1
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Hecht ES, Obiorah EC, Liu X, Morrison L, Shion H, Lauber M. Microflow size exclusion chromatography to preserve micromolar affinity complexes and achieve subunit separations for native state mass spectrometry. J Chromatogr A 2022; 1685:463638. [DOI: 10.1016/j.chroma.2022.463638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
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Proteomic Analysis of Exudates from Chronic Ulcer of Diabetic Foot Treated with Scorpion Antimicrobial Peptide. Mediators Inflamm 2022; 2022:5852786. [PMID: 36225537 PMCID: PMC9550419 DOI: 10.1155/2022/5852786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/26/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
Scorpion peptides have good therapeutic effect on chronic ulcer of diabetic foot, but the related pharmacological mechanism has remained unclear. The different proteins and bacteria present in ulcer exudates from chronic diabetic foot patients, treated with scorpion antimicrobial peptide at different stages, were analyzed using isobaric tags for quantification-labeled proteomics and bacteriological methods. According to the mass spectrometry data, a total of 1865 proteins were identified qualitatively, and the number of the different proteins was 130 (mid/early), 401 (late/early), and 310 (mid, late/early). In addition, functional annotation, cluster analysis of effects and the analysis of signal pathway, transcription regulation, and protein-protein interaction network were carried out. The results showed that the biochemical changes of wound microenvironment during the treatment involved activated biological functions such as protein synthesis, cell proliferation, differentiation, migration, movement, and survival. Inhibited biological functions such as cell death, inflammatory response, immune diseases, and bacterial growth were also involved. Bacteriological analysis showed that Burkholderia cepacia was the main bacteria in the early and middle stage of ulcer exudate and Staphylococcus epidermidis in the late stage. This study provides basic data for further elucidation of the molecular mechanism of diabetic foot.
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3
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Wang C, Liang Y, Zhao B, Liang Z, Zhang L, Zhang Y. Ethane-Bridged Hybrid Monolithic Column with Large Mesopores for Boosting Top-Down Proteomic Analysis. Anal Chem 2022; 94:6172-6179. [PMID: 35412811 DOI: 10.1021/acs.analchem.1c05234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Top-down proteomics is challenged by the high complexity of biological samples. The coelution of intact proteins results in overlapped mass spectra, and hence, an increased peak capacity for protein separation is needed. Herein, ethane-bridged hybrid monoliths with well-defined large mesopores were successfully prepared based on the sol-gel condensation of 1,2-bis(trimethoxysilyl)ethane and tetramethoxysilane, followed by two-step base etching of the Si-O-Si domain while maintaining the Si-C-C-Si domain in the structure. Relatively homogeneous macropores of 1.1 μm and large mesopores of 24 nm were obtained, permitting fast mass transfer of large molecules and efficient diffusion without obstruction. The use of less hydrophobic C1 ligand further sharpened the peak shape and improved peak capacity. A 120 cm-long capillary column was used for top-down proteomic analysis of E. coli lysates under low backpressure with 16 MPa. High peak capacity of 646 was achieved within 240 min gradient. With MS/MS analysis, 959 proteoforms corresponding to 263 proteins could be unambiguously identified from E. coli lysates in a single run. Furthermore, to illustrate the separation performance for large proteoforms, such monoliths were applied to top-down analysis of the SEC fraction of E. coli lysates with Mw ranging from 30 to 70 kDa. With highly effective separation, 347 large proteoforms with Mw higher than 30 kDa were detected in the single 75 min run. These results showed great potential for top-down proteomic analysis in complex samples.
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Affiliation(s)
- Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Baofeng Zhao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Shimizu H, Toyoda K, Mawatari K, Terabe S, Kitamori T. Femtoliter Gradient Elution System for Liquid Chromatography Utilizing Extended Nanofluidics. Anal Chem 2019; 91:3009-3014. [PMID: 30661360 DOI: 10.1021/acs.analchem.8b05302] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A gradient system was developed for the separation of proteins on a femtoliter scale utilizing nanofluidic channels. In the history of chromatography, miniaturization of the separation column has been important for efficient separation and downsizing of instruments. Previously, our group developed a small and highly efficient chromatography system utilizing nanofluidic channels, although a flexible design of the gradient was difficult and separation of proteins was not achieved. Here, we propose a flexible gradient system using standard HPLC pumps and an auxiliary mixer with a simple sample injection system. In contrast to our previous sample injection system using pressure balance, the system enables a femtoliter-scale sample injection which is compatible with gradient elution using HPLC pumps. The system was carefully designed, verified for sample injection and gradient elution, and finally applied to the separation of proteins from model and real samples. This femtoliter-scale, efficient separation system will contribute to omics studies at the single-cell level.
