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Nie X, He Q, Zhou B, Huang D, Chen J, Chen Q, Yang S, Yu X. Exploring the five-paced viper ( Deinagkistrodon acutus) venom proteome by integrating a combinatorial peptide ligand library approach with shotgun LC-MS/MS. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20200196. [PMID: 34745239 PMCID: PMC8547348 DOI: 10.1590/1678-9199-jvatitd-2020-0196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/18/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Snake venoms are complex mixtures of toxic proteins or peptides encoded by various gene families that function synergistically to incapacitate prey. In the present study, in order to unravel the proteomic repertoire of Deinagkistrodon acutus venom, some trace abundance components were analyzed. METHODS Shotgun proteomic approach combined with shotgun nano-LC-ESI-MS/MS were employed to characterize the medically important D. acutus venom, after collected samples were enriched with the combinatorial peptide ligand library (CPLL). RESULTS This avenue helped us find some trace components, undetected before, in D. acutus venom. The results indicated that D. acutus venom comprised 84 distinct proteins from 10 toxin families and 12 other proteins. These results are more than twice the number of venom components obtained from previous studies, which were only 29 distinct proteins obtained through RP-HPLC for the venom of the same species. The present results indicated that in D. acutus venom, the most abundant components (66.9%) included metalloproteinases, serine proteinases, and C-type lectin proteins; the medium abundant components (13%) comprised phospholipases A2 (PLA2) and 5'-nucleotidases and nucleases; whereas least abundant components (6%) were aminopeptidases, L-amino acid oxidases (LAAO), neurotoxins and disintegrins; and the trace components. The last were undetected before the use of conventional shotgun proteomics combined with shotgun nano-LC-ESI-MS/MS, such as cysteine-rich secretory proteins Da-CRPa, phospholipases B-like 1, phospholipases B (PLB), nerve growth factors (NGF), glutaminyl-peptide cyclortransferases (QC), and vascular non-inflammatory molecules 2 (VNN2). CONCLUSION These findings demonstrated that the CPLL enrichment method worked well in finding the trace toxin proteins in D. acutus venom, in contrast with the previous venomic characterization of D. acutus by conventional LC-MS/MS. In conclusion, this approach combined with the CPLL enrichment was effective for allowing us to explore the hidden D. acutus venomic profile and extended the list of potential venom toxins.
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Affiliation(s)
- Xuekui Nie
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Qiyi He
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Bin Zhou
- Library, Chongqing Normal University, Chongqing, China
| | - Dachun Huang
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Junbo Chen
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Qianzi Chen
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Shuqing Yang
- Emergency Department, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, China
| | - Xiaodong Yu
- Animal Toxin Group, Engineering Research Center of Active Substance and Biotechnology, Ministry of Education, College of Life Sciences, Chongqing Normal University, Chongqing, China
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Gouveia D, Grenga L, Pible O, Armengaud J. Quick microbial molecular phenotyping by differential shotgun proteomics. Environ Microbiol 2020; 22:2996-3004. [PMID: 32133743 PMCID: PMC7496289 DOI: 10.1111/1462-2920.14975] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
Differential shotgun proteomics identifies proteins that discriminate between sets of samples based on differences in abundance. This methodology can be easily applied to study (i) specific microorganisms subjected to a variety of growth or stress conditions or (ii) different microorganisms sampled in the same condition. In microbiology, this comparison is particularly successful because differing microorganism phenotypes are explained by clearly altered abundances of key protein players. The extensive description and quantification of proteins from any given microorganism can be routinely obtained for several conditions within a few days by tandem mass spectrometry. Such protein-centred microbial molecular phenotyping is rich in information. However, well-designed experimental strategies, carefully parameterized analytical pipelines, and sound statistical approaches must be applied if the shotgun proteomic data are to be correctly interpreted. This minireview describes these key items for a quick molecular phenotyping based on label-free quantification shotgun proteomics.
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Affiliation(s)
- Duarte Gouveia
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D)Service de Pharmacologie et Immunoanalyse (SPI)CEA, INRAE, F‐30207 Bagnols‐sur‐CèzeFrance
| | - Lucia Grenga
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D)Service de Pharmacologie et Immunoanalyse (SPI)CEA, INRAE, F‐30207 Bagnols‐sur‐CèzeFrance
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D)Service de Pharmacologie et Immunoanalyse (SPI)CEA, INRAE, F‐30207 Bagnols‐sur‐CèzeFrance
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D)Service de Pharmacologie et Immunoanalyse (SPI)CEA, INRAE, F‐30207 Bagnols‐sur‐CèzeFrance
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3
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Batista ANL, Santos-Pinto JRAD, Batista JM, Souza-Moreira TM, Santoni MM, Zanelli CF, Kato MJ, López SN, Palma MS, Furlan M. The Combined Use of Proteomics and Transcriptomics Reveals a Complex Secondary Metabolite Network in Peperomia obtusifolia. JOURNAL OF NATURAL PRODUCTS 2017; 80:1275-1286. [PMID: 28422496 DOI: 10.1021/acs.jnatprod.6b00827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Peperomia obtusifolia, an ornamental plant from the Piperaceae family, accumulates a series of secondary metabolites with interesting biological properties. From a biosynthesis standpoint, this species produces several benzopyrans derived from orsellinic acid, which is a polyketide typically found in fungi. Additionally, the chiral benzopyrans were reported as racemic and/or as diastereomeric mixtures, which raises questions about the level of enzymatic control in the cyclization step for the formation of the 3,4-dihydro-2H-pyran moiety. Therefore, this article describes the use of shotgun proteomic and transcriptome studies as well as phytochemical profiling for the characterization of the main biosynthesis pathways active in P. obtusifolia. This combined approach resulted in the identification of a series of proteins involved in its secondary metabolism, including tocopherol cyclase and prenyltransferases. The activity of these enzymes was supported by the phytochemical profiling performed in different organs of P. obtusifolia. However, the polyketide synthases possibly involved in the production of orsellinic acid could not be identified, suggesting that orsellinic acid may be produced by endophytes intimately associated with the plant.
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Affiliation(s)
- Andrea N L Batista
- Instituto de Química, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14800-060, Brazil
| | | | - João M Batista
- Departamento de Química, Universidade Federal de São Carlos-UFSCar , São Carlos, SP 13565-905, Brazil
| | - Tatiana M Souza-Moreira
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14801-902, Brazil
| | - Mariana M Santoni
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14801-902, Brazil
| | - Cleslei F Zanelli
- Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14801-902, Brazil
| | - Massuo J Kato
- Instituto de Química, Universidade de São Paulo-USP , São Paulo, SP 05508-000, Brazil
| | - Silvia N López
- CONICET, Farmacognosia, Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario , Rosario, Santa Fe S2002LRK, Argentina
| | - Mario S Palma
- Instituto de Biociências, Universidade Estadual Paulista (Unesp) , Rio Claro, SP 13506-900, Brazil
| | - Maysa Furlan
- Instituto de Química, Universidade Estadual Paulista (Unesp) , Araraquara, SP 14800-060, Brazil
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van Oosten LN, Pieterse M, Pinkse MWH, Verhaert PDEM. Screening Method for the Discovery of Potential Bioactive Cysteine-Containing Peptides Using 3D Mass Mapping. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2039-2050. [PMID: 26552389 PMCID: PMC4654750 DOI: 10.1007/s13361-015-1282-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 09/18/2015] [Accepted: 09/24/2015] [Indexed: 06/05/2023]
Abstract
Animal venoms and toxins are a valuable source of bioactive peptides with pharmacologic relevance as potential drug leads. A large subset of biologically active peptides discovered up till now contain disulfide bridges that enhance stability and activity. To discover new members of this class of peptides, we developed a workflow screening specifically for those peptides that contain inter- and intra-molecular disulfide bonds by means of three-dimensional (3D) mass mapping. Two intrinsic properties of the sulfur atom, (1) its relatively large negative mass defect, and (2) its isotopic composition, allow for differentiation between cysteine-containing peptides and peptides lacking sulfur. High sulfur content in a peptide decreases the normalized nominal mass defect (NMD) and increases the normalized isotopic shift (NIS). Hence in a 3D plot of mass, NIS, and NMD, peptides with sulfur appear in this plot with a distinct spatial localization compared with peptides that lack sulfur. In this study we investigated the skin secretion of two frog species; Odorrana schmackeri and Bombina variegata. Peptides from the crude skin secretions were separated by nanoflow LC, and of all eluting peptides high resolution zoom scans were acquired in order to accurately determine both monoisotopic mass and average mass. Both the NMD and the NIS were calculated from the experimental data using an in-house developed MATLAB script. Candidate peptides exhibiting a low NMD and high NIS values were selected for targeted de novo sequencing, and this resulted in the identification of several novel inter- and intra-molecular disulfide bond containing peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Luuk N van Oosten
- Department of Biotechnology, Delft University of Technology, 2628 BC, Delft, The Netherlands
| | - Mervin Pieterse
- Department of Biotechnology, Delft University of Technology, 2628 BC, Delft, The Netherlands
| | - Martijn W H Pinkse
- Department of Biotechnology, Delft University of Technology, 2628 BC, Delft, The Netherlands
| | - Peter D E M Verhaert
- Department of Biotechnology, Delft University of Technology, 2628 BC, Delft, The Netherlands.
