: 17297930 DOI: 10.1021/ac0613737] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein identification and characterization often requires cleavage into distinct fragments. Current methods require proteolytic enzymes or chemical agents and typically a second reagent to discontinue cleavage. We have developed a selective cleavage process for peptides and proteins using light-generated radicals from titanium dioxide. The hydroxyl radicals, produced at the TiO(2) surface using UV light, are present for only hundreds of microseconds and are confined to a defined reagent zone. Peptides and proteins can be moved past the "reagent zone", and cleavage is tunable through residence time, illumination time, and intensity. Using this method, products are observed consistent with cleavage at proline residues. These initial experiments indicate the method is rapid, specific, and reproducible. In certain configurations, cleavage products are produced in less than 10 s. Reproducible product patterns consistent with cleavage of the peptide bond at proline for angiotensin I, Lys-bradykinin, and myoglobin are demonstrated using capillary electrophoresis. Mass characterization of fragments produced in the cleavage of angiotensin I was obtained using liquid chromatography-mass spectrometry. In addition to the evidence supporting cleavage at proline, enkephalin and peptide A-779, two peptides that do not contain proline, showed no evidence of cleavage under the same conditions.
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27
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Coussot G, Hawke DH, Mularz A, Koomen JM, Kobayashi R. A method for the isolation of blocked N-terminal peptides. Anal Biochem 2007; 361:302-4. [PMID: 17188638 DOI: 10.1016/j.ab.2006.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Revised: 11/02/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Affiliation(s)
- Gaëlle Coussot
- Department of Molecular Pathology, University of Texas, M. D. Anderson Cancer Center, Houston, TX 77230, USA
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28
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Leitner A, Lindner W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics 2007; 6:5418-34. [PMID: 16972287 DOI: 10.1002/pmic.200600255] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As proteomics matures from a purely descriptive to a function-oriented discipline of the life sciences, there is strong demand for novel methodologies that increase the depth of information that can be obtained from proteomic studies. MS has long played a central role for protein identification and characterization, often in combination with dedicated chemical modification reactions. Today, chemistry is helping to advance the field of proteomics in numerous ways. In this review, we focus on those methodologies that have a significant impact for the large-scale study of proteins and peptides. This includes approaches that allow the introduction of affinity tags for the enrichment of subclasses of peptides or proteins and strategies for in vitro stable isotope labeling for quantification purposes, among others. Particular attention is given to the study of PTMs where recent advancements have been promising, but many interesting targets are not yet being addressed.
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Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Vienna, Austria.
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29
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Gevaert K, Van Damme P, Ghesquière B, Vandekerckhove J. Protein processing and other modifications analyzed by diagonal peptide chromatography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1801-10. [PMID: 17035109 DOI: 10.1016/j.bbapap.2006.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 09/06/2006] [Accepted: 09/06/2006] [Indexed: 11/29/2022]
Abstract
Diagonal peptide chromatography consists of two consecutive, identical peptide separations with in between an enzymatic or chemical alteration of the side-chain structure of selected peptides. Such selected and altered peptides acquire different chromatographic properties thereby segregating from non-altered peptides in a series of secondary peptide separations. Originally described by Brown and Hartley in 1966, we have modified the technique such that it can be used for higher throughput gel-free proteomics. Our technique is termed COmbined FRActional DIagonal Chromatography (COFRADIC) and exploits evoked differences of the hydrophobicity of peptides in reverse-phase liquid chromatography. One important advantage of COFRADIC is its versatility: by changing the alteration reaction, different classes of peptides are sorted and finally analyzed. We previously published protocols and applications for separating methionyl, cysteinyl, amino terminal and phosphorylated peptides. In this review, we assess the potential of COFRADIC for the analysis of several posttranslational modifications emphasizing on in vivo protein processing events. Additional modifications that can be analyzed include phosphorylation and N-glycosylation. The potential of COFRADIC for isolating peptides holding such modified amino acids are discussed here.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
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30
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Wei C, Yang J, Zhu J, Zhang X, Leng W, Wang J, Xue Y, Sun L, Li W, Wang J, Jin Q. Comprehensive Proteomic Analysis ofShigellaflexneri2a Membrane Proteins. J Proteome Res 2006; 5:1860-5. [PMID: 16889407 DOI: 10.1021/pr0601741] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Shigella flexneri is the causative agent of most shigellosis cases in developing countries. We used different proteolytic enzymes to selectively shave the protruding proteins on the surface of purified bacterial membrane sheets or vesicles, and recovered peptides were subsequently identified using 2-D LC-MS/MS. As a result, a total of 666 proteins were unambiguously assigned, including 159 integral membrane proteins, 35 outer membrane proteins and 114 proteins previously annotated as hypothetical. The former had an average grand average hydrophobicity score of 0.362 and were predicted to separate within a pH range of 4.1-10.6 with molecular mass 8-148 kDa, which represents the largest validated set of integral membrane proteins in this organism to date. A functional classification revealed that a large proportion of the identified proteins were involved in cell envelope biogenesis and energy production and conversion. For the first time, this work provides a global view of the S. flexneri 2a membrane subproteome.