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Affiliation(s)
- Hisashi Shimizu
- International Research Center for Neurointelligence , The University of Tokyo , 7-3-1, Hongo , Bunkyo, Tokyo 113-0033 , Japan
| | - Kouto Toyoda
- Department of Applied Chemistry, School of Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo, Tokyo 113-8656 , Japan
| | - Kazuma Mawatari
- Department of Applied Chemistry, School of Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo, Tokyo 113-8656 , Japan
| | - Shigeru Terabe
- Graduate School of Material Science , University of Hyogo , 3-2-1, Kouto , Kamigori , Hyogo 678-1297 , Japan
| | - Takehiko Kitamori
- Department of Applied Chemistry, School of Engineering , The University of Tokyo , 7-3-1, Hongo , Bunkyo, Tokyo 113-8656 , Japan
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Wang EH, Nagarajan Y, Carroll F, Schug KA. Reversed-phase separation parameters for intact proteins using liquid chromatography with triple quadrupole mass spectrometry. J Sep Sci 2016; 39:3716-3727. [DOI: 10.1002/jssc.201600764] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/01/2016] [Accepted: 08/01/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Evelyn H. Wang
- Department of Chemistry & Biochemistry; The University of Texas at Arlington; Arlington TX USA
| | - Yashaswini Nagarajan
- Department of Chemistry & Biochemistry; The University of Texas at Arlington; Arlington TX USA
| | | | - Kevin A. Schug
- Department of Chemistry & Biochemistry; The University of Texas at Arlington; Arlington TX USA
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6
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Efficient separations of intact proteins using slip-flow with nano-liquid chromatography-mass spectrometry. Anal Chem 2014; 86:1592-8. [PMID: 24383398 PMCID: PMC3982985 DOI: 10.1021/ac403233d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
A capillary with a pulled tip, densely
packed with silica particles
of 0.47 μm in diameter, is shown to provide higher peak capacity
and sensitivity in the separation of intact proteins by reversed-phase
liquid chromatography–mass spectrometry (LC–MS). For
a C18 bonded phase, slip flow gave a 10-fold flow enhancement to allow
for stable nanospray with a 4-cm column length. Model proteins were
studied: ribonuclease A, trypsin inhibitor, and carbonic anhydrase,
where the latter had impurities of superoxide dismutase and ubiquitin.
The proteins were well separated at room temperature with negligible
peak tailing. The peak capacity for ubiquitin was 195 for a 10-min
gradient and 315 for a 40-min gradient based on Gaussian fitting of
the entire peak, rather than extrapolating the full-width at half-maximum.
Separation of a cell lysate with a 60 min gradient showed extremely
high peak capacities of 750 and above for a peptide and relatively
homogeneous proteins. Clean, low noise mass spectra for each model
protein were obtained. The physical widths of the peaks were an order
of magnitude narrower than those of conventional columns, giving increased
sensitivity. All proteins except ubiquitin exhibited significant heterogeneity
apparently due to multiple proteoforms, as indicated by both peak
shapes and mass spectra. The chromatograms exhibited excellent reproducibility
in retention time, with relative standard deviations of 0.09 to 0.34%.
The results indicate that submicrometer particles are promising for
improving the separation dimension of LC in top-down proteomics.
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Bobály B, Tóth E, Drahos L, Zsila F, Visy J, Fekete J, Vékey K. Influence of acid-induced conformational variability on protein separation in reversed phase high performance liquid chromatography. J Chromatogr A 2014; 1325:155-62. [DOI: 10.1016/j.chroma.2013.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 12/03/2013] [Accepted: 12/06/2013] [Indexed: 12/23/2022]
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Lagrain B, Brunnbauer M, Rombouts I, Koehler P. Identification of intact high molecular weight glutenin subunits from the wheat proteome using combined liquid chromatography-electrospray ionization mass spectrometry. PLoS One 2013; 8:e58682. [PMID: 23520527 PMCID: PMC3592795 DOI: 10.1371/journal.pone.0058682] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/05/2013] [Indexed: 11/25/2022] Open
Abstract
The present paper describes a method for the identification of intact high molecular weight glutenin subunits (HMW-GS), the quality determining proteins from the wheat storage proteome. The method includes isolation of HMW-GS from wheat flour, further separation of HMW-GS by reversed-phase high-performance liquid chromatography (RP-HPLC), and their subsequent molecular identification with electrospray ionization mass spectrometry using a quadrupole-time-of-flight mass analyzer. For HMW-GS isolation, wheat proteins were reduced and extracted from flour with 50% 1-propanol containing 1% dithiothreitol. HMW-GS were then selectively precipitated from the protein mixture by adjusting the 1-propanol concentration to 60%. The composition of the precipitated proteins was first evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis with Coomassie staining and RP-HPLC with ultraviolet detection. Besides HMW-GS (≥65%), the isolated proteins mainly contained ω5-gliadins. Secondly, the isolated protein fraction was analyzed by liquid chromatography-mass spectrometry. Optimal chromatographic separation of HMW-GS from the other proteins in the isolated fraction was obtained when the mobile phase contained 0.1% trifluoroacetic acid as ion-pairing agent. Individual HMW-GS were then identified by determining their molecular masses from the high-resolution mass spectra and comparing these with theoretical masses calculated from amino acid sequences. Using formic acid instead of trifluoroacetic acid in the mobile phase increased protein peak intensities in the base peak mass chromatogram. This allowed the detection of even traces of other wheat proteins than HMW-GS in the isolated fraction, but the chromatographic separation was inferior with a major overlap between the elution ranges of HMW-GS and ω-gliadins. Overall, the described method allows a rapid assessment of wheat quality through the direct determination of the HMW-GS composition and offers a basis for further top-down proteomics of individual HMW-GS and the entire wheat glutenin fraction.