- Department of Biomedical Sciences, Antwerp University, 2610, Antwerp, Belgium.
- CEBMMS (Center of Excellence in Biological and Medical Mass Spectrometry), Department of Clinical Sciences, Lund University, 221 85, Lund, Sweden.
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Prediction of spontaneous regression of cervical intraepithelial neoplasia lesions grades 2 and 3 by proteomic analysis. INTERNATIONAL JOURNAL OF PROTEOMICS 2014; 2014:129064. [PMID: 25018881 PMCID: PMC4082862 DOI: 10.1155/2014/129064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/29/2014] [Accepted: 05/14/2014] [Indexed: 02/07/2023]
Abstract
Regression of cervical intraepithelial neoplasia (CIN) 2-3 to CIN 1 or less is associated with immune response as demonstrated by immunohistochemistry in formaldehyde-fixed paraffin-embedded (FFPE) biopsies. Proteomic analysis of water-soluble proteins in supernatants of biopsy samples with LC-MS (LTQ-Orbitrap) was used to identify proteins predictive of CIN2-3 lesions regression. CIN2-3 in the biopsies and persistence (CIN2-3) or regression (≤CIN1) in follow-up cone biopsies was validated histologically by two experienced pathologists. In a learning set of 20 CIN2-3 (10 regressions and 10 persistence cases), supernatants were depleted of seven high abundance proteins prior to unidimensional LC-MS/MS protein analysis. Mean protein concentration was 0.81 mg/mL (range: 0.55–1.14). Multivariate statistical methods were used to identify proteins that were able to discriminate between regressive and persistent CIN2-3. The findings were validated in an independent test set of 20 CIN2-3 (10 regressions and 10 persistence cases). Multistep identification criteria identified 165 proteins. In the learning set, zinc finger protein 441 and phospholipase D6 independently discriminated between regressive and persistent CIN2-3 lesions and correctly classified all 20 patients. Nine regression and all persistence cases were correctly classified in the validation set. Zinc finger protein 441 and phospholipase D6 in supernatant samples detected by LTQ-Orbitrap can predict regression of CIN2-3.
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Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2014; 3:129-42. [PMID: 16445357 DOI: 10.1586/14789450.3.1.129] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
2D electrophoresis (2DE) is a prominent separation method for complex proteomes. Although recent advances have increased the utility of this method in quantitative proteomics studies, many sources of variance still exist. This review discusses the post-electrophoretic sources of variance in current 2DE analysis. The essential improvements in protein visualization and software algorithms that have made 2DE a leading quantitative proteomics method are briefly reviewed. A number of shortcomings in the post-electrophoretic analysis of 2DE data that require further attention are highlighted. Topics discussed include protein visualization and image acquisition, internal standards and normalization methods, background subtraction algorithms, normality of distribution, and the need for standardized tests for the evaluation of 2DE analysis software packages.
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Affiliation(s)
- Asa M Wheelock
- Kyoto University, Bioinformatics Center, Institute for Chemical Research, Uji, Kyoto, 611-0011, Japan.
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7
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Ruse CI, Peacock S, Ghiban C, Rivera K, Pappin DJ, Leopold P. A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide-spectrum matches in shotgun proteomics experiments. Proteomics 2013; 13:2386-97. [PMID: 23733317 PMCID: PMC3994887 DOI: 10.1002/pmic.201300022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 05/06/2013] [Accepted: 05/11/2013] [Indexed: 11/06/2022]
Abstract
Chromatographed peptide signals form the basis of further data processing that eventually results in functional information derived from data-dependent bottom-up proteomics assays. We seek to rank LC/MS parent ions by the quality of their extracted ion chromatograms. Ranked extracted ion chromatograms act as an intuitive physical/chemical preselection filter to improve the quality of MS/MS fragment scans submitted for database search. We identify more than 4900 proteins when considering detector shifts of less than 7 ppm. High quality parent ions for which the database search yields no hits become candidates for subsequent unrestricted analysis for PTMs. Following this rational approach, we prioritize identification of more than 5000 spectrum matches from modified peptides and confirmed the presence of acetylaldehyde-modified His/Lys. We present a logical workflow that scores data-dependent selected ion chromatograms and leverage information about semianalytical LC/LC dimension prior to MS. Our method can be successfully used to identify unexpected modifications in peptides with excellent chromatography characteristics, independent of fragmentation pattern and activation methods. We illustrate analysis of ion chromatograms detected in two different modes by RF linear ion trap and electrostatic field orbitrap.
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Affiliation(s)
- Cristian I Ruse
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Hsieh EJ, Bereman MS, Durand S, Valaskovic GA, MacCoss MJ. Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:148-153. [PMID: 23197307 PMCID: PMC3554873 DOI: 10.1007/s13361-012-0508-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/27/2012] [Accepted: 09/27/2012] [Indexed: 05/20/2023]
Abstract
Reversed-phase liquid chromatography is the most commonly used separation method for shotgun proteomics. Nanoflow chromatography has emerged as the preferred chromatography method for its increased sensitivity and separation. Despite its common use, there are a wide range of parameters and conditions used across research groups. These parameters have an effect on the quality of the chromatographic separation, which is critical to maximizing the number of peptide identifications and minimizing ion suppression. Here we examined the relationship between column lengths, gradient lengths, peptide identifications, and peptide peak capacity. We found that while longer column and gradient lengths generally increase peptide identifications, the degree of improvement is dependent on both parameters and is diminished at longer column and gradients. Peak capacity, in comparison, showed a more linear increase with column and gradient lengths. We discuss the discrepancy between these two results and some of the considerations that should be taken into account when deciding on the chromatographic conditions for a proteomics experiment.
