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Strategy for purification and mass spectrometry identification of SELDI peaks corresponding to low-abundance plasma and serum proteins. J Proteomics 2010; 74:420-30. [PMID: 21184852 DOI: 10.1016/j.jprot.2010.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 12/22/2022]
Abstract
Analysis by SELDI-TOF-MS of low abundance proteins makes it possible to select peaks as candidate biomarkers. Our aim was to define a purification strategy to optimise identification by MS of peaks detected by SELDI-TOF-MS from plasma or serum, regardless of any treatment by a combinatorial peptide ligand library (CPLL). We describe 2 principal steps in purification. First, choosing the appropriate sample containing the selected peak requires setting up a databank that records all the m/z peaks detected from samples in different conditions. Second, the specific purification process must be chosen: separation was achieved with either chromatographic columns or liquid-phase isoelectric focusing, both combined when appropriate with reverse-phase chromatography. After purification, peaks were separated by gel electrophoresis and the candidate proteins were analyzed by nano-liquid-chromatography-MS/MS. We chose 4m/z peaks (9400, 13,571, 13,800 and 15,557) selected for their differential expression between two conditions, as examples to explain the different strategies of purification, and we successfully identified 3 of them. Despite some limitations, our strategy to purify and identify peaks selected from SELDI-TOF-MS analysis was effective.
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103
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Beseme O, Fertin M, Drobecq H, Amouyel P, Pinet F. Combinatorial peptide ligand library plasma treatment: Advantages for accessing low-abundance proteins. Electrophoresis 2010; 31:2697-704. [PMID: 20665525 DOI: 10.1002/elps.201000188] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Depletion of major blood proteins is one of the most promising approaches to accessing low-abundance biomarkers. This study compared the use of combinatorial peptide ligand library (CPLL) and albumin and immunoglobulins (IgGs) depletion technology for accessing these low-abundance proteins in plasma using 2-DE in an acidic restricted pH range (4-7). Compared with native plasma, both techniques enlarge the visibility of other proteins than albumin and IgG, but there were marked differences in their composition. An increase of the number of spots was detected compared with native plasma (157 spots) with 427 and 557 spots, respectively, detected with albumin and IgG depletion, and CPLL treatment. We selected 70 spots to be identified by MALDI-TOF related to their absence in the 2-D gels from native or albumin and IgG-depleted plasma. The 42 spots identified corresponded to 24 different proteins, with more than half of the proteins which did not belong to the major plasma proteins. CPLL treatment allowed the accessibility to proteolytic fragments obtained from major plasma proteins. We found a large superiority of the CPLL approach over the albumin and IgG depletion process. These findings show the utility of depleting major blood proteins to be able to access low-abundance proteins and the potential of CPLL to select and identify candidate biomarkers in clinical studies.
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104
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Makridakis M, Vlahou A. Secretome proteomics for discovery of cancer biomarkers. J Proteomics 2010; 73:2291-305. [DOI: 10.1016/j.jprot.2010.07.001] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 06/14/2010] [Accepted: 07/05/2010] [Indexed: 12/11/2022]
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105
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Fakelman F, Felix K, Büchler MW, Werner J. New pre-analytical approach for the deep proteome analysis of sera from pancreatitis and pancreas cancer patients. Arch Physiol Biochem 2010; 116:208-17. [PMID: 20815689 DOI: 10.3109/13813455.2010.510891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
UNLABELLED The presence of high-abundance proteins and the wide dynamic range of protein-distribution complicates the proteome analysis of crude serum. The aim was to establish a new preanalytical protocol for analysis of the deep serum-proteome for biomarker discovery. METHODS We investigated the stability and functionality of ProteoMiner™ and tested the new protocol by SELDI-TOF-MS profiling with serum samples obtained from patients with different pancreatic diseases. RESULTS We developed a high-throughput protocol and proved the convenience of ProteoMiner™ in the 96-well format to provide insights into the deep serum proteome and facilitate the detection of novel serum biomarkers. Serum samples spiked with defined amounts of insulin, processed with ProteoMiner™ and analyzed by SELDI-TOF-MS revealed that the concentration of the spiked insulin was not altered by ProteoMiner™ treatment. CONCLUSION ProteoMiner™ technology is robust preanalytical step and can be used in a high-throughput format for analysis of low-abundant proteins in serum.
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Affiliation(s)
- Frederik Fakelman
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
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106
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Ahn JY, Lee SW, Kang HS, Jo M, Lee DK, Laurell T, Kim S. Aptamer microarray mediated capture and mass spectrometry identification of biomarker in serum samples. J Proteome Res 2010; 9:5568-73. [PMID: 20806970 DOI: 10.1021/pr100300t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sensitive detection of molecular biomarkers in clinical samples is crucially important in disease diagnostics. This paper reports the development of an aptamer microarray platform combined with sol-gel technology to identify low-abundance targets in complex serum samples. Because of the nanoporous structure of the sol-gel, a high capacity to immobilize the affinity specific aptamers is accomplished which allows binding and detection of target molecules with high sensitivity. The captured protein is digested in situ and the obtained digest was analyzed by ESI-MS without any interference from the affinity probe. TBP (TATA Box Protein) and its specific aptamers were chosen as a model system. A proof of concept with protein concentrations ranging between nanomolar to micromolar is reported, showing a good linearity up to 400 nM when characterized in an aptamer sandwich assay. Moreover, as low as 0.001% of target protein present in total serum proteins could be identified without any pretreatment step using ESI MS/MS mass spectrometry. We believe this novel strategy could become an efficient method for aptamer-based biomarker detection linked directly to mass spectrometry readout.