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Affiliation(s)
- Bert Lagrain
- German Research Center for Food Chemistry, Freising, Germany.
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Han C, Geng J, Xie X, Wang X, Ren H, Gao S. Determination of phosphite in a eutrophic freshwater lake by suppressed conductivity ion chromatography. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:10667-10674. [PMID: 22954139 DOI: 10.1021/es300771a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The establishment of a sensitive and specific method for the detection of reduced phosphorus (P) is crucial for understanding P cycle. This paper presents the quantitative evidence of phosphite (P, +3) from the freshwater matrix correspondent to the typically eutrophic Lake Taihu in China. By ion chromatography coupled with gradient elution procedure, efficient separation of micromolar levels of phosphite is possible in the presence of millimolar levels of interfering ions, such as chloride, sulfate, and hydrogen carbonate in freshwater lakes. Optimal suppressed ion chromatography conditions include the use of 500 μL injection volumes and an AS11 HC analytical column heated to 30 °C. The method detection limit of 0.002 μM for phosphite was successfully applied for phosphite determination in natural water samples with recoveries ranging from 90.7 ± 3.2% to 108 ± 1.5%. Phosphite in the freshwater matrix was also verified using a two-dimensional capillary ion chromatography and ion chromatography coupled with mass spectrometry. Results confirmed the presence of phosphite in Lake Taihu ranging from 0.01 ± 0.01 to 0.17 ± 0.01 μM, which correlated to 1-10% of the phosphate. Phosphite is an important component of P and may influence biogeochemical P cycle in lakes.
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Affiliation(s)
- Chao Han
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210046, China
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Stastna M, Van Eyk JE. Analysis of protein isoforms: can we do it better? Proteomics 2012; 12:2937-48. [PMID: 22888084 DOI: 10.1002/pmic.201200161] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/12/2012] [Accepted: 06/18/2012] [Indexed: 12/23/2022]
Abstract
Protein isoforms/splice variants can play important roles in various biological processes and can potentially be used as biomarkers or therapeutic targets/mediators. Thus, there is a need for efficient and, importantly, accurate methods to distinguish and quantify specific protein isoforms. Since protein isoforms can share a high percentage of amino acid sequence homology and dramatically differ in their cellular concentration, the task for accuracy and efficiency in methodology and instrumentation is challenging. The analysis of intact proteins has been perceived to provide a more accurate and complete result for isoform identification/quantification in comparison to analysis of the corresponding peptides that arise from protein enzymatic digestion. Recently, novel approaches have been explored and developed that can possess the accuracy and reliability important for protein isoform differentiation and isoform-specific peptide targeting. In this review, we discuss the recent development in methodology and instrumentation for enhanced detection of protein isoforms as well as the examples of their biological importance.