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Affiliation(s)
- Edward J Hsieh
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Wright P, Noirel J, Ow SY, Fazeli A. A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 2012; 77:738-765.e52. [DOI: 10.1016/j.theriogenology.2011.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 12/27/2022]
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Savino R, Terracciano R. Mesopore-assisted profiling strategies in clinical proteomics for drug/target discovery. Drug Discov Today 2012; 17:143-52. [DOI: 10.1016/j.drudis.2011.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/23/2011] [Accepted: 10/07/2011] [Indexed: 12/29/2022]
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Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies. PLoS One 2011; 6:e26554. [PMID: 22087229 PMCID: PMC3210124 DOI: 10.1371/journal.pone.0026554] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/28/2011] [Indexed: 11/19/2022] Open
Abstract
Background The recent outbreak of severe infections with Shiga toxin (Stx) producing Escherichia coli (STEC) serotype O104:H4 highlights the need to understand horizontal gene transfer among E. coli strains, identify novel virulence factors and elucidate their pathogenesis. Quantitative shotgun proteomics can contribute to such objectives, allowing insights into the part of the genome translated into proteins and the connectivity of biochemical pathways and higher order assemblies of proteins at the subcellular level. Methodology/Principal Findings We examined protein profiles in cell lysate fractions of STEC strain 86-24 (serotype O157:H7), following growth in cell culture or bacterial isolation from intestines of infected piglets, in the context of functionally and structurally characterized biochemical pathways of E. coli. Protein solubilization in the presence of Triton X-100, EDTA and high salt was followed by size exclusion chromatography into the approximate Mr ranges greater than 280 kDa, 280-80 kDa and 80-10 kDa. Peptide mixtures resulting from these and the insoluble fraction were analyzed by quantitative 2D-LC-nESI-MS/MS. Of the 2521 proteins identified at a 1% false discovery rate, representing 47% of all predicted E. coli O157:H7 gene products, the majority of integral membrane proteins were enriched in the high Mr fraction. Hundreds of proteins were enriched in a Mr range higher than that predicted for a monomer supporting their participation in protein complexes. The insoluble STEC fraction revealed enrichment of aggregation-prone proteins, including many that are part of large structure/function entities such as the ribosome, cytoskeleton and O-antigen biosynthesis cluster. Significance Nearly all E. coli O157:H7 proteins encoded by prophage regions were expressed at low abundance levels or not detected. Comparative quantitative analyses of proteins from distinct cell lysate fractions allowed us to associate uncharacterized proteins with membrane attachment, potential participation in stable protein complexes, and susceptibility to aggregation as part of larger structural assemblies.
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Tang K, Page JS, Marginean I, Kelly RT, Smith RD. Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1318-25. [PMID: 21953185 PMCID: PMC3187566 DOI: 10.1007/s13361-011-0135-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 01/19/2011] [Accepted: 01/22/2011] [Indexed: 05/08/2023]
Abstract
In this work, the subambient pressure ionization with nanoelectrospray (SPIN) ion source and interface, which operates at ~15-30 Torr, is demonstrated to be compatible with gradient reversed-phase liquid chromatography-MS applications, exemplified here with the analysis of complex samples (a protein tryptic digest and a whole cell lysate). A low liquid chromatographic flow rate (100-400 nL/min) allowed stable electrospray to be established while avoiding electrical breakdown. Efforts to increase the operating pressure of the SPIN source relative to previously reported designs prevented solvent freezing and enhanced charged cluster/droplet desolvation. A 5- to 12-fold improvement in sensitivity relative to a conventional atmospheric pressure nanoelectrospray ionization (ESI) source was obtained for detected peptides.
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Affiliation(s)
- Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Uleberg KE, Munk AC, Brede C, Gudlaugsson E, van Diermen B, Skaland I, Malpica A, Janssen EA, Hjelle A, Baak JP. Discrimination of grade 2 and 3 cervical intraepithelial neoplasia by means of analysis of water soluble proteins recovered from cervical biopsies. Proteome Sci 2011; 9:36. [PMID: 21711556 PMCID: PMC3142202 DOI: 10.1186/1477-5956-9-36] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/28/2011] [Indexed: 12/24/2022] Open
Abstract
Background Cervical intraepithelial neoplasia (CIN) grades 2 and 3 are usually grouped and treated in the same way as "high grade", in spite of their different risk to cancer progression and spontaneous regression rates. CIN2-3 is usually diagnosed in formaldehyde-fixed paraffin embedded (FFPE) punch biopsies. This procedure virtually eliminates the availability of water-soluble proteins which could have diagnostic and prognostic value. Aim To investigate whether a water-soluble protein-saving biopsy processing method followed by a proteomic analysis of supernatant samples using LC-MS/MS (LTQ Orbitrap) can be used to distinguish between CIN2 and CIN3. Methods Fresh cervical punch biopsies from 20 women were incubated in RPMI1640 medium for 24 hours at 4°C for protein extraction and subsequently subjected to standard FFPE processing. P16 and Ki67-supported histologic consensus review CIN grade (CIN2, n = 10, CIN3, n = 10) was assessed by independent gynecological pathologists. The biopsy supernatants were depleted of 7 high abundance proteins prior to uni-dimensional LC-MS/MS analysis for protein identifications. Results The age of the patients ranged from 25-40 years (median 29.7), and mean protein concentration was 0.81 mg/ml (range 0.55 - 1.14). After application of multistep identification criteria, 114 proteins were identified, including proteins like vimentin, actin, transthyretin, apolipoprotein A-1, Heat Shock protein beta 1, vitamin D binding protein and different cytokeratins. The identified proteins are annotated to metabolic processes (36%), signal transduction (27%), cell cycle processes (15%) and trafficking/transport (9%). Using binary logistic regression, Cytokeratin 2 was found to have the strongest independent discriminatory power resulting in 90% overall correct classification. Conclusions 114 proteins were identified in supernatants from fresh cervical biopsies and many differed between CIN2 and 3. Cytokeratin 2 is the strongest discriminator with 90% overall correct classifications.
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Affiliation(s)
- Kai-Erik Uleberg
- Pathology Department, Stavanger University Hospital, Armauer Hansen Road 20, Stavanger, Norway.
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High-efficiency liquid chromatography–mass spectrometry separations with 50mm, 250mm, and 1m long polymer-based monolithic capillary columns for the characterization of complex proteolytic digests. J Chromatogr A 2010; 1217:6610-5. [DOI: 10.1016/j.chroma.2010.03.037] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/17/2010] [Accepted: 03/23/2010] [Indexed: 12/20/2022]
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Abstract
The complementary disciplines of genomics and proteomics offer better insights into the molecular mechanisms of diseases. While genomics hunts for defining our static genetic substrate, proteomics explores the structure and function of proteins expressed by a cell or tissue type under specified conditions. In the past decade, proteomics has been revolutionized by the application of techniques such as two-dimensional gel electrophoresis (2DGE), mass spectrometry (MS), and protein arrays. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of islet and diabetes research. This chapter will highlight the contributions of proteomic technologies toward the dissection of complex network of signaling molecules regulating islet function, the identification of potential biomarkers, and the understanding of mechanisms involved in the pathogenesis of diabetes.
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Brunner A, Keidel EM, Dosch D, Kellermann J, Lottspeich F. ICPLQuant - A software for non-isobaric isotopic labeling proteomics. Proteomics 2010; 10:315-26. [PMID: 19953540 DOI: 10.1002/pmic.200900174] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The main goal of many proteomics experiments is an accurate and rapid quantification and identification of regulated proteins in complex biological samples. The bottleneck in quantitative proteomics remains the availability of efficient software to evaluate and quantify the tremendous amount of mass spectral data acquired during a proteomics project. A new software suite, ICPLQuant, has been developed to accurately quantify isotope-coded protein label (ICPL)-labeled peptides on the MS level during LC-MALDI and peptide mass fingerprint experiments. The tool is able to generate a list of differentially regulated peptide precursors for subsequent MS/MS experiments, minimizing time-consuming acquisition and interpretation of MS/MS data. ICPLQuant is based on two independent units. Unit 1 performs ICPL multiplex detection and quantification and proposes peptides to be identified by MS/MS. Unit 2 combines MASCOT MS/MS protein identification with the quantitative data and produces a protein/peptide list with all the relevant information accessible for further data mining. The accuracy of quantification, selection of peptides for MS/MS-identification and the automated output of a protein list of regulated proteins are demonstrated by the comparative analysis of four different mixtures of three proteins (Ovalbumin, Horseradish Peroxidase and Rabbit Albumin) spiked into the complex protein background of the DGPF Proteome Marker.