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Affiliation(s)
- Ji-Young Ahn
- Department of Biomedical Engineering, Dongguk University, Joong-Gu, Seoul, 100-715, Korea
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107
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Righetti PG, Boschetti E, Kravchuk AV, Fasoli E. The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries. Expert Rev Proteomics 2010; 7:373-85. [PMID: 20536309 DOI: 10.1586/epr.10.25] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The latest advances in combinatorial peptide ligand libraries, with their unique performance in discovering low-abundance species in proteomes, are reviewed here. Explanations of mechanism, potential applications, capture of proteomes at different pH values to enhance the total catch and quantitative elutions, such as boiling in the presence of 5% sodium dodecyl sulfate and 3% dithiothreitol are included. The reproducibility of protein capture among different experiments with the same batch of beads or with different batches is also reported to be very high, with coefficient of variations in the order of 10-20%. Miniaturized operations, consisting of capture with as little as 20 or even 5 microl of peptide beads are reported, thus demonstrating that the described technology could be exploited for routine biomarker discovery in a biomedical environment. Finally, it is shown that the signal of captured proteins is linear over approximately three orders of magnitude, ranging from nM to microM, thus ensuring that differential quantitative proteomics for biomarker discovery can be fully implemented, providing species do not saturate their ligands.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Via Mancinelli 7, Politecnico di Milano, Milano, Italy.
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108
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Overgaard AJ, Thingholm TE, Larsen MR, Tarnow L, Rossing P, McGuire JN, Pociot F. Quantitative iTRAQ-Based Proteomic Identification of Candidate Biomarkers for Diabetic Nephropathy in Plasma of Type 1 Diabetic Patients. Clin Proteomics 2010; 6:105-114. [PMID: 21124997 PMCID: PMC2970822 DOI: 10.1007/s12014-010-9053-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Introduction As part of a clinical proteomics programme focused on diabetes and its complications, it was our goal to investigate the proteome of plasma in order to find improved candidate biomarkers to predict diabetic nephropathy. Methods Proteins derived from plasma from a cross-sectional cohort of 123 type 1 diabetic patients previously diagnosed as normoalbuminuric, microalbuminuric or macroalbuminuric were enriched with hexapeptide library beads and subsequently pooled within three groups. Proteins from the three groups were compared by online liquid chromatography and tandem mass spectrometry in three identical repetitions using isobaric mass tags (iTRAQ). The results were further analysed with ingenuity pathway analysis. Levels of apolipoprotein A1, A2, B, C3, E and J were analysed and validated by a multiplex immunoassay in 20 type 1 diabetic patients with macroalbuminuria and 10 with normoalbuminuria. Results A total of 112 proteins were identified in at least two out of three replicates. The global protein ratios were further evaluated by ingenuity pathway analysis, resulting in the recognition of apolipoprotein A2, B, C3, D and E as key nodes in the top-rated network. The multiplex immunoassay confirmed the overall protein expression patterns observed by the iTRAQ analysis. Conclusion The candidate biomarkers discovered in this cross-sectional cohort may turn out to be progression biomarkers and might have several clinical applications in the treatment and monitoring of diabetic nephropathy; however, they need to be confirmed in a longitudinal cohort. Electronic supplementary material The online version of this article (doi:10.1007/s12014-010-9053-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Julie Overgaard
- Hagedorn Research Institute, Novo Nordisk A/S, Niels Steensens Vej 1, 2820 Gentofte, Denmark
| | - Tine E. Thingholm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Lise Tarnow
- Steno Diabetes Center, Niels Steensens Vej 1, 2820 Gentofte, Denmark
| | - Peter Rossing
- Steno Diabetes Center, Niels Steensens Vej 1, 2820 Gentofte, Denmark
| | - James N. McGuire
- Hagedorn Research Institute, Novo Nordisk A/S, Niels Steensens Vej 1, 2820 Gentofte, Denmark
| | - Flemming Pociot
- Hagedorn Research Institute, Novo Nordisk A/S, Niels Steensens Vej 1, 2820 Gentofte, Denmark
- CRC, University of Lund, Malmö, Sweden
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109
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D'Amato A, Kravchuk AV, Bachi A, Righetti PG. Noah's nectar: the proteome content of a glass of red wine. J Proteomics 2010; 73:2370-7. [PMID: 20813213 DOI: 10.1016/j.jprot.2010.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/24/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
Abstract
Combinatorial peptide ligand libraries (CPLLs) have been adopted for harvesting and identifying traces of proteins present in red wines. Surprisingly, although it is stated that red wines are in general fined with egg albumin, for all Italian wines investigated (in the areas around Chiari and Verona as well as in the Chianti area) we find that the only fining agent used is bovine casein, just like in white wines. Although the typical levels of casein found range between 45 to 85μg/L, in one case as little as 3.8μg/L of casein could be detected, an extremely high level of sensitivity, close to our lower detection limit of 1μg/L reported for white wines. As a result of such treatments, very small amounts of residual proteins in red wines could be identified: essentially no residual grape proteins (except for thaumatin), but only traces of proteins from Saccharomyces cerevisiae and a few proteins from plant pathogens and fungi (e.g., Botryotinia fuckeliana, Sclerotinia sclerotiorum, Aspergillus aculeatus). Contrary to what has been found in white wines, the best capture efficiency with CPLLs has occurred at pH 7.2 and pH 9.3, with minimal capture at pH 3.3. The fact that such very low levels of fining agents can still be detected in treated red wines should be taken into consideration by winemakers in labelling their products and by EC rulers in issuing proper regulations.