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Affiliation(s)
- Miroslava Stastna
- Johns Hopkins Bayview Proteomics Center, Department of Medicine, Division of Cardiology, School of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA
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Munigunti R, Calderón AI. Development of liquid chromatography/mass spectrometry based screening assay for PfTrxR inhibitors using relative quantitation of intact thioredoxin. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2051-2056. [PMID: 22847705 DOI: 10.1002/rcm.6316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE Plasmodium falciparum (Pf) thioredoxin reductase (TrxR) catalyzes the reduction of thioredoxin disulfide (Trx-S(2)) to thioredoxin dithiol (Trx-(SH)(2)) that is essential for antioxidant defense mechanism and DNA synthesis in the parasite and is a validated drug target for new antimalarial agents. METHODS In this study, we have developed a liquid chromatography/mass spectrometry (LC/MS)-based functional assay to identify inhibitors of PfTrxR by quantifying the product formed (Trx-(SH)(2)) in the enzymatic reaction. Relative quantitation of the reaction product (intact Trx-(SH)(2)) was carried out using an Agilent 6520 QTOF mass spectrometer equipped with a positive mode electrospray ionization (ESI) source. RESULTS The calibration curve prepared for Trx-(SH)(2) at concentrations ranging from 1.8 to 116.5 µg/mL was linear (R(2) >0.998). The limit of detection (LOD) and limit of quantification (LOQ) of Trx-(SH)(2) were at 0.45 and 1.8 µg/mL respectively. To validate the developed functional assay we have screened reference compounds 1, 2 and 3 for their PfTrxR inhibitory activity and ten natural compounds (at 10 μM) which were earlier identified as ligands of PfTrxR by a UF-LC/MS based binding assay. CONCLUSIONS The developed LC/MS-based functional assay for identification of inhibitors of PfTrxR is a sensitive and reliable method that is also amendable for high-throughput format. This is the first representation of a relative quantitation of intact Trx-(SH)(2) using LC/MS.
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Affiliation(s)
- Ranjith Munigunti
- Department of Pharmacal Sciences, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA
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12
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Collier TS, Muddiman DC. Analytical strategies for the global quantification of intact proteins. Amino Acids 2012; 43:1109-17. [PMID: 22821264 DOI: 10.1007/s00726-012-1285-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
The quantification of intact proteins is a relatively recent development in proteomics. In eukaryotic organisms, proteins are present as multiple isoforms as the result of variations in genetic code, alternative splicing, post-translational modification and other processing events. Understanding the identities and biological functions of these isoforms and how their concentrations vary across different states is the central goal of proteomics. To date, the bulk of proteomics research utilizes a "bottom-up" approach, digesting proteins into their more manageable constitutive peptides, but sacrificing information about the specific isoform and combinations of post-translational modifications present on the protein. Very specific strategies for protein quantification such as the enzyme-linked immunosorbent assay and Western blot are commonplace in laboratories and clinics, but impractical for the study of global biological changes. Herein, we describe strategies for the quantification of intact proteins, their distinct advantages, and challenges to their employment. Techniques contained in this review include the more traditional and widely employed methodology of differential gel electrophoresis and more recently developed mass spectrometry-based techniques including metabolic labeling, chemical labeling, and label-free methodologies.
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Affiliation(s)
- Timothy S Collier
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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13
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Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Calligaris D, Villard C, Lafitte D. Advances in top-down proteomics for disease biomarker discovery. J Proteomics 2011; 74:920-34. [DOI: 10.1016/j.jprot.2011.03.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/01/2011] [Accepted: 03/29/2011] [Indexed: 11/16/2022]
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Abstract
The commercialization of ultra-performance liquid chromatography (UPLC) has allowed more researchers to take advantage of the benefits of this work. Many researchers are exploring this technique to reduce analytical throughput and to increase resolution. The majority of this work has focused on small molecule analysis; however, this technique can provide the same advantages for the analysis of proteins. Traditionally, protein chromatography has suffered from a number of issues such as carryover, peak splitting, peak broadening, and poor peak shape. Because UPLC utilizes a smaller particle at a higher pressure and flow rate, many of these issues are remedied. When used in combination with mass spectrometry, UPLC becomes a powerful tool for protein identification, characterization, and quantitation. In this work we show how UPLC/MS can be used to separate and identify intact proteins.
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Affiliation(s)
- Timothy R Croley
- US Food and Drug Administration Center for Food Safety and Applied Nutrition, 5100 Paint Branch Parkway, College Park, USA
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16
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Callipo L, Capriotti AL, Cavaliere C, Gubbiotti R, Samperi R, Laganà A. Evaluation of different two-dimensional chromatographic techniques for proteomic analysis of mouse cardiac tissue. Biomed Chromatogr 2010; 25:594-9. [PMID: 20652868 DOI: 10.1002/bmc.1487] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/24/2010] [Accepted: 06/02/2010] [Indexed: 11/09/2022]
Abstract
In proteomics experiments the first critical step after sampling is certainly sample preparation. Multidimensional chromatography techniques have emerged as a powerful tool for the large-scale analysis of such complex samples as biological samples. In order to evaluate these separation techniques, microgram quantities of protein extracted from mouse heart tissue were fractionated by four different chromatographic methods. Regarding peptide-level fractionation, the first dimension of separation was performed with high-pH reversed-phase chromatography (pH-RP) and strong cation exchange chromatography (SCX). Regarding protein-level fractionation, C(8) protein reversed-phase (C(8) -RP Prot) and high-recovery protein reversed-phase (hr-RP Prot) were used instead. The second dimension consisted of a reversed-phase nano-HPLC on-Chip coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The peptide-level pH-RP and the hr-RP Prot protein-level separations were the best methods, identifying 1338 and 1303 proteins, respectively. The peptide-level SCX, with 509 proteins identified, was the worst method.