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Affiliation(s)
- Achim Brunner
- Max-Planck-Institute of Biochemistry, Martinsried, Germany.
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Pitroda SP, Wakim BT, Sood RF, Beveridge MG, Beckett MA, MacDermed DM, Weichselbaum RR, Khodarev NN. STAT1-dependent expression of energy metabolic pathways links tumour growth and radioresistance to the Warburg effect. BMC Med 2009; 7:68. [PMID: 19891767 PMCID: PMC2780454 DOI: 10.1186/1741-7015-7-68] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 11/05/2009] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The Signal Transducer and Activator of Transcription 1 (STAT1) has traditionally been regarded as a transmitter of interferon signaling and a pro-apoptotic tumour suppressor. Recent data have identified new functions of STAT1 associated with tumourigenesis and resistance to genotoxic stress, including ionizing radiation (IR) and chemotherapy. To investigate the mechanisms contributing to the tumourigenic functions of STAT1, we performed a combined transcriptomic-proteomic expressional analysis and found that STAT1 is associated with regulation of energy metabolism with potential implication in the Warburg effect. METHODS We generated a stable knockdown of STAT1 in the SCC61 human squamous cell carcinoma cell line, established tumour xenografts in athymic mice, and compared transcriptomic and proteomic profiles of STAT1 wild-type (WT) and knockdown (KD) untreated or irradiated (IR) tumours. Transcriptional profiling was based on Affymetrix Human GeneChip(R) Gene 1.0 ST microarrays. Proteomes were determined from the tandem mass spectrometry (MS/MS) data by searching against the human subset of the UniProt database. Data were analysed using Significance Analysis of Microarrays for ribonucleic acid and Visualize software for proteins. Functional analysis was performed with Ingenuity Pathway Analysis with statistical significance measured by Fisher's exact test. RESULTS Knockdown of STAT1 led to significant growth suppression in untreated tumours and radio sensitization of irradiated tumours. These changes were accompanied by alterations in the expression of genes and proteins of glycolysis/gluconeogenesis (GG), the citrate cycle (CC) and oxidative phosphorylation (OP). Of these pathways, GG had the most concordant changes in gene and protein expression and demonstrated a STAT1-dependent expression of genes and proteins consistent with tumour-specific glycolysis. In addition, IR drastically suppressed the GG pathway in STAT1 KD tumours without significant change in STAT1 WT tumours. CONCLUSION Our results identify a previously uncharacterized function of STAT1 in tumours: expressional regulation of genes encoding proteins involved in glycolysis, the citrate cycle and mitochondrial oxidative phosphorylation, with predominant regulation of glycolytic genes. STAT1-dependent expressional regulation of glycolysis suggests a potential role for STAT1 as a transcriptional modulator of genes responsible for the Warburg effect.
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Affiliation(s)
- Sean P Pitroda
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, IL 60637, USA.
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Li YF, Arnold RJ, Li Y, Radivojac P, Sheng Q, Tang H. A bayesian approach to protein inference problem in shotgun proteomics. J Comput Biol 2009; 16:1183-93. [PMID: 19645593 DOI: 10.1089/cmb.2009.0018] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The protein inference problem represents a major challenge in shotgun proteomics. In this article, we describe a novel Bayesian approach to address this challenge by incorporating the predicted peptide detectabilities as the prior probabilities of peptide identification. We propose a rigorious probabilistic model for protein inference and provide practical algoritmic solutions to this problem. We used a complex synthetic protein mixture to test our method and obtained promising results.
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Affiliation(s)
- Yong Fuga Li
- School of Informatics, Indiana University , Bloomington, IN 47408, USA
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19
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Proteomics at the center of nutrigenomics: Comprehensive molecular understanding of dietary health effects. Nutrition 2009; 25:1085-93. [DOI: 10.1016/j.nut.2009.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 05/31/2009] [Indexed: 11/18/2022]
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20
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Meng W, Zhang H, Guo T, Pandey C, Zhu Y, Kon OL, Sze SK. One-step procedure for peptide extraction from in-gel digestion sample for mass spectrometric analysis. Anal Chem 2009; 80:9797-805. [PMID: 18986172 DOI: 10.1021/ac801344z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein identification from samples resolved by one-dimensional and two-dimensional gel electrophoresis is highly dependent on the recovery of trypsin-digested peptides prior to mass spectrometric analysis. The commonly used two-step protocol for extracting tryptic peptides, involving high-volume organic solvent extraction and cleanup via microscale reversed-phase micropipet tip or microcolumn is not only limited by significant sample loss but is also costly and very labor-intensive. We report here a simple one-step procedure for simultaneous peptide extraction and cleanup by incubating a small piece of C18 Empore Disk (3M) with the in-gel digested solution. We show that the direct Empore Disk-based peptide extraction procedure is convenient, economical, and has higher efficiency as compared with the commonly used two-step protocol for peptide preparation prior to MS analysis.
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Affiliation(s)
- Wei Meng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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21
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Giorgi A, Di Francesco L, Principe S, Mignogna G, Sennels L, Mancone C, Alonzi T, Sbriccoli M, De Pascalis A, Rappsilber J, Cardone F, Pocchiari M, Maras B, Schininà ME. Proteomic profiling of PrP27-30-enriched preparations extracted from the brain of hamsters with experimental scrapie. Proteomics 2009; 9:3802-14. [DOI: 10.1002/pmic.200900085] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Isolation and proteomic analysis of the halotolerant alga Dunaliella salina flagella using shotgun strategy. Mol Biol Rep 2009; 37:711-6. [PMID: 19437132 DOI: 10.1007/s11033-009-9563-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 05/01/2009] [Indexed: 10/20/2022]
Abstract
Previous studies have demonstrated that flagella/cilia are critical organelles and play diverse roles of motility, sensory perception and development in many eukaryotic cells. However, there is very little information available about flagella composition in Dunaliella salina, a halotolerant, unicellular biflagellate green alga. In the present study, we used strategy of shotgun proteomics to identify flagella proteins after flagella were released and collected from D. salina. A total of 520 groups of proteins were identified under a stringent filter condition (Xcorr > or =1.9, > or =2.2 and > or =3.75; DeltaCn >/= 0.1). In addition to six kinds of known flagella proteins, the putative flagella proteins of D. salina identified by one or more peptides are abundant in signaling, cell division, metabolism, etc. The findings provide guidance for further studies to elucidate the roles of these proteins in the function and assembly of this organelle in microalgae.
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23
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Ow SY, Wright PC. Current trends in high throughput proteomics in cyanobacteria. FEBS Lett 2009; 583:1744-52. [DOI: 10.1016/j.febslet.2009.03.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/17/2009] [Accepted: 03/27/2009] [Indexed: 02/07/2023]
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Alex P, Gucek M, Li X. Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies. Inflamm Bowel Dis 2009; 15:616-29. [PMID: 18844215 PMCID: PMC2667948 DOI: 10.1002/ibd.20652] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inflammatory bowel diseases (IBD) are chronic, heterogeneous, and multifactorial intestinal inflammatory disorders. Major challenges in IBD research include identification of major pathogenic alterations of genes/proteins as well as effective biomarkers for early diagnosis, prognosis, and prediction of therapeutic response. Since proteins govern cellular structure and biological function, a wide selection of proteomic approaches enables effective characterization of IBD pathogenesis by investigating the dynamic nature of protein expression, cellular and subcellular distribution, posttranslational modifications, and interactions at both the cellular and subcellular levels. The aims of this review are to 1) highlight the current status of proteomic studies of IBD, and 2) introduce the available and emerging proteomic technologies that have potential applications in the study of IBD. These technologies include various mass spectrometry technologies, quantitative proteomics (2D-PAGE, ICAT, SILAC, iTRAQ), protein/antibody arrays, and multi-epitope-ligand cartography. This review also presents information and methodologies, from sample selection and enrichment to protein identification, that are not only essential but also particularly relevant to IBD research. The potential future application of these technologies is expected to have a significant impact on the discovery of novel biomarkers and key pathogenic factors for IBD.