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Affiliation(s)
- Alfonsina D'Amato
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
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Fahiminiya S, Labas V, Dacheux JL, Gérard N. Improvement of 2D-PAGE Resolution of Human, Porcine and Equine Follicular Fluid by Means of Hexapeptide Ligand Library. Reprod Domest Anim 2010; 46:561-3. [DOI: 10.1111/j.1439-0531.2010.01683.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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111
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Proteomics of wine additives: Mining for the invisible via combinatorial peptide ligand libraries. J Proteomics 2010; 73:1732-9. [DOI: 10.1016/j.jprot.2010.05.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 05/05/2010] [Accepted: 05/18/2010] [Indexed: 10/19/2022]
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112
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Bandow JE. Comparison of protein enrichment strategies for proteome analysis of plasma. Proteomics 2010; 10:1416-25. [PMID: 20127685 DOI: 10.1002/pmic.200900431] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Efforts to discover protein biomarkers in plasma are hampered by the high abundance of few proteins, which interfere with the detection of low-abundant proteins. Different commercially available protein-partitioning products were tested for their ability to lower the detection limit of proteins in 2-D gels. Immuno-depletion using polyclonal antibodies raised against the proteins of highest abundance (Seppro IgY14 System) was compared with a two-step immuno-depletion strategy, where depletion with the Seppro IgY14 column was followed by depletion with the Seppro IgY-SuperMix system. The third strategy tested was protein pre-fractionation using the ProteoMiner kit, where proteins compete for binding sites on bead-bound peptide hexamers with different binding properties. The pre-fractionated protein samples were analyzed using 2-DE, which revealed stunning differences in protein patterns. However, detectable protein spots in the different plasma fractions contained exclusively high-abundant proteins normally present in plasma at concentrations between 1 microg and 40 mg/mL.
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Affiliation(s)
- Julia E Bandow
- Pfizer Global Research and Development, Pfizer Inc, Ann Arbor, MI, USA.
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113
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114
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Kawashima Y, Fukutomi T, Tomonaga T, Takahashi H, Nomura F, Maeda T, Kodera Y. High-yield peptide-extraction method for the discovery of subnanomolar biomarkers from small serum samples. J Proteome Res 2010; 9:1694-705. [PMID: 20184378 DOI: 10.1021/pr9008018] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serum proteins/peptides reflect physiological or pathological states in humans and are an attractive target for the discovery of disease biomarkers. However, the existence of high-abundance proteins and the large dynamic range of serum proteins/peptides make any quantitative analysis of low-abundance proteins/peptides challenging. Furthermore, analyses of peptides, including the cleaved fragments of proteins, are difficult because of carrier protein binding. Here, we developed a differential solubilization (DS) method to extract low-molecular-weight proteins/peptides in serum with good reproducibility and yield as compared to typical peptide-extraction methods such as organic solvent precipitation and ultrafiltration. Using the DS method combined with reverse-phase HPLC fractionation followed by MALDI-TOF-MS, we performed high-quality comparative analyses of more than 1500 peptides from 1 microL of serum samples, including low-abundance peptides in the subnanomolar range and containing many peptides bound to carrier proteins such as albumin. We applied this method and successfully discovered four new biomarker candidates of colon cancer, none of which have previously been observed in serum and one of which is a fragment of the protein zyxin that possibly originated from tumor cells. Our results indicate that serum peptide analyses based on the DS method should greatly contribute to the discovery of novel low-abundance biomarkers.
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Affiliation(s)
- Yusuke Kawashima
- Laboratory of Biomolecular Dynamics, Department of Physics, Kitasato University School of Science, Sagamihara, Kanagawa, Japan
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Abstract
In this review, we discuss several important issues concerning the discovery of protein biomarkers for complex human diseases, with a focus on type 1 diabetes. Serum or plasma is the first choice of specimen due to its richness in biological information and relatively easy availability. It is a challenging task to comprehensively characterize the serum/plasma proteome because of the large dynamic range of protein concentration. Therefore, sample pretreatment is required in order to explore the low- to medium-abundance proteins contained in serum/plasma. In this regard, enrichment of low-abundance proteins using random hexapeptide library beads has distinct advantages over the traditional immune-depletion methods, including higher efficiency, higher binding capacity, and lower cost. In-depth mining of serum/plasma proteome using different separation techniques have also been evaluated and are discussed in this review. Overall, the shotgun proteomics-multidimensional separation of digested peptides followed by mass spectrometry analysis--is highly efficient and therefore has become a preferred method for protein biomarker discovery.
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Affiliation(s)
- Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, Georgia 30912, USA
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116
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A proteomic approach for plasma biomarker discovery with 8-plex iTRAQ labeling and SCX-LC-MS/MS. Mol Cell Biochem 2010; 343:91-9. [PMID: 20526653 DOI: 10.1007/s11010-010-0502-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 05/12/2010] [Indexed: 10/19/2022]
Abstract
Plasma is recognized as a promising source of disease-related biomarkers, and proteomic approaches for identifying novel plasma biomarkers are in great demand. However, the complexity and dynamic protein concentration range of plasma remain the main obstacles for current research in this field. In this study, plasma proteins were prefractioned by immunodepletion and Protein Equalizer Technology to remove high abundant proteins, then labeled with an 8-plex isobaric tags for relative and absolute quantitation (iTRAQ) to improve the peptide ionization, and analyzed by strong-cation-exchange(SCX) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our results showed that both prefraction methods were complementary, with regard to the number of identified proteins. Good chromatographic technique is important to further fractionate the iTRAQ labeling peptides, which allowed 320 and 248 different proteins to be characterized from two prefraction methods, respectively, encompassing a wide array of biological functions and a broad dynamic range of 10(7). Furthermore, the accuracy of iTRAQ relative quantitation for differentially expressed proteins is associated with the number of peptides hits per protein.