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Affiliation(s)
- Luciano Callipo
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
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Collier TS, Sarkar P, Rao B, Muddiman DC. Quantitative top-down proteomics of SILAC labeled human embryonic stem cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:879-889. [PMID: 20199872 DOI: 10.1016/j.jasms.2010.01.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 05/28/2023]
Abstract
Human embryonic stem cells (hESCs) are self-renewing pluripotent cells with relevance to treatment of numerous medical conditions. However, a global understanding of the role of the hESC proteome in maintaining pluripotency or triggering differentiation is still largely lacking. The emergence of top-down proteomics has facilitated the identification and characterization of intact protein forms that are not readily apparent in bottom-up studies. Combined with metabolic labeling techniques such as stable isotope labeling by amino acids in cell culture (SILAC), quantitative comparison of intact protein expression under differing experimental conditions is possible. Herein, quantitative top-down proteomics of hESCs is demonstrated using the SILAC method and nano-flow reverse phase chromatography directly coupled to a linear-ion-trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FT-ICR-MS). In this study, which to the best of our knowledge represents the first top-down analysis of hESCs, we have confidently identified 11 proteins by accurate intact mass, MS/MS, and amino acid counting facilitated by SILAC labeling. Although quantification is challenging due to the incorporation of multiple labeled amino acids (i.e., lysine and arginine) and arginine to proline conversion, we are able to quantitatively account for these phenomena using a mathematical model.
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Affiliation(s)
- Timothy S Collier
- W. M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Ali I, Aboul-Enein HY, Singh P, Singh R, Sharma B. Separation of biological proteins by liquid chromatography. Saudi Pharm J 2010; 18:59-73. [PMID: 23960722 DOI: 10.1016/j.jsps.2010.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 11/03/2009] [Indexed: 01/11/2023] Open
Abstract
After the success of human genome project, proteome is a new emerging field of biochemistry as it provides the knowledge of enzymes (proteins) interactions with different body organs and medicines administrated into human body. Therefore, the study of proteomics is very important for the development of new and effective drugs to control many lethal diseases. In proteomics study, analyses of proteome is essential and significant from the pathological point of views, i.e., in several serious diseases such as cancer, Alzheimer's disease and aging, heart diseases and also for plant biology. The separation and identification of proteomics is a challenging job due to their complex structures and closely related physico-chemical behaviors. However, the recent advances in liquid chromatography make this job easy. Various kinds of liquid chromatography, along with different detectors and optimization strategies, have been discussed in this article. Besides, attempts have been made to include chirality concept in proteomics for understanding mechanism and medication of various disease controlled by different body proteins.
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Key Words
- 2D-nano LC, two-dimensional nano liquid chromatography quadrupole
- ACN, acetonitrile
- AIEC, anion exchange chromatography
- CEC, capillary electro-chromatography
- CIEF, capillary isoelectric focusing
- CSF, cerebrospinal fluid
- Chirality
- EC, electro-chromatography
- ESI-LC–MS, electrospray ionization liquid chromatography–mass spectrometry
- FA, formic acid
- FLP, FMRF amide-like peptide
- FT-ICR-MS, ion cyclotron resonance-mass spectrometry
- GPI-APs, glycosylphosphadylinositol anchored proteins
- GSH, glutathione stimulating hormone
- GSTs, glutathione-S-transferase isoenzyme
- Gene
- HFBA, heptafluorobutyric acid
- HPLC, high performance liquid chromatography
- ICAT, isotope coded affinity tag
- IEF-SEC, isoelectrofocussing size-exclusion chromatography
- IMCD, inner medullary collecting duct
- LC-Q-TOF, liquid chromatography-quadrupole time-of-flight tandem mass
- LC-dual ESI, liquid chromatography dual electrospray ionization-Fourier transform
- LC–MS, liquid chromatography–mass spectrometry
- Liquid chromatography
- MALDI-TOF, matrix-assisted laser desorption/ionization-time-of flight
- MFGM, milk fat globule membranes
- MMA, mass measurement accuracy
- MPC, mesenchymal progenitor cell
- MS/MS, spectrometry
- NLFs, Nasal lavage fluids
- NLP, neuropeptide like protein
- Nano detection
- PC2, prohormone convertase-2
- PS II, photosystem II
- Preparation
- Proteomics
- Q-TOFMS/MS, time-of-flight tandem-mass spectrometry
- RPLC, reversed phase liquid chromatography
- SCX, strong cation exchange
- SEC, size-exclusion chromatography
- TFA, trifluoroacetic acid
- TIC, total ion current
- TRAF, tumor necrosis factor receptor
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Affiliation(s)
- Imran Ali
- Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi 110 025, India