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Affiliation(s)
- Philip Alex
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
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25
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Abstract
Over the past two decades, mass spectrometry (MS) has ceased to be a fairly exotic technique banished from the protein scientists' mind to become a seminal tool for deciphering the information encoded in the genomes of many biological species. Clues to this shift in the modus operandi for characterizing their proteomes stem from the progressive availability of full genome sequences and well-annotated protein databases of many model (micro)organisms, the development both of soft ionization methods for large biomolecules (peptides and proteins) and of innovative instrumentation designs, and the introduction of sophisticated search algorithms able to correlate MS information with sequence databases, to name but a few. Here we integrate the typical MS-based strategy for identifying proteins of Candida albicans, an opportunistic fungal pathogen of humans, which have proved to be present during systemic infection and targeted by the immune system as a consequence of its interaction with the host (i.e., the C. albicans immunome).
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Schlüter H, Hildebrand D, Gallin C, Schulz A, Thiemann J, Trusch M. Mass spectrometry for monitoring protease reactions. Anal Bioanal Chem 2008; 392:783-92. [PMID: 18584157 PMCID: PMC7080141 DOI: 10.1007/s00216-008-2213-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 05/27/2008] [Accepted: 05/28/2008] [Indexed: 12/02/2022]
Abstract
More than 560 genes are annotated as proteases in the human genome. About half of the genes are not or are only marginally characterized. Over the past decade, mass spectrometry has become the basis for proteomics, especially for protein identification, performed in a high-throughput manner. This development was also very fruitful for exploring the complex systems associated with protease functions, as briefly reviewed here. Mass spectrometry is an ideal tool for monitoring protease reactions, as will be highlighted in this review.
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Affiliation(s)
- H Schlüter
- Charite-Core Facility Protein Analysis, Tucholskystr. 2, 10117, Berlin, Germany.
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28
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Page JS, Tang K, Kelly RT, Smith RD. Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry. Anal Chem 2008; 80:1800-5. [PMID: 18237189 DOI: 10.1021/ac702354b] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A nanoelectrospray ionization mass spectrometry (ESI-MS) source and interface has been designed that enables efficient ion production and transmission in a 30 Torr pressure environment using solvents compatible with typical reversed-phase liquid chromatography (RPLC) separations. In this design, the electrospray emitter is located inside the mass spectrometer in the same region as an electrodynamic ion funnel. This avoids the use of a conductance limiting ion inlet, as required by a conventional atmospheric pressure ESI source, and allows more efficient ion transmission to the mass analyzer. The new subambient pressure ionization with nanoelectrospray (SPIN) source improves instrument sensitivity and enables new electrospray interface designs, including the use of multi-emitter approaches. Performance of the SPIN source was evaluated by electrospraying standard solutions at 300 nL/min and comparing results with those obtained from a standard atmospheric pressure ESI source that used a heated capillary inlet. This initial study demonstrated an approximately 5-fold improvement in sensitivity when the SPIN source was used compared to a standard atmospheric pressure ESI source. The importance of desolvation was also investigated by electrospraying at different flow rates, which showed that the ion funnel provided an effective desolvation region to aid the creation of gas-phase analyte ions.
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Affiliation(s)
- Jason S Page
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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29
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Mauri P, Dehò G. Chapter 6 A Proteomic Approach to the Analysis of RNA Degradosome Composition in Escherichia coli. Methods Enzymol 2008; 447:99-117. [DOI: 10.1016/s0076-6879(08)02206-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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30
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Emrich CA, Medintz IL, Chu WK, Mathies RA. Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling. Anal Chem 2007; 79:7360-6. [PMID: 17822308 DOI: 10.1021/ac0711485] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A microfluidic separation system is developed to perform two-dimensional differential gel electrophoretic (DIGE) separations of complex, cellular protein mixtures produced by induced protein expression in E. coli. The micro-DIGE analyzer is a two-layer borosilicate glass microdevice consisting of a single 3.75 cm long channel for isoelectric focusing, which is sampled in parallel by 20 channels effecting a second-dimension separation by native electrophoresis. The connection between the orthogonal separation systems is accomplished by smaller channels comprising a microfluidic interface (MFI) that prevents media leakage between the two dimensions and enables facile loading of discontinuous gel systems in each dimension. Proteins are covalently labeled with Cy2 and Cy3 DIGE and detected simultaneously with a rotary confocal fluorescence scanner. Reproducible two-dimensional separations of both purified proteins and complex protein mixtures are performed with minimal run-to-run variation by including 7 M urea in the second-dimension separation matrix. The capabilities of the micro-DIGE analyzer are demonstrated by following the induced expression of maltose binding protein in E. coli. Although the absence of sodium dodecyl sulfate (SDS) in the second-dimension sizing separation limits the orthogonality and peak capacity of the separation, this analyzer is a significant first step toward the reproducible two-dimensional analysis of complex protein samples in microfabricated devices. Furthermore, the microchannel interface structures developed here will facilitate other multidimensional separations in microdevices.
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Affiliation(s)
- Charles A Emrich
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
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Page JS, Kelly RT, Tang K, Smith RD. Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1582-90. [PMID: 17627841 DOI: 10.1016/j.jasms.2007.05.018] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 05/24/2007] [Accepted: 05/25/2007] [Indexed: 05/03/2023]
Abstract
The ionization and transmission efficiencies of an electrospray ionization (ESI) interface were investigated to advance the understanding of how these factors affect mass spectrometry (MS) sensitivity. In addition, the effects of the ES emitter distance to the inlet, solution flow rate, and inlet temperature were characterized. Quantitative measurements of ES current loss throughout the ESI interface were accomplished by electrically isolating the front surface of the interface from the inner wall of the heated inlet capillary, enabling losses on the two surfaces to be distinguished. In addition, the ES current lost to the front surface of the ESI interface was spatially profiled with a linear array of 340-microm-diameter electrodes placed adjacent to the inlet capillary entrance. Current transmitted as gas-phase ions was differentiated from charged droplets and solvent clusters by measuring sensitivity with a single quadrupole mass spectrometer. The study revealed a large sampling efficiency into the inlet capillary (>90% at an emitter distance of 1 mm), a global rather than a local gas dynamic effect on the shape of the ES plume resulting from the gas flow conductance limit of the inlet capillary, a large (>80%) loss of analyte ions after transmission through the inlet arising from incomplete desolvation at a solution flow rate of 1.0 microL/min, and a decrease in analyte ions peak intensity at lower temperatures, despite a large increase in ES current transmission efficiency.