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117
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In-depth exploration of Hevea brasiliensis latex proteome and “hidden allergens” via combinatorial peptide ligand libraries. J Proteomics 2010; 73:1368-80. [DOI: 10.1016/j.jprot.2010.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/02/2010] [Accepted: 03/04/2010] [Indexed: 11/18/2022]
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118
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Chevalier F. Highlights on the capacities of "Gel-based" proteomics. Proteome Sci 2010; 8:23. [PMID: 20426826 PMCID: PMC2873371 DOI: 10.1186/1477-5956-8-23] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 04/28/2010] [Indexed: 11/18/2022] Open
Abstract
Gel-based proteomic is the most popular and versatile method of global protein separation and quantification. This is a mature approach to screen the protein expression at the large scale, and a cheaper approach as compared with gel-free proteomics. Based on two independent biochemical characteristics of proteins, two-dimensional electrophoresis combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass. The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis and finally protein identification by mass spectrometry. For the study of differentially expressed proteins, two-dimensional electrophoresis allows simultaneously to detect, quantify and compare up to thousand protein spots isoforms, including post-translational modifications, in the same gel and in a wide range of biological systems. In this review article, the limits, benefits, and perspectives of gel-based proteomic approaches are discussed using concrete examples.
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119
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Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis. Talanta 2010; 82:245-54. [PMID: 20685463 DOI: 10.1016/j.talanta.2010.04.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Revised: 03/31/2010] [Accepted: 04/16/2010] [Indexed: 11/23/2022]
Abstract
In most diseases, the clinical need for serum/plasma markers has never been so crucial, not only for diagnosis, but also for the selection of the most efficient therapies, as well as exclusion of ineffective or toxic treatment. Due to the high sample complexity, prefractionation is essential for exploring the deep proteome and finding specific markers. In this study, three different sample preparation methods (i.e., highly abundant protein precipitation, restricted access materials (RAM) combined with IMAC chromatography and peptide ligand affinity beads) were investigated in order to select the best fractionation step for further differential proteomic experiments focusing on the LMW proteome (MW inferior to 40,000 Da). Indeed, the aim was not to cover the entire plasma/serum proteome, but to enrich potentially interesting tissue leakage proteins. These three methods were evaluated on their reproducibility, on the SELDI-TOF-MS peptide/protein peaks generated after fractionation and on the information supplied. The studied methods appeared to give complementary information and presented good reproducibility (below 20%). Peptide ligand affinity beads were found to provide efficient depletion of HMW proteins and peak enrichment in protein/peptide profiles.
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120
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Keidel EM, Ribitsch D, Lottspeich F. Equalizer technology - Equal rights for disparate beads. Proteomics 2010; 10:2089-98. [DOI: 10.1002/pmic.200900767] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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121
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Fertin M, Beseme O, Duban S, Amouyel P, Bauters C, Pinet F. Deep plasma proteomic analysis of patients with left ventricular remodeling after a first myocardial infarction. Proteomics Clin Appl 2010; 4:654-73. [PMID: 21137084 DOI: 10.1002/prca.200900178] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 02/10/2010] [Accepted: 02/27/2010] [Indexed: 11/10/2022]
Abstract
PURPOSE Depletion of major blood proteins is one of the most promising approaches to accessing low abundance biomarkers for proteomics studies. The use of combinatorial peptide ligand library (CPLL) for accessing these low abundance proteins in plasma from patients with a myocardial infarction (MI) was tested to identify candidate protein biomarkers of left ventricular remodeling (LVR). EXPERIMENTAL DESIGN Serial blood samples of MI patients followed for one year (at inclusion, 1 month, 3 months, and 1 year) were treated with CPLL and analyzed by SELDI-TOF-MS. RESULT The use of CPLL increased resolution, with loss of most abundant plasma proteins, reproducibly and improved the intensity of low-abundance proteins. Longitudinal information allowed us to reduce by 55% the final number of peaks identified as significantly modulated throughout the 1-year follow-up after MI. Interestingly, 19 of the 26 peaks finally selected were detected only in samples treated from CPLL. The 2777 m/z peak, found in less elevated level in high remodeling patients, was identified as being DAHKSEVAHR FKDLGEENFKALVL, the N-terminal peptide (24-48 aa) generated from albumin by pepsin cleavage. CONCLUSIONS AND CLINICAL RELEVANCE This finding shows the potential of CPLL in accessing low-abundance proteins to select and identify candidate biomarkers in patients with LVR.
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122
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Tan Q, Dong D, Ye L, Li R. Combined usage of cascade affinity fractionation and LC-MS/MS for the proteomics of adult mouse testis. J Sep Sci 2010; 32:3871-9. [PMID: 19890842 DOI: 10.1002/jssc.200900477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this report, the proteomics of adult mouse testis were analyzed by the combined usage of cascade affinity fractionation and LC-MS/MS. The differences between the selected affinity ligands in size, shape, structure, and biochemical characteristics, result in each ligand exhibiting a specific affinity to some protein groups. Therefore, a cascade composition of different ligands can be applied to the fractionation of complex tissue proteins. Ultimately, the fractions collected from cascade affinity fractionation were analyzed by LC-MS/MS, which resulted in high confidence identification of a total of 1378 non-redundant mouse testis protein groups, over 2.6 times as many proteins as were detected in the un-fractionated sample (526). All detected proteins were bioinformatically categorized according to their physicochemical characteristics (such as relative molecular mass, pI, grand average hydrophobicity value, and transmembrane helices), subcellular location, and function annotation. This approach highlighted the sensitivity of this method to a wide variety of protein classes. Utilizing a combination of cascade affinity fractionation and LC-MS/MS, we have established the largest proteomic database for adult mouse testis at the present time.