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Della Donna L, Ronci M, Sacchetta P, Di Ilio C, Biolatti B, Federici G, Nebbia C, Urbani A. A food safety control low mass-range proteomics platform for the detection of illicit treatments in veal calves by MALDI-TOF-MS serum profiling. Biotechnol J 2009; 4:1596-609. [DOI: 10.1002/biot.200900085] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Tran BQ, Loftheim H, Reubsaet L, Lundanes E, Greibrokk T. On-Line multitasking analytical proteomics: How to separate, reduce, alkylate and digest whole proteins in an on-Line multidimensional chromatography system coupled to MS. J Sep Sci 2008; 31:2913-23. [DOI: 10.1002/jssc.200800275] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Dowell JA, Frost DC, Zhang J, Li L. Comparison of two-dimensional fractionation techniques for shotgun proteomics. Anal Chem 2008; 80:6715-23. [PMID: 18680313 DOI: 10.1021/ac8007994] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional (2D) fractionation is a commonly used tool to increase dynamic range and proteome coverage for bottom-up, shotgun proteomics. However, there are few reports comparing the relative separation efficiencies of 2D methodologies using low-microgram sample quantities. In order to systematically evaluate 2D separation techniques, we fractionated microgram quantities of E. coli protein extract by seven different methods. The first dimension of separation was performed with either reversed-phase high-pressure liquid chromatography (RP-HPLC), gel electrophoresis (SDS-PAGE), or strong cation exchange (SCX-HPLC). The second dimension consisted of a standard reversed-phase capillary HPLC coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The overall performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The protein-level RP-HPLC and the high-pH RP-HPLC peptide-level separations performed the best, identifying 281 and 266 proteins, respectively. The online pH variance SCX and the SDS-PAGE returned modest performances with 178 and 139 proteins identified, respectively. The offline SCX had the worst performance with 81 proteins identified. We also examined various chromatographic factors that contribute to separation efficiency, including resolving power, orthogonality, and sample loss.
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Affiliation(s)
- James A Dowell
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA
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22
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Collier TS, Hawkridge AM, Georgianna DR, Payne GA, Muddiman DC. Top-down identification and quantification of stable isotope labeled proteins from Aspergillus flavus using online nano-flow reversed-phase liquid chromatography coupled to a LTQ-FTICR mass spectrometer. Anal Chem 2008; 80:4994-5001. [PMID: 18512951 DOI: 10.1021/ac800254z] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Online liquid chromatography-mass spectrometric (LC-MS) analysis of intact proteins (i.e., top-down proteomics) is a growing area of research in the mass spectrometry community. A major advantage of top-down MS characterization of proteins is that the information of the intact protein is retained over the vastly more common bottom-up approach that uses protease-generated peptides to search genomic databases for protein identification. Concurrent to the emergence of top-down MS characterization of proteins has been the development and implementation of the stable isotope labeling of amino acids in cell culture (SILAC) method for relative quantification of proteins by LC-MS. Herein we describe the qualitative and quantitative top-down characterization of proteins derived from SILAC-labeled Aspergillus flavus using nanoflow reversed-phase liquid chromatography directly coupled to a linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FTICR-MS). A. flavus is a toxic filamentous fungus that significantly impacts the agricultural economy and human health. SILAC labeling improved the confidence of protein identification, and we observed 1318 unique protein masses corresponding to 659 SILAC pairs, of which 22 were confidently identified. However, we have observed some limiting issues with regard to protein quantification using top-down MS/MS analyses of SILAC-labeled proteins. The role of SILAC labeling in the presence of competing endogenously produced amino acid residues and its impact on quantification of intact species are discussed in detail.
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Affiliation(s)
- Timothy S Collier
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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Tang J, Gao M, Deng C, Zhang X. Recent development of multi-dimensional chromatography strategies in proteome research. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:123-32. [PMID: 18289947 PMCID: PMC7185551 DOI: 10.1016/j.jchromb.2008.01.029] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 01/15/2008] [Accepted: 01/18/2008] [Indexed: 11/23/2022]
Abstract
As a complementary approach to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), multi-dimensional chromatography separation methods have been widely applied in all kinds of biological sample investigations. Multi-dimensional liquid chromatography (MDLC) coupled with bio-mass spectrometry (MS) is playing important roles in proteome research due to its high speed, high resolution and high sensitivity. Proteome analysis strategies mainly include bottom-up and top-down approaches which carry out biological sample separation based on peptide and protein levels, respectively. Electrophoretic methods combined with liquid chromatography like IEF-HPLC and HPLC-SDS-PAGE have been successful applied for protein separations. As for MDLC strategy, ion-exchange chromatography (IEX) together with reversed phase liquid chromatography (RPLC) is still a most widely used chromatography in proteome analysis, other chromatographic methods are also frequently used in protein pre-fractionations, while affinity chromatography is usually adopted for specific functional protein analysis. Recent MDLC technologies and applications to variety of proteome analysis have been achieved great development. A digest peptide-based approach as so-called "bottom-up" and intact protein-based approach "top-down" analysis of proteome samples were briefly reviewed in this paper. The diversity of combinations of different chromatography modes to set up MDLC systems was demonstrated and discussed. Novel developments of MDLC techniques such as high-abundance protein depletion and chromatography array were also included in this review.