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Affiliation(s)
- Jason S Page
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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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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The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments. BMC Bioinformatics 2007; 8:255. [PMID: 17631686 PMCID: PMC1939855 DOI: 10.1186/1471-2105-8-255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Accepted: 07/15/2007] [Indexed: 12/25/2022] Open
Abstract
Background Isotope-coded affinity tags (ICAT) is a method for quantitative proteomics based on differential isotopic labeling, sample digestion and mass spectrometry (MS). The method allows the identification and relative quantification of proteins present in two samples and consists of the following phases. First, cysteine residues are either labeled using the ICAT Light or ICAT Heavy reagent (having identical chemical properties but different masses). Then, after whole sample digestion, the labeled peptides are captured selectively using the biotin tag contained in both ICAT reagents. Finally, the simplified peptide mixture is analyzed by nanoscale liquid chromatography-tandem mass spectrometry (LC-MS/MS). Nevertheless, the ICAT LC-MS/MS method still suffers from insufficient sample-to-sample reproducibility on peptide identification. In particular, the number and the type of peptides identified in different experiments can vary considerably and, thus, the statistical (comparative) analysis of sample sets is very challenging. Low information overlap at the peptide and, consequently, at the protein level, is very detrimental in situations where the number of samples to be analyzed is high. Results We designed a method for improving the data processing and peptide identification in sample sets subjected to ICAT labeling and LC-MS/MS analysis, based on cross validating MS/MS results. Such a method has been implemented in a tool, called EIPeptiDi, which boosts the ICAT data analysis software improving peptide identification throughout the input data set. Heavy/Light (H/L) pairs quantified but not identified by the MS/MS routine, are assigned to peptide sequences identified in other samples, by using similarity criteria based on chromatographic retention time and Heavy/Light mass attributes. EIPeptiDi significantly improves the number of identified peptides per sample, proving that the proposed method has a considerable impact on the protein identification process and, consequently, on the amount of potentially critical information in clinical studies. The EIPeptiDi tool is available at with a demo data set. Conclusion EIPeptiDi significantly increases the number of peptides identified and quantified in analyzed samples, thus reducing the number of unassigned H/L pairs and allowing a better comparative analysis of sample data sets.
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Speers AE, Blackler AR, Wu CC. Shotgun Analysis of Integral Membrane Proteins Facilitated by Elevated Temperature. Anal Chem 2007; 79:4613-20. [PMID: 17500534 DOI: 10.1021/ac0700225] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The beneficial effects on peak selectivity and resolution of conducting liquid chromatography (LC) at elevated temperature (e.g., 30-80 degrees C) are generally well-known; however, its importance for peptide recovery is not nearly as well recognized. This report demonstrates that microLC analysis of membrane proteomic samples significantly benefits from the application of heat. Enriched membrane and membrane-embedded peptides (the latter obtained by membrane shaving) were analyzed by microLC-tandem mass spectrometry (MS/MS) from 20 to 60 degrees C using a standard reversed-phase material. Maximal protein and hydrophobic peptide recovery was obtained at 60 degrees C. The membrane-shaving method employed, a recently optimized version of the high pH/proteinase K protocol, provided significant integral membrane protein enrichment: 98% of identified proteins were predicted to have at least one transmembrane domain (87% to have at least three), and 68% of peptides were predicted to contain transmembrane segments. Analysis of this highly enriched sample at elevated temperature increased protein identifications by 400%, and peptide identifications by 500%, as compared to room-temperature separation. Given that most microLC-MS/MS analyses are currently conducted at room temperature, the findings described herein should be of considerable value for improving the comprehensive study of integral membrane proteins.
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Affiliation(s)
- Anna E Speers
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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35
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Kelly RT, Page JS, Tang K, Smith RD. Array of Chemically Etched Fused-Silica Emitters for Improving the Sensitivity and Quantitation of Electrospray Ionization Mass Spectrometry. Anal Chem 2007; 79:4192-8. [PMID: 17472340 DOI: 10.1021/ac062417e] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An array of emitters has been developed for increasing the sensitivity of electrospray ionization mass spectrometry (ESI-MS). The linear array consists of 19 chemically etched fused-silica capillaries arranged with 500 microm (center-to-center) spacing. The multiemitter device has a low dead volume to facilitate coupling to capillary liquid chromatography (LC) separations. The high aspect ratio of the emitters enables operation at flow rates as low as 20 nL/min/emitter, effectively extending the benefits of nanoelectrospray to higher flow rate analyses. To accommodate the larger ion current produced by the emitter array, a multicapillary inlet to the mass spectrometer was also constructed. The inlet, which matched the dimensions of the emitter array, preserved ion transmission efficiency. Standard reserpine solutions of varying concentration were electrosprayed at 1 microL/min using the multiemitter/multi-inlet combination, and the results were compared to those from a standard, single-emitter configuration. A 9-fold sensitivity enhancement was observed for the multiemitter relative to the single emitter. A bovine serum albumin tryptic digest was also analyzed, and a sensitivity increase ranging from 2.4- to 12.3-fold for the detected tryptic peptides resulted; the varying response was attributed to reduced ion suppression under the nanoESI conditions afforded by the emitter array. An equimolar mixture of leucine enkephalin and maltopentaose was studied to verify that ion suppression is indeed reduced for the multiplexed ESI (multi-ESI) array relative to a single emitter over a range of flow rates.
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Affiliation(s)
- Ryan T Kelly
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:312-34. [PMID: 17206599 PMCID: PMC3426914 DOI: 10.1002/jms.1163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 microg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis.
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Affiliation(s)
- Chul Yoo
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Tasneem H. Patwa
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Paweena Kreunin
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Fred R. Miller
- Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Christian G. Huber
- Department of Chemistry, Instrumental Analysis and Bioanalysis, Saarland University, 66123 Saarbrucken, Germany
| | - Alexey I. Nesvizhskii
- Department of Pathology, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - David M. Lubman
- Department of Surgery, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, The University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Correspondence to: David M. Lubman, University of Michigan Medical Center, Department of Surgery, MSRBI, A510B, Box 0658, Ann Arbor, MI 48109, USA.
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Rohrbough JG, Galgiani JN, Wysocki VH. The Application of Proteomic Techniques to Fungal Protein Identification and Quantification. Ann N Y Acad Sci 2007; 1111:133-46. [PMID: 17344531 DOI: 10.1196/annals.1406.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The number of sequenced genomes has increased rapidly in the last few years, supporting a revolution in bioinformatics that has been leveraged by scientists seeking to analyze the proteomes of numerous biological systems. The primary technique employed for the identification of peptides and proteins from biological sources is mass spectrometry (MS). This analytical process is usually in the form of whole-protein analysis (termed "top-down" proteomics) or analysis of enzymatically produced peptides (known as the "bottom-up" approach). This article will focus primarily on the more common bottom-up proteomics to include topics such as sample preparation, separation strategies, MS instrumentation, data analysis, and techniques for protein quantification. Strategies for preparation of samples for proteomic analysis, as well as tools for protein and peptide separation will be discussed. A general description of common MS instruments along with tandem mass spectrometry (MS/MS) will be given. Different methodologies of sample ionization including matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) will be discussed. Data analysis methods including database search algorithms and tools for protein sequence analysis will be introduced. We will also discuss experimental strategies for MS protein quantification using stable isotope labeling techniques and fluorescent labeling. We will introduce several fungal proteomic studies to illustrate the use of these methods. This article will allow investigators to gain a working knowledge of proteomics along with some strengths and weaknesses associated with the techniques presented.
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Katayama H, Oda Y. Chemical proteomics for drug discovery based on compound-immobilized affinity chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 855:21-7. [PMID: 17241823 DOI: 10.1016/j.jchromb.2006.12.047] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 12/19/2006] [Accepted: 12/30/2006] [Indexed: 10/23/2022]
Abstract
Chemical proteomics is an effective approach to focused proteomics, having the potential to find specific interactors in moderate-scale comprehensive analysis. Unlike chemical genetics, chemical proteomics directly and comprehensively identifies proteins that bind specifically to candidate compounds by means of affinity chromatographic purification using the immobilized candidate, combined with mass spectrometric identification of interacting proteins. This is an effective approach for discovering unknown protein functions, identifying the molecular mechanisms of drug action, and obtaining information for optimization of lead compounds. However, immobilized-small molecule affinity chromatography always suffers from the problem of non-specific binders. Although several approaches were reported to reduce non-specific binding proteins, these are mainly focused on the use of low-binding-affinity beads or insertion of a spacer between the bead and the compound. Stable isotope labeling strategies have proven particularly advantageous for the discrimination of true interactors from many non-specific binders, including carrier proteins, such as serum albumin, and are expected to be valuable for drug discovery.