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Affiliation(s)
- Qingqiao Tan
- MOE Key Laboratory of Microbial Metabolism, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
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123
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Fasoli E, Sanz L, Wagstaff S, Harrison RA, Righetti PG, Calvete JJ. Exploring the venom proteome of the African puff adder, Bitis arietans, using a combinatorial peptide ligand library approach at different pHs. J Proteomics 2010; 73:932-42. [DOI: 10.1016/j.jprot.2009.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/09/2009] [Accepted: 12/09/2009] [Indexed: 12/28/2022]
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124
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Candiano G, Santucci L, Petretto A, Bruschi M, Dimuccio V, Urbani A, Bagnasco S, Ghiggeri GM. 2D-electrophoresis and the urine proteome map: Where do we stand? J Proteomics 2010; 73:829-44. [DOI: 10.1016/j.jprot.2009.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/30/2009] [Accepted: 12/02/2009] [Indexed: 12/19/2022]
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125
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Gadher SJ, Jarkovska K, Kovarova H. Reproductive therapies and a need for potential biomarkers for prognostic and diagnostic screening of women desperate to conceive. Expert Rev Proteomics 2010; 6:591-3. [PMID: 19929604 DOI: 10.1586/epr.09.79] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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126
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Plucking, pillaging and plundering proteomes with combinatorial peptide ligand libraries. J Chromatogr A 2010; 1217:893-900. [DOI: 10.1016/j.chroma.2009.08.070] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 08/19/2009] [Accepted: 08/27/2009] [Indexed: 11/23/2022]
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127
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Jmeian Y, El Rassi Z. Multicolumn separation platform for simultaneous depletion and prefractionation prior to 2-DE for facilitating in-depth serum proteomics profiling. J Proteome Res 2010; 8:4592-603. [PMID: 19670910 DOI: 10.1021/pr900399q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report, we describe an integrated fluidic platform composed of tandem affinity columns for the depletion of high-abundance proteins from human serum and on-line fractionation/concentration of medium- and low-abundance proteins by tandem immobilized metal-ion affinity chromatography (IMAC) columns and reversed phase (RP) column for in-depth proteomics analysis. The depletion columns were based on monolithic polymethacrylate with surface immobilized protein A, protein G', and antibodies for depleting the top 8 high-abundance proteins. The IMAC fractionation/concentration columns consisted of monolithic stationary phases with surface bound iminodiacetic acid (IDA) chelated with Zn2+, Ni2+ and Cu2+, while the RP column was packed with nonpolar polymer beads. The integrated multicolumn fluidic platform was very effective in reducing simultaneously both the dynamic range differences among the protein constituents of serum and the complexity of the proteomics samples, thus, facilitating the in-depth proteomics analysis by 2-DE followed by MALDI-TOF and LC-MS/MS. In fact, the number of detected spots was approximately 1450 using SYPRO fluorescent stain from which 384 spots were subsequently detected by Coomassie Blue. Since the investigation was simply a proof of concept, 295 proteins were readily identified in some selected spots by MALDI-TOF and LC-MS/MS.
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Affiliation(s)
- Yazen Jmeian
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078-3071, USA
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128
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Fasoli E, Farinazzo A, Sun CJ, Kravchuk AV, Guerrier L, Fortis F, Boschetti E, Righetti PG. Interaction among proteins and peptide libraries in proteome analysis: pH involvement for a larger capture of species. J Proteomics 2010; 73:733-42. [DOI: 10.1016/j.jprot.2009.10.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 10/05/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
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129
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Mouton-Barbosa E, Roux-Dalvai F, Bouyssié D, Berger F, Schmidt E, Righetti PG, Guerrier L, Boschetti E, Burlet-Schiltz O, Monsarrat B, Gonzalez de Peredo A. In-depth exploration of cerebrospinal fluid by combining peptide ligand library treatment and label-free protein quantification. Mol Cell Proteomics 2010; 9:1006-21. [PMID: 20093276 DOI: 10.1074/mcp.m900513-mcp200] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cerebrospinal fluid (CSF) is the biological fluid in closest contact with the brain and thus contains proteins of neural cell origin. Hence, CSF is a biochemical window into the brain and is particularly attractive for the search for biomarkers of neurological diseases. However, as in the case of other biological fluids, one of the main analytical challenges in proteomic characterization of the CSF is the very wide concentration range of proteins, largely exceeding the dynamic range of current analytical approaches. Here, we used the combinatorial peptide ligand library technology (ProteoMiner) to reduce the dynamic range of protein concentration in CSF and unmask previously undetected proteins by nano-LC-MS/MS analysis on an LTQ-Orbitrap mass spectrometer. This method was first applied on a large pool of CSF from different sources with the aim to better characterize the protein content of this fluid, especially for the low abundance components. We were able to identify 1212 proteins in CSF, and among these, 745 were only detected after peptide library treatment. However, additional difficulties for clinical studies of CSF are the low protein concentration of this fluid and the low volumes typically obtained after lumbar puncture, precluding the conventional use of ProteoMiner with large volume columns for treatment of patient samples. The method has thus been optimized to be compatible with low volume samples. We could show that the treatment is still efficient with this miniaturized protocol and that the dynamic range of protein concentration is actually reduced even with small amounts of beads, leading to an increase of more than 100% of the number of identified proteins in one LC-MS/MS run. Moreover, using a dedicated bioinformatics analytical work flow, we found that the method is reproducible and applicable for label-free quantification of series of samples processed in parallel.