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Affiliation(s)
- Jia Tang
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Xiangming Zhang
- Department of Chemistry Fudan University, 220 Handan Road, Shanghai 200433, China
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24
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Everley RA, Croley TR. Ultra-performance liquid chromatography/mass spectrometry of intact proteins. J Chromatogr A 2008; 1192:239-47. [PMID: 18417140 DOI: 10.1016/j.chroma.2008.03.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 03/18/2008] [Accepted: 03/19/2008] [Indexed: 10/22/2022]
Abstract
Given that numerous small molecule applications of ultra-performance liquid chromatography (UPLC) have been published, efforts were made to examine the potential of UPLC to enhance the separation of intact proteins. Beginning with typically employed conditions, column temperature and organic solvent were optimized followed by an HPLC vs. UPLC comparison. When applied to a mixture of 10 protein standards, the optimized method yielded improved chromatographic resolution, enhanced sensitivity, and a threefold increase in throughput. Subsequent cell lysate analysis demonstrated no compromise in chromatographic or mass spectral data quality at 1/3 of the original run time.
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Affiliation(s)
- Robert A Everley
- Commonwealth of Virginia, Division of Consolidated Laboratory Services, 600 N. 5th Street, Richmond, VA 23219, USA
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Bunger MK, Cargile BJ, Ngunjiri A, Bundy JL, Stephenson JL. Automated Proteomics of E. coli via Top-Down Electron-Transfer Dissociation Mass Spectrometry. Anal Chem 2008; 80:1459-67. [DOI: 10.1021/ac7018409] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maureen K. Bunger
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Benjamin J. Cargile
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Anne Ngunjiri
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - Jonathan L. Bundy
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
| | - James L. Stephenson
- Mass Spectrometry Research Program, Research Triangle Institute, 3040 Cornwallis Road, Research Triangle Park, North Carolina 27709
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Yassine MM, Guo N, Zhong H, Li L, Lucy CA. Off-line coupling of preparative capillary zone electrophoresis with microwave-assisted acid hydrolysis and matrix-assisted laser desorption ionization mass spectrometry for protein sequencing. Anal Chim Acta 2007; 597:41-9. [PMID: 17658311 DOI: 10.1016/j.aca.2007.05.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 05/25/2007] [Accepted: 05/31/2007] [Indexed: 11/16/2022]
Abstract
An off-line coupling of capillary electrophoresis (CE) with microwave-assisted acid hydrolysis/matrix-assisted laser desorption ionization mass spectrometry (MAAH/MALDI) has been developed for protein identification and characterization. Preparative scale protein separations enable collection of 10-50 pmol of purified cytochrome c for subsequent sequencing using MAAH/MALDI. To reduce protein adsorption onto the silica surface, the cationic surfactant-based coatings, dimethylditetradecylammonium bromide and dimethyldioctadecylammonium bromide, are employed. The choice of the buffer conditions is critical for both the preparative CE and MAAH/MALDI method. The use of high buffer concentrations (100 mM Bis-tris) reduces electromigration dispersion, but suppressed MALDI ionization such that a peptide sequence coverage of only 80% was achieved at a sample loading of 40 g L(-1) of each cytochrome c. By reducing the buffer concentration to 25 mM Bis-tris, the sequence coverage increased to 95% at a sample loading of 40 g L(-1).
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Affiliation(s)
- Mahmoud M Yassine
- Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T, Drabik A, Suder P, Noga M, Jarzebinska J, Silberring J. Methods for samples preparation in proteomic research. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:1-31. [PMID: 17113834 DOI: 10.1016/j.jchromb.2006.10.040] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 10/23/2006] [Indexed: 01/04/2023]
Abstract
Sample preparation is one of the most crucial processes in proteomics research. The results of the experiment depend on the condition of the starting material. Therefore, the proper experimental model and careful sample preparation is vital to obtain significant and trustworthy results, particularly in comparative proteomics, where we are usually looking for minor differences between experimental-, and control samples. In this review we discuss problems associated with general strategies of samples preparation, and experimental demands for these processes.