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Affiliation(s)
- Hiroyuki Katayama
- Eisai Co., Ltd., Laboratory of Seed Finding Technology, Tsukuba, Ibaraki, Japan
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Hu J, Qian J, Borisov O, Pan S, Li Y, Liu T, Deng L, Wannemacher K, Kurnellas M, Patterson C, Elkabes S, Li H. Optimized proteomic analysis of a mouse model of cerebellar dysfunction using amine-specific isobaric tags. Proteomics 2006; 6:4321-34. [PMID: 16800037 PMCID: PMC2553677 DOI: 10.1002/pmic.200600026] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recent proteomic applications have demonstrated their potential for revealing the molecular mechanisms underlying neurodegeneration. The present study quantifies cerebellar protein changes in mice that are deficient in plasma membrane calcium ATPase 2 (PMCA2), an essential neuronal pump that extrudes calcium from cells and is abundantly expressed in Purkinje neurons. PMCA2-null mice display motor dyscoordination and unsteady gait deficits observed in neurological diseases such as multiple sclerosis and ataxia. We optimized an amine-specific isobaric tags (iTRAQ)-based shotgun proteomics workflow for this study. This workflow took consideration of analytical variance as a function of ion signal intensity and employed biological repeats to aid noise reduction. Even with stringent protein identification criteria, we could reliably quantify nearly 1000 proteins, including many neuronal proteins that are important for synaptic function. We identified 21 proteins that were differentially expressed in PMCA2-null mice. These proteins are involved in calcium homeostasis, cell structure and chromosome organization. Our findings shed light on the molecular changes that underlie the neurological deficits observed in PMCA2-null mice. The optimized workflow presented here will be valuable for others who plan to implement the iTRAQ method.
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Affiliation(s)
- Jun Hu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Jin Qian
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Oleg Borisov
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Sanqiang Pan
- Department of Anatomy, Medical School of Jinan University, Guangzhou, Guangdong, P. R. China
| | - Yan Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Tong Liu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Longwen Deng
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Kenneth Wannemacher
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Michael Kurnellas
- Department of Neurology and Neuroscience, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
- Neurology Service, Veterans Affairs, East Orange, NJ, USA
| | - Christa Patterson
- Department of Neurology and Neuroscience, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
- Neurology Service, Veterans Affairs, East Orange, NJ, USA
| | - Stella Elkabes
- Department of Neurology and Neuroscience, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
- Neurology Service, Veterans Affairs, East Orange, NJ, USA
| | - Hong Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
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McDonald T, Sheng S, Stanley B, Chen D, Ko Y, Cole RN, Pedersen P, Van Eyk JE. Expanding the subproteome of the inner mitochondria using protein separation technologies: one- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis. Mol Cell Proteomics 2006; 5:2392-411. [PMID: 17000643 DOI: 10.1074/mcp.t500036-mcp200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Currently no single proteomics technology has sufficient analytical power to allow for the detection of an entire proteome of an organelle, cell, or tissue. One approach that can be used to expand proteome coverage is the use of multiple separation technologies especially if there is minimal overlap in the proteins observed by the different methods. Using the inner mitochondrial membrane subproteome as a model proteome, we compared for the first time the ability of three protein separation methods (two-dimensional liquid chromatography using the ProteomeLab PF 2D Protein Fractionation System from Beckman Coulter, one-dimensional reversed phase high performance liquid chromatography, and two-dimensional gel electrophoresis) to determine the relative overlap in protein separation for these technologies. Data from these different methods indicated that a strikingly low number of proteins overlapped with less than 24% of proteins common between any two technologies and only 7% common among all three methods. Utilizing the three technologies allowed the creation of a composite database totaling 348 non-redundant proteins. 82% of these proteins had not been observed previously in proteomics studies of this subproteome, whereas 44% had not been identified in proteomics studies of intact mitochondria. Each protein separation method was found to successfully resolve a unique subset of proteins with the liquid chromatography methods being more suited for the analysis of transmembrane domain proteins and novel protein discovery. We also demonstrated that both the one- and two-dimensional LC allowed for the separation of the alpha-subunit of F1F0 ATP synthase that differed due to a change in pI or hydrophobicity.
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Affiliation(s)
- Todd McDonald
- Department of Medicine, The Technical Implementation and Coordination Core of The Johns Hopkins NHLBI Proteomics Center, The Johns Hopkins University, Baltimore, MD 21224, USA
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Hoehenwarter W, Ackermann R, Zimny-Arndt U, Kumar NM, Jungblut PR. The necessity of functional proteomics: protein species and molecular function elucidation exemplified by in vivo alpha A crystallin N-terminal truncation. Amino Acids 2006; 31:317-23. [PMID: 16964561 DOI: 10.1007/s00726-005-0377-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Accepted: 12/15/2005] [Indexed: 11/24/2022]
Abstract
Ten years after the establishment of the term proteome, the science surrounding it has yet to fulfill its potential. While a host of technologies have generated lists of protein names, there are only a few reported studies that have examined the individual proteins at the covalent chemical level defined as protein species in 1997 and their function. In the current study, we demonstrate that this is possible with two-dimensional gel electrophoresis (2-DE) and mass spectrometry by presenting clear evidence of in vivo N-terminal alpha A crystallin truncation and relating this newly detected protein species to alpha crystallin activity regulation by protease cleavage in the healthy young murine lens. We assess the present state of technology and suggest a shift in resources and paradigm for the routine attainment of the protein species level in proteomics.
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Affiliation(s)
- W Hoehenwarter
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany
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Abstract
Considerable effort has been invested in the development of integrated microfluidic devices for fast and highly efficient proteomic studies. Among various fabrication techniques for the preparation of analytical components (separation columns, reactors, extractors, valves, etc.) in integrated microchips, in situ fabrication of monolithic media is receiving increasing attention. This is mainly due to the ease and simplicity of preparation of monolithic media and the availability of various precursors and chemistries. In addition, UV-initiated photopolymerization technique enables the incorporation of multiple analytical components into specified parts of a single microchip using photomasks. This review summarizes preparation methods for monolithic media and their application as microfluidic analytical components in microchips.
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Affiliation(s)
- Kyung Won Ro
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
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Tassone P, Tagliaferri P, Rossi M, Gaspari M, Terracciano R, Venuta S. Genetics and molecular profiling of multiple myeloma: novel tools for clinical management? Eur J Cancer 2006; 42:1530-8. [PMID: 16820292 DOI: 10.1016/j.ejca.2006.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 04/03/2006] [Indexed: 10/24/2022]
Abstract
The understanding of molecular events involved in multiple myeloma (MM) development as well as of mechanisms underlying sensitivity/resistance to anticancer drugs has been dramatically increased by the wide-spread use of modern technologies for genetic analysis, global gene expression and proteomic profiling. Such analytical approaches, which are presently supported by reliable bioinformatic tools, have depicted a new scenario for the development of molecular-based anti-MM agents and for predicting clinical outcome. IgH translocations or a hyperdiploid state are emerging as early genetic signatures of MM which lead to deregulated expression of cyclin D. At present however, the major challenge remains the definition of the potential role of cytogenetic techniques and molecular profiling technologies in individual patient management. Here we will describe the prospective potential and current achievements of such technologies which might produce major advancements in the treatment of this still incurable disease.