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Affiliation(s)
- Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, 205 route de Narbonne, 31077 Toulouse, France
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130
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Dwivedi RC, Krokhin OV, Cortens JP, Wilkins JA. Assessment of the Reproducibility of Random Hexapeptide Peptide Library-Based Protein Normalization. J Proteome Res 2010; 9:1144-9. [DOI: 10.1021/pr900608z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ravi C. Dwivedi
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg MB, Canada, R3E 3P4
| | - Oleg V. Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg MB, Canada, R3E 3P4
| | - John P. Cortens
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg MB, Canada, R3E 3P4
| | - John A. Wilkins
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg MB, Canada, R3E 3P4
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131
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Advances in urinary proteome analysis and biomarker discovery in pediatric renal disease. Pediatr Nephrol 2010; 25:27-35. [PMID: 19603189 DOI: 10.1007/s00467-009-1251-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
Recent progress in proteomic analysis and strategies for the identification of clinically useful biomarkers in biofluids has led to the identification of urine as an excellent non-invasive reservoir for biomarkers of disease. Urinary biomarkers have been identified and validated on independent cohorts in different high-incidence adult renal diseases, including diabetic nephropathy, chronic kidney disease and immunoglobulin A-nephropathy, but also in extrarenal disease, such as coronary artery disease. Unfortunately, this type of research is underrepresented in the pediatric population. Here, we present the rare studies in the pediatric population that identified potential clinically useful urinary biomarkers in ureteropelvic junction (UPJ) obstruction and renal Fanconi syndrome. These studies, although limited in number, clearly show the potential of urinary proteomics, especially in the pediatric population. It is anticipated that the advances made in the adult population, the lessons learned on the use of appropriate statistics and the inclusion of independent blinded validation cohorts in these types of studies will rapidly lead to clinical useful urinary biomarkers for other pediatric (renal) disease in a population where non-invasive analysis is particularly appreciated.
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132
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Righetti PG, Boschetti E. Blood proteomics and the dynamic range: some light at the end of the tunnel? J Proteomics 2010; 73:627-8. [DOI: 10.1016/j.jprot.2009.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 09/11/2009] [Indexed: 11/28/2022]
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133
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Challenges for biomarker discovery in body fluids using SELDI-TOF-MS. J Biomed Biotechnol 2009; 2010:906082. [PMID: 20029632 PMCID: PMC2793423 DOI: 10.1155/2010/906082] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 09/01/2009] [Indexed: 01/17/2023] Open
Abstract
Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy for biomarker discovery are presented. This paper also reviews biological fluids generally available including a description of their peculiar properties and the preanalytical challenges inherent to sample collection and storage. Finally, some new insights for biomarker identification and validation challenges are provided.
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134
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Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ). J Biomed Biotechnol 2009; 2010:952047. [PMID: 19902006 PMCID: PMC2774473 DOI: 10.1155/2010/952047] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 08/21/2009] [Indexed: 11/24/2022] Open
Abstract
Currently no specific biomarkers exist for the screening of pregnancies at risk for down
syndrome (DS). Since a quantitative proteomic approach with isobaric labelling (iTRAQ) has
recently been suggested to be highly suitable for the discovery of novel plasma biomarkers, we
have now used this method to examine for potential quantitative changes in the plasma
proteome of the pregnancies bearing DS fetuses in comparison to normal healthy babies. In our
study, we used plasma from six women with DS pregnancies and six with uncomplicated
pregnancies care were taken to match cases and controls for gestational and maternal age, as
these could be a confounder.
In our quantitative proteomics analysis we were able to detect 178 proteins using iTRAQ
labelling in conjunction with 4800 MALDI TOF/TOF. Amongst these we observed changes in βHCG, a known screening marker for DS, indicating that our assay was functional. We found a
number of elevated proteins Ig lambda chain C region, serum amyloid P-component, amyloid
beta A4, and under expressed proteins like gamma-actin and titin in DS pregnancies. These proteins
are also found in the sera of patients with Alzheimer disease, which share similar pathologies of
DS. Our study therefore indicates that the iTRAQ labelling approach may be indeed useful for the
detection of novel biomarkers.
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135
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A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation. J Biomed Biotechnol 2009; 2010:927917. [PMID: 19888438 PMCID: PMC2771280 DOI: 10.1155/2010/927917] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/17/2009] [Accepted: 08/03/2009] [Indexed: 11/18/2022] Open
Abstract
Human blood plasma contains a plethora of proteins, encompassing not only proteins that have plasma-based functionalities, but also possibly every other form of low concentrated human proteins. As it circulates through the tissues, the plasma picks up proteins that are released from their origin due to physiological events such as tissue remodeling and cell death. Specific disease processes or tumors are often characterized by plasma “signatures,” which may become obvious via changes in the plasma proteome profile, for example, through over expression of proteins. However, the wide dynamic range of proteins present in plasma makes their analysis very challenging, because high-abundance proteins tend to mask those of lower abundance. In the present study, we used a strategy combining iTRAQ as a reagent which improved the peptide ionization and peptide OFFGEL fractionation that has already been shown, in our previous research, to improve the proteome coverage of cellular extracts. Two prefractioning methods were compared: immunodepletion and a bead-based library of combinatorial hexapeptide technology. Our data suggested that both methods were complementary, with regard to the number of identified proteins. iTRAQ labelling, in association with OFFGEL fractionation, allowed more than 300 different proteins to be characterized from 400 μg of plasma proteins.