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Affiliation(s)
- Candong Wei
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, CAMS, Beijing 100730, Peoples Republic of China
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31
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Guillaume E, Panchaud A, Affolter M, Desvergnes V, Kussmann M. Differentially isotope-coded N-terminal protein sulphonation: combining protein identification and quantification. Proteomics 2006; 6:2338-49. [PMID: 16526082 DOI: 10.1002/pmic.200500527] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most proteomic labelling technologies intend to improve protein quantification and/or facilitate (de novo) peptide sequencing. We present here a novel stable-isotope labelling method to simultaneously identify and quantify protein components in complex mixtures by specifically derivatizing the N-terminus of proteins with 4-sulphophenyl isothiocyanate (SPITC). Our approach combines protein identification with quantification through differential isotope-coded labelling at the protein N-terminus prior to digestion. The isotope spacing of 6 Da (unlabelled vs. six-fold 13C-labelled tag) between derivatized peptide pairs enables the detection on different MS platforms (MALDI and ESI). Optimisation of the reaction conditions using SPITC was performed on three model proteins. Improved detection of the N-terminally derivatized peptide compared to the native analogue was observed in negative-ion MALDI-MS. Simpler fragmentation patterns compared to native peptides facilitated protein identification. The 13C-labelled SPITC resulted in convenient peptide pair spacing without isotopic overlap and hence facilitated relative quantification by MALDI-TOF/TOF and LC-ESI-MS/MS. The combination of facilitated identification and quantification achieved by differentially isotope-coded N-terminal protein tagging with light/heavy SPITC represents, to our knowledge, a new approach to quantitative proteomics.
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Affiliation(s)
- Elisabeth Guillaume
- Department of Bioanalytical Science, Functional Genomics Group, Nestlé Research Centre, Nestec, Lausanne, Switzerland
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32
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McDonald L, Robertson DHL, Hurst JL, Beynon RJ. Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat Methods 2005; 2:955-7. [PMID: 16299481 DOI: 10.1038/nmeth811] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 10/03/2005] [Indexed: 11/09/2022]
Abstract
Bottom-up proteomics is the analysis of peptides derived from single proteins or protein mixtures, and because each protein generates tens of peptides, there is scope for controlled reduction in complexity. We report here a new strategy for selective isolation of the N-terminal peptides of a protein mixture, yielding positionally defined peptides. The method is tolerant of several fragmentation methods, and the databases that must be searched are substantially less complex.
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Affiliation(s)
- Lucy McDonald
- Protein Function Group, Faculty of Veterinary Science, University of Liverpool, Crown Street, Liverpool L69 7ZJ, UK
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33
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Gevaert K, Van Damme P, Martens L, Vandekerckhove J. Diagonal reverse-phase chromatography applications in peptide-centric proteomics: Ahead of catalogue-omics? Anal Biochem 2005; 345:18-29. [PMID: 16181830 DOI: 10.1016/j.ab.2005.01.038] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Revised: 11/29/2004] [Accepted: 01/04/2005] [Indexed: 10/25/2022]
Abstract
Diagonal electrophoresis/chromatography was described 40 years ago and was used to isolate specific sets of peptides from simple peptide mixtures such as protease digests of purified proteins. Recently, we have adapted the core technology of diagonal chromatography so that the technique can be used in so-called gel-free, peptide-centric proteome studies. Here we review the different procedures we have developed over the past few years, sorting of methionyl, cysteinyl, amino terminal, and phosphorylated peptides. We illustrate the power of the technique, termed COFRADIC (combined fractional diagonal chromatography), in the case of a peptide-centric analysis of a sputum sol phase sample of a patient suffering from chronic obstructive pulmonary disease (COPD). We were able to identify an unexpectedly high number of intracellular proteins next to known biomarkers.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
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34
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Kuhn K, Prinz T, Schäfer J, Baumann C, Schärfke M, Kienle S, Schwarz J, Steiner S, Hamon C. Protein sequence tags: A novel solution for comparative proteomics. Proteomics 2005; 5:2364-8. [PMID: 15887190 DOI: 10.1002/pmic.200401306] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Comparative proteome profiling using stable isotope peptide labelling and mass spectrometry has emerged as a promising strategy. Here, we show the broad potential of our proprietary protein sequence tag (PST) technology. A special feature of PST is its ability to detect a wide variety of proteins including the pharmaceutically relevant membrane and nuclear proteins. This procedure addresses a similar number of proteins, compared to the multidimensional protein identification technology approach, but offers additionally a quantitative analysis with its recently developed quantitative PST version.