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Affiliation(s)
- Anna Bodzon-Kulakowska
- Department of Neurobiochemistry, Faculty of Chemistry, Jagiellonian University, Ingardena St. 3, 30-060 Krakow, Poland
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Simpson DC, Ahn S, Pasa-Tolic L, Bogdanov B, Mottaz HM, Vilkov AN, Anderson GA, Lipton MS, Smith RD. Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling. Electrophoresis 2006; 27:2722-33. [PMID: 16732621 PMCID: PMC1769308 DOI: 10.1002/elps.200600037] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Bottom-up proteomics (analyzing peptides that result from protein digestion) has demonstrated capability for broad proteome coverage and good throughput. However, due to incomplete sequence coverage, this approach is not ideally suited to the study of modified proteins. The modification complement of a protein can best be elucidated by analyzing the intact protein. 2-DE, typically coupled with the analysis of peptides that result from in-gel digestion, is the most frequently applied protein separation technique in MS-based proteomics. As an alternative, numerous column-based liquid phase techniques, which are generally more amenable to automation, are being investigated. In this work, the combination of size-exclusion chromatography (SEC) fractionation with RPLC-Fourier-transform ion cyclotron resonance (FTICR)-MS is compared with the combination of RPLC fractionation with CIEF-FTICR-MS for the analysis of the Shewanella oneidensis proteome. SEC-RPLC-FTICR-MS allowed the detection of 297 proteins, as opposed to 166 using RPLC-CIEF-FTICR-MS, indicating that approaches based on LC-MS provide better coverage. However, there were significant differences in the sets of proteins detected and both approaches provide a basis for accurately quantifying changes in protein and modified protein abundances.
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Affiliation(s)
| | | | - Ljiljana Pasa-Tolic
- Corresponding Author: Ljiljana Pasa-Tolic, Telephone:
+1 509 376 8859, Facsimile: +1 509 376
2303, Electronic Mail:
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29
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Yassine MM, Lucy CA. Preparative capillary zone electrophoresis using a dynamic coated wide-bore capillary. Electrophoresis 2006; 27:3066-74. [PMID: 16807937 DOI: 10.1002/elps.200500862] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Preparative capillary zone electrophoresis separations of cytochrome c from bovine and horse heart are performed efficiently in a surfactant-coated capillary. The surfactant, dimethylditetradecylammonium bromide (2C(14)DAB), effectively eliminated protein adsorption from the capillary surface, such that symmetrical peaks with efficiencies of 0.7 million plates/m were observed in 50-microm id capillaries when low concentrations of protein were injected. At protein concentrations greater than 1 g/L, electromigration dispersion became the dominant source of band broadening and the peak shape distorted to triangular fronting. Matching of the mobility of the buffer co-ion to that of the cytochrome c resulted in dramatic improvements in the efficiency and peak shape. Using 100 mM bis(2-hydroxyethyl)imino-tris(hydroxymethyl)methane phosphate buffer at pH 7.0 with a 100-microm id capillary, the maximum sample loading capacity in a single run was 160 pmol (2.0 microg) of each protein.
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Affiliation(s)
- Mahmoud M Yassine
- Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Akashi S, Suzuki K, Arai A, Yamada N, Suzuki EI, Hirayama K, Nakamura S, Nishimura Y. Top-down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:1932-8. [PMID: 16715472 DOI: 10.1002/rcm.2541] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A system of microchip capillary electrophoresis/electrospray ionization mass spectrometry (microchip-CE/ESI-MS) for rapid characterization of proteins has been developed. Capillary electrophoresis (CE) enables rapid analysis of a sample present in very small quantity, such as at femtomole levels, at high resolution. Faster CE/MS analysis is expected by downsizing the normal capillary to the microchip (microchip) capillary. Although rapidity and high resolution are advantages of CE separation, electroosmotic flow (EOF) instability caused by the interaction between proteins and the microchannel surface results in low reproducibility in the analysis of basic proteins under neutral pH conditions. By coating the microchannel surface with a basic polymer, polyE-323, basic proteins, which have pI values of over 7.5, could be separated and detected by microchip-CE/MS on quadrupole (Q) and time-of-flight (TOF) hybrid instruments. By increasing the cone and collision voltages during the analysis by microchip-CE/ESI-MS of a small protein, some product ions, which contain the sequence information, could also be obtained, i.e., 'top-down' analysis of the protein could be accomplished with this microchip-CE/MS system. To our knowledge, this is the first report of 'top-down' analysis of a protein by microchip-CE/MS. Since it requires a much shorter time and a smaller sample amount for analysis than the conventional liquid chromatography (LC)/ESI-MS method, microchip-CE/MS promises to be suitable for the high-throughput characterization of proteins.
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Affiliation(s)
- Satoko Akashi
- International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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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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