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136
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Gander S, Martin D, Hauri S, Moes S, Poletto G, Pagano MA, Marin O, Meggio F, Jenoe P. A Modified KESTREL Search Reveals a Basophilic Substrate Consensus for the Saccharomyces cerevisiae Npr1 Protein Kinase. J Proteome Res 2009; 8:5305-16. [DOI: 10.1021/pr9005469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefan Gander
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Dietmar Martin
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Simon Hauri
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Suzette Moes
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Giorgia Poletto
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Mario A. Pagano
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Oriano Marin
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Flavio Meggio
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
| | - Paul Jenoe
- Department of Biochemistry, Biozentrum of the University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland, Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany, and Department of Biological Chemistry, University of Padova, Viale G. Colombo, 3, I-35121 Padova, Italy
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137
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Calvete JJ, Fasoli E, Sanz L, Boschetti E, Righetti PG. Exploring the venom proteome of the western diamondback rattlesnake, Crotalus atrox, via snake venomics and combinatorial peptide ligand library approaches. J Proteome Res 2009; 8:3055-67. [PMID: 19371136 DOI: 10.1021/pr900249q] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the proteomic characterization of the venom of the medically important North American western diamondback rattlesnake, Crotalus atrox, using two complementary approaches: snake venomics (to gain an insight of the overall venom proteome), and two solid-phase combinatorial peptide ligand libraries (CPLL), followed by 2D electrophoresis and mass spectrometric characterization of in-gel digested protein bands (to capture and "amplify" low-abundance proteins). The venomics approach revealed approximately 24 distinct proteins belonging to 2 major protein families (snake venom metalloproteinases, SVMP, and serine proteinases), which represent 69.5% of the total venom proteins, 4 medium abundance families (medium-size disintegrin, PLA(2), cysteine-rich secretory protein, and l-amino acid oxidase) amounting to 25.8% of the venom proteins, and 3 minor protein families (vasoactive peptides, endogenous inhibitor of SVMP, and C-type lectin-like). This toxin profile potentially explains the cytotoxic, myotoxic, hemotoxic, and hemorrhagic effects evoked by C. atrox envenomation. Further, our results showing that C. atrox exhibits a similar level of venom variation as Sistrurus miliarius points to a "diversity gain" scenario in the lineage leading to the Sistrurus catenatus taxa. On the other hand, the two combinatorial hexapeptide libraries captured distinct sets of proteins. Although the CPLL-treated samples did not retain a representative venom proteome, protein spots barely, or not at all, detectable in the whole venom were enriched in the two CPLL-treated samples. The amplified low copy number C. atrox venom proteins comprised a C-type lectin-like protein, several PLA(2) molecules, PIII-SVMP isoforms, glutaminyl cyclase isoforms, and a 2-cys peroxiredoxin highly conserved across the animal kingdom. Peroxiredoxin and glutaminyl cyclase may participate, respectively, in redox processes leading to the structural/functional diversification of toxins, and in the N-terminal pyrrolidone carboxylic acid formation required in the maturation of bioactive peptides such as bradykinin-potentiating peptides and endogenous inhibitors of metalloproteases. Our findings underscore the usefulness of combinatorial peptide libraries as powerful tools for mining below the tip of the iceberg, complementing thereby the data gained using the snake venomics protocol toward a complete visualization of the venom proteome.
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Affiliation(s)
- Juan J Calvete
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas (CSIC), Jaume Roig 11, 46010 Valencia, Spain.
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138
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Colzani M, Waridel P, Laurent J, Faes E, Rüegg C, Quadroni M. Metabolic Labeling and Protein Linearization Technology Allow the Study of Proteins Secreted by Cultured Cells in Serum-Containing Media. J Proteome Res 2009; 8:4779-88. [DOI: 10.1021/pr900476b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- M. Colzani
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland, and National Center of Competence in Research (NCCR) Molecular Oncology, ISREC, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - P. Waridel
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland, and National Center of Competence in Research (NCCR) Molecular Oncology, ISREC, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - J. Laurent
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland, and National Center of Competence in Research (NCCR) Molecular Oncology, ISREC, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - E. Faes
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland, and National Center of Competence in Research (NCCR) Molecular Oncology, ISREC, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - C. Rüegg
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland, and National Center of Competence in Research (NCCR) Molecular Oncology, ISREC, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - M. Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV), University of Lausanne, Lausanne, Switzerland, and National Center of Competence in Research (NCCR) Molecular Oncology, ISREC, School of Life Sciences, EPFL, Lausanne, Switzerland
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139
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Sigdel TK, Klassen RB, Sarwal MM. Interpreting the proteome and peptidome in transplantation. Adv Clin Chem 2009; 47:139-69. [PMID: 19634780 DOI: 10.1016/s0065-2423(09)47006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Publication of the human proteome has prompted efforts to develop high-throughput techniques that can catalogue and quantify proteins and peptides present in different tissue types. The field of proteomics aims to identify, quantify, analyze, and functionally define a large number of proteins in cellular processes in different disease states on a global scale. Peptidomics, a newer name in the -omics world, measures and identifies naturally occurring low molecular weight peptides, also providing an insight into enzymatic processes and molecular events occurring in the system of interest. One area of major interest is the use of proteomics to identify diagnostic and prognostic biomarkers for different diseases as well as for various clinical phenotypes in organ transplantation that can advance targeted therapy for various forms of graft injury. Outcomes in organ transplantation can be potentially improved by identifying noninvasive biomarkers that will serve as triggers that predate graft injury, and can offer a means to customize patient treatment by differentiating among causes of acute and chronic graft injury. Proteomic and peptidomic strategies can be harnessed for frequent noninvasive measurements in tissue fluids, allowing for serial monitoring of organ disease. In this review, we describe the basic techniques used in proteomic and peptidomic approaches, point out special considerations in using these methods, and discuss their applications in recently published studies in organ transplantation.