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Affiliation(s)
- Pierfrancesco Tassone
- Medical Oncology Unit, University of Magna Graecia and T. Campanella Cancer Center, Campus Germaneto, Viale Europa, 88100 Catanzaro, Italy
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Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, Yamada T. Label-free Quantitative Proteomics Using Large Peptide Data Sets Generated by Nanoflow Liquid Chromatography and Mass Spectrometry. Mol Cell Proteomics 2006; 5:1338-47. [PMID: 16552026 DOI: 10.1074/mcp.t500039-mcp200] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We developed an integrated platform consisting of machinery and software modules that can apply vast amounts of data generated by nanoflow LC-MS to differential protein expression analyses. Unlabeled protein samples were completely digested with modified trypsin and separated by low speed (200 nl/min) one-dimensional HPLC. Mass spectra were obtained every 1 s by using the survey mode of a hybrid Q-TOF mass spectrometer and displayed in a two-dimensional plane with m/z values along the x axis, and retention time was displayed along the y axis. The time jitter of nano-LC was adjusted using newly developed software based on a dynamic programming algorithm. The comprehensiveness (60,000-160,000 peaks above the predetermined threshold detectable in 60-microg cell protein samples), reproducibility (average coefficient of variance of 0.35-0.39 and correlation coefficient of over 0.92 between duplicates), and accurate quantification with a wide dynamic range (over 10(3)) of our platform warrant its application to various types of experimental and translational proteomics.
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Affiliation(s)
- Masaya Ono
- Chemotherapy Division and Cancer Proteomics Project, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Hoehenwarter W, Klose J, Jungblut PR. Eye lens proteomics. Amino Acids 2006; 30:369-89. [PMID: 16583312 DOI: 10.1007/s00726-005-0283-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Accepted: 09/01/2005] [Indexed: 01/12/2023]
Abstract
The eye lens is a fascinating organ as it is in essence living transparent matter. Lenticular transparency is achieved through the peculiarities of lens morphology, a semi-apoptotic process where cells elongate and loose their organelles and the precise molecular arrangement of the bulk of soluble lenticular proteins, the crystallins. The 16 crystallins ubiquitous in mammals and their modifications have been extensively characterized by 2-DE, liquid chromatography, mass spectrometry and other protein analysis techniques. The various solubility dependant fractions as well as subproteomes of lenticular morphological sections have also been explored in detail. Extensive post translational modification of the crystallins is encountered throughout the lens as a result of ageing and disease resulting in a vast number of protein species. Proteomics methodology is therefore ideal to further comprehensive understanding of this organ and the factors involved in cataractogenesis.
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Affiliation(s)
- W Hoehenwarter
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany
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Ro KW, Liu J, Knapp DR. Plastic microchip liquid chromatography-matrix-assisted laser desorption/ionization mass spectrometry using monolithic columns. J Chromatogr A 2006; 1111:40-7. [PMID: 16480733 DOI: 10.1016/j.chroma.2006.01.105] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 01/10/2006] [Accepted: 01/24/2006] [Indexed: 10/25/2022]
Abstract
A prototype array of monolithic liquid chromatography (LC) columns was prepared in a plastic microfluidic device for the off-line interface with matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The microfluidic channels were fabricated on a cyclic olefin copolymer (COC) plate by hot embossing. An array of methacrylate monolithic columns was prepared in the microfluidic channels by UV-initiated polymerization. The deposition system employed a pulsed electric field to transfer the effluents from multiple columns directly onto MALDI targets with a non-contact deposition method reported by Ericson et al. [C. Ericson, Q.T. Phung, D.M. Horn, E.C. Peters, J.R. Fitchett, S.B. Ficarro, A.R. Salmon, L.M. Brill, A. Brock, Anal. Chem. 75 (2003) 2309]. To characterize the off-line interface of the multiple-channel microchip LC and the MALDI-MS for the analysis of peptide mixtures, the separation efficiency and reproducibility tests in each column were carried out by separating a peptide mixture from tryptic digested proteins and depositing the multiple effluents simultaneously on the MALDI target plate. Using a MALDI-TOF mass spectrometer with a mass accuracy of +/-1 Da for peptide assignments of digested bovine serum albumin (BSA), amino acid sequence coverage of around 59% was obtained for the microchip LC-MALDI-MS compared to 23% obtained by the MALDI-MS method without LC separation. In sensitivity tests for the detection of low abundance proteins in the presence of high concentration protein mixtures, as low as 10 fmol/mul (S/N = 10) of a spiked peptide in 1 microg of digested BSA could be detected. In the analysis of a mixture of three digested proteins (BSA, myoglobin, and cytochrome c), more than twice the amino acid sequence coverage was obtained for the microchip LC-MALDI-MS compared to MALDI-MS alone.
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Affiliation(s)
- Kyung Won Ro
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, 29425, USA
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Abstract
Proteomics reveals complex protein expression, function, interactions and localization in different phenotypes of neuron. As proteomics, regarded as a highly complex screening technology, moves from a theoretical approach to practical reality, neuroscientists have to determine the most-appropriate applications for this technology. Even though proteomics compliments genomics, it is in sheer contrast to the basically constant genome due to its dynamic nature. Neuroscientists have to surmount difficulties particular to the research in neuroscience; such as limited sample amounts, heterogeneous cellular compositions in samples and the fact that many proteins of interest are hydrophobic proteins. The necessity of exclusive technology, sophisticated software and skilled manpower tops the challenge. This review examines subcellular organelle isolation, protein fractionation and separation using two-dimensional gel electrophoresis (2-DGE) as well as multi-dimensional liquid chromatography (LC) followed by mass spectrometry (MS). The methods for quantifying relative gene product expression between samples (e.g., two-dimensional difference in gel electrophoresis (2D-DIGE), isotope-coded affinity tag (ICAT) and iTRAQ) are elaborated. An overview of the techniques used currently to assign post-translational modification status on a proteomics scale is also evaluated. The feasible coverage of the proteome, ability to detect unique cell components such as post-synaptic densities and membrane proteins, resource requirements and quantitative as well as qualitative reliability of different approaches is also discussed. While there are many challenges in neuroproteomics, this field promises many returns in the future.
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Sheng S, Chen D, Van Eyk JE. Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome: optimization and protein database. Mol Cell Proteomics 2005; 5:26-34. [PMID: 16188874 DOI: 10.1074/mcp.t500019-mcp200] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In biomarker discovery, the detection of proteins with low abundance in the serum proteome can be achieved by optimization of protein separation methods as well as selective depletion of the higher abundance proteins such as immunoglobins (e.g. IgG) and albumin. A relative newcomer to the proteomic separation arena is the commercial instrument PF2D from Beckman Coulter that separates proteins in the first dimension using chromatofocusing followed in line by reversed phase chromatography in the second dimension, thereby separating intact proteins based on pI and hydrophobicity. In this study, assessment and optimization of serum separation (undepleted serum and albumin-IgG-depleted serum) by the PF2D is presented. Protein databases were created for serum obtained from a healthy individual under traditional and optimized methods and under different sample preparation protocols. Separation of the doubly depleted serum using the PF2D with 20% isopropanol present in the first dimension running buffer allowed us to unambiguously identify 150 non-redundant serum proteins (excluding all immunoglobulin and albumin, a minimum of two peptide matches with acceptable Mascot score) in which 81 have not been identified previously in serum. Among them, numerous cellular proteins were identified to be specifically the skeletal muscle isoform, such as skeletal muscle fast twitch isoforms of troponin T, myosin alkali light chain 1, and sarcoplasmic/endoplasmic reticulum calcium ATPase. The detection of specific skeletal muscle protein isoforms in the serum from healthy individuals reflects the physiological turnover that occurs in skeletal muscle, which will have an impact on the ability to use generic "cellular" proteins as biomarkers without further characterization of the precise isoforms or post-translational modifications present.
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Affiliation(s)
- Simon Sheng
- Department of Medicine, The Johns Hopkins University, Baltimore, Maryland 21224, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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