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Affiliation(s)
- Karsten Kuhn
- Proteome Sciences R&D, Frankfurt am Main, Germany
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35
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Affiliation(s)
- Jean-Philippe Lambert
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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36
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Prinz T, Müller J, Kuhn K, Schäfer J, Thompson A, Schwarz J, Hamon C. Characterization of Low Abundant Membrane Proteins Using the Protein Sequence Tag Technology. J Proteome Res 2004; 3:1073-81. [PMID: 15473698 DOI: 10.1021/pr049925u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
About 25% of open reading frames in fully sequenced genomes are estimated to encode transmembrane proteins that represent valuable targets for drugs. However, the global analysis of membrane proteins has been proven to be problematic, e.g., because of their very amphiphilic nature. In this paper, we show that the recently published Protein Sequence Tag (PST) technology combined with an efficient sample preparation is a powerful method to perform protein analysis of highly enriched membrane fractions. The PST approach is a gel-free proteomics tool for the analysis of proteins, which relies on a "sampling" strategy by isolating N-terminal protein sequence tags from cyanogen bromide cleaved proteins. The identification of these N-terminal PST peptides is based on LC-MS/MS. The effectiveness of the technology is demonstrated for a membrane fraction, which was isolated from crude mitochondria of yeast after alkaline sodium carbonate treatment. The PST approach performed on this fraction analyzed 148 proteins, whereas 84% are identified as membrane proteins. More interestingly, among these membrane proteins 56% are predicted to be of low abundance. These encouraging results are an important step toward the development of a quantitative PST approach (qPST) for the differential display of membrane protein analysis.
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Affiliation(s)
- Thorsten Prinz
- Proteome Sciences R&D, Industriepark Höchst, Building G865a, D-65929 Frankfurt am Main, Germany
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37
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Boja ES, Sokoloski EA, Fales HM. Divinyl Sulfone as a Postdigestion Modifier for Enhancing the a1 Ion in MS/MS and Postsource Decay: Potential Applications in Proteomics. Anal Chem 2004; 76:3958-70. [PMID: 15253630 DOI: 10.1021/ac049774e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Divinyl sulfone reacts at pH 8-9 with the alpha-amino groups of N-terminal residues, proline, the epsilon-amino groups of lysine, and the histidine side chains of peptides. This reaction leads to great enhancement of the abundance of the normally weak or missing "a(1)" fragment ion in MS/MS analysis defining the N-terminal residue of a peptide in a digest. This provides "one-step Edman-like" information that, together with a fairly accurately determined mass, often enables one to correctly identify a protein or family of proteins. The applicability of this procedure in proteomics was demonstrated with several peptides and tryptic digests of protein mixtures by LC-MS/MS experiments using a QTOF and MALDI-PSD analyses. Advantages of this approach are its simple chemistry, retention of charge multiplicity, and possibly, shortening of database search time. Used with other MS/MS data, it provides higher confidence in the scores and identification of a protein found in peptide mass fingerprinting. Moreover, this approach has an advantage in "de novo" sequencing due to its ability to decipher the first amino acid of a peptide whose information is normally unavailable in MS/MS spectra.
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Affiliation(s)
- Emily S Boja
- Laboratory of Biophysical Chemistry, NHLBI, NIH, 50 South Drive, Bethesda, Maryland 20892-8014, USA
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