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Affiliation(s)
- Tara K Sigdel
- Department of Pediatrics-Nephrology, Stanford University Medical School, Stanford University, Stanford, California 94305, USA
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140
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D’Amato A, Bachi A, Fasoli E, Boschetti E, Peltre G, Sénéchal H, Righetti PG. In-Depth Exploration of Cow’s Whey Proteome via Combinatorial Peptide Ligand Libraries. J Proteome Res 2009; 8:3925-36. [DOI: 10.1021/pr900221x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alfonsina D’Amato
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Angela Bachi
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Elisa Fasoli
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Egisto Boschetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Gabriel Peltre
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Helène Sénéchal
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
| | - Pier Giorgio Righetti
- San Raffaele Scientific Institute, 20132 Milano, Italy, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, 20131 Milano, Italy, Bio Rad Laboratories, C/o CEA-Saclay, 91181 Gif-sur-Yvette, France, and Laboratoire Environnement et Chimie Analytique, UMR CNRS 7121, ESPCI, Paris, France
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141
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Candiano G, Dimuccio V, Bruschi M, Santucci L, Gusmano R, Boschetti E, Righetti PG, Ghiggeri GM. Combinatorial peptide ligand libraries for urine proteome analysis: Investigation of different elution systems. Electrophoresis 2009; 30:2405-11. [DOI: 10.1002/elps.200800762] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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142
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Searching for specific motifs in affinity capture in proteome analysis. J Proteomics 2009; 72:791-802. [DOI: 10.1016/j.jprot.2009.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 03/20/2009] [Accepted: 04/07/2009] [Indexed: 11/18/2022]
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143
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Applications of chemical tagging approaches in combination with 2DE and mass spectrometry. Methods Mol Biol 2009; 519:83-101. [PMID: 19381578 DOI: 10.1007/978-1-59745-281-6_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Chemical modification reactions play an important role in various protocols for mass-spectrometry-based proteome analysis; this applies to both gel-based and gel-free proteomics workflows. In combination with two-dimensional gel electrophoresis (2DE), the addition of "tags" by means of chemical reactions serves several purposes. Potential benefits include increased sensitivity or sequence coverage for peptide mass fingerprinting and improved peptide fragmentation for de novo sequencing studies. Tagging strategies can also be used to obtain complementary quantitative information in addition to densitometry, and they may be employed for the study of post-translational modifications. In combination with the unique advantages of 2DE as a separation technique, such approaches provide a powerful toolbox for proteomic research. In this review, relevant examples from recent literature will be given to illustrate the capabilities of chemical tagging approaches, and methodological requirements will be discussed.
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144
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Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci 2009; 32:771-98. [PMID: 19219839 DOI: 10.1002/jssc.200800622] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine at East Carolina University, Greenville, NC, USA.
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145
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Farinazzo A, Fasoli E, Kravchuk AV, Candiano G, Aldini G, Regazzoni L, Righetti PG. En bloc elution of proteomes from combinatorial peptide ligand libraries. J Proteomics 2009; 72:725-30. [DOI: 10.1016/j.jprot.2009.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 02/23/2009] [Indexed: 10/21/2022]
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146
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Fasoli E, Pastorello EA, Farioli L, Scibilia J, Aldini G, Carini M, Marocco A, Boschetti E, Righetti PG. Searching for allergens in maize kernels via proteomic tools. J Proteomics 2009; 72:501-10. [DOI: 10.1016/j.jprot.2009.01.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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147
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Callesen AK, Madsen JS, Vach W, Kruse TA, Mogensen O, Jensen ON. Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 2009; 9:1428-41. [DOI: 10.1002/pmic.200800382] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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148
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Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 2009; 9:1492-510. [DOI: 10.1002/pmic.200800389] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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149
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Duncan MW, Roder H, Hunsucker SW. Quantitative matrix-assisted laser desorption/ionization mass spectrometry. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 7:355-70. [PMID: 19106161 DOI: 10.1093/bfgp/eln041] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the essential characteristics of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS), especially as they relate to its applications in quantitative analysis. Approaches to quantification by MALDI-TOF MS are presented and published applications are critically reviewed.
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Affiliation(s)
- Mark W Duncan
- Division of Endocrinology, Metabolism and Diabetes, School of Medicine, University of Colorado Denver, Mail Stop 8106, 12801 East 17th Avenue, Aurora, CO 80045, USA.
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150
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Combinatorial peptide ligand libraries and plant proteomics: A winning strategy at a price. J Chromatogr A 2009; 1216:1215-22. [DOI: 10.1016/j.chroma.2008.11.098] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 11/22/2008] [Accepted: 11/26/2008] [Indexed: 12/16/2022]
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