51
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Blackwell DL, Bean SR. Separation of alcohol soluble sorghum proteins using non-porous cation-exchange columns. J Chromatogr A 2012; 1230:48-53. [DOI: 10.1016/j.chroma.2012.01.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/18/2012] [Accepted: 01/23/2012] [Indexed: 11/25/2022]
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52
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Yang Y, Geng X. Mixed-mode chromatography and its applications to biopolymers. J Chromatogr A 2011; 1218:8813-25. [DOI: 10.1016/j.chroma.2011.10.009] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 10/06/2011] [Accepted: 10/06/2011] [Indexed: 10/16/2022]
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53
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Screening and confirmation analysis of stimulants, narcotics and beta-adrenergic agents in human urine by hydrophilic interaction liquid chromatography coupled to mass spectrometry. J Chromatogr A 2011; 1218:8156-67. [DOI: 10.1016/j.chroma.2011.09.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 09/02/2011] [Accepted: 09/08/2011] [Indexed: 11/21/2022]
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54
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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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55
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Multi-modal applicability of a reversed-phase/weak-anion exchange material in reversed-phase, anion-exchange, ion-exclusion, hydrophilic interaction and hydrophobic interaction chromatography modes. Anal Bioanal Chem 2011; 400:2517-30. [PMID: 21336792 DOI: 10.1007/s00216-011-4755-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/28/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
We recently introduced a mixed-mode reversed-phase/weak anion-exchange type separation material based on silica particles which consisted of a hydrophobic alkyl strand with polar embedded groups (thioether and amide functionalities) and a terminal weak anion-exchange-type quinuclidine moiety. This stationary phase was designed to separate molecules by lipophilicity and charge differences and was mainly devised for peptide separations with hydroorganic reversed-phase type elution conditions. Herein, we demonstrate the extraordinary flexibility of this RP/WAX phase, in particular for peptide separations, by illustrating its applicability in various chromatographic modes. The column packed with this material can, depending on the solute character and employed elution conditions, exploit attractive or repulsive electrostatic interactions, and/or hydrophobic or hydrophilic interactions as retention and selectivity increments. As a consequence, the column can be operated in a reversed-phase mode (neutral compounds), anion-exchange mode (acidic compounds), ion-exclusion chromatography mode (cationic solutes), hydrophilic interaction chromatography mode (polar compounds), and hydrophobic interaction chromatography mode (e.g., hydrophobic peptides). Mixed-modes of these chromatographic retention principles may be materialized as well. This allows an exceptionally flexible adjustment of retention and selectivity by tuning experimental conditions. The distinct separation mechanisms will be outlined by selected examples of peptide separations in the different modes.
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56
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Bicker W, Wu J, Yeman H, Albert K, Lindner W. Retention and selectivity effects caused by bonding of a polar urea-type ligand to silica: A study on mixed-mode retention mechanisms and the pivotal role of solute–silanol interactions in the hydrophilic interaction chromatography elution mode. J Chromatogr A 2011; 1218:882-95. [DOI: 10.1016/j.chroma.2010.10.073] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 10/12/2010] [Accepted: 10/18/2010] [Indexed: 10/18/2022]
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57
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Tian Z, Zhao R, Tolić N, Moore RJ, Stenoien DL, Robinson EW, Smith RD, Paša-Tolić L. Two-dimensional liquid chromatography system for online top-down mass spectrometry. Proteomics 2011; 10:3610-20. [PMID: 20879039 DOI: 10.1002/pmic.201000367] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An online metal-free weak cation exchange-hydrophilic interaction LC/RPLC system has been developed for sensitive, high-throughput top-down MS. Here, we report results for analyzing PTMs of core histones, with a focus on histone H4, using this system. With just ∼24 μg on-column of core histones (H4, H2B, H2A, and H3) purified from human fibroblasts, 41 H4 isoforms were identified, with the type and location of PTMs unambiguously mapped for 20 of these variants. Compared to corresponding offline studies reported previously, the online weak cation exchange-hydrophilic interaction LC/RPLC platform offers significant improvement in sensitivity, with several orders of magnitude reduction in sample requirements and a reduction in the overall analysis time. To the best of our knowledge, this study represents the first online 2-D LC-MS/MS characterization of core histone mixture at the intact protein level.
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Affiliation(s)
- Zhixin Tian
- Pacific Northwest National Laboratory, Richland, WA, USA
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58
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Hao P, Zhang H, Sze SK. Application of electrostatic repulsion hydrophilic interaction chromatography to the characterization of proteome, glycoproteome, and phosphoproteome using nano LC-MS/MS. Methods Mol Biol 2011; 790:305-18. [PMID: 21948424 DOI: 10.1007/978-1-61779-319-6_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In shotgun proteomics, peptide fractionation is essential for in-depth characterization of proteomes and the mapping of protein posttranslational modifications. Recently, a mix-mode chromatography [i.e., electrostatic repulsion hydrophilic interaction chromatography (ERLIC)] has been developed and found to be a versatile method in proteome characterization. Here, we use ERLIC to characterize the glycoproteome and phosphoproteome simultaneously. We also demonstrate that the ERLIC can be an alternative to the commonly used strong cation exchange chromatography for higher recovery of proteins during whole proteome analysis. These protocols can be easily adopted in most proteomics laboratories.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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59
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Vitorino R, Krenkova J, Foret F, Domingues P, Amado F. Protein identification using nano-HPLC-MS: ESI-MS and MALDI-MS interfaces. Methods Mol Biol 2011; 790:31-46. [PMID: 21948404 DOI: 10.1007/978-1-61779-319-6_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Body fluids and body tissues have a myriad of peptides and proteins that, very often, the traditional methodologies of proteomics, such as conventional gel electrophoresis or mass spectrometry, are unable to characterize. We describe two protocols to characterize high molecular weight peptides (>3 kDa) and intact proteins involving on-line trypsin digestion, separation of the digests by nano-HPLC, and analysis by mass spectrometry using two different ionization sources (matrix-assisted laser desorption and electrospray ionization). These protocols have the advantage of promoting protein denaturation in an aqueous-organic solvent, which reduces the derivatization of the sample and facilitates an in-depth analysis for detection and identification of proteins. Additional advantages include the following: (1) integration of these protocols into standard proteomic workflows after the preprocessing of samples and separation; (2) use of high-resolution monolithic columns; and (3) the ability to acquire information from minimal amounts of sample.
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Affiliation(s)
- Rui Vitorino
- Department of Chemistry, Mass Spectrometry Center, QOPNA, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal.
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60
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Hao P, Guo T, Li X, Adav SS, Yang J, Wei M, Sze SK. Novel application of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) in shotgun proteomics: comprehensive profiling of rat kidney proteome. J Proteome Res 2010; 9:3520-6. [PMID: 20450224 DOI: 10.1021/pr100037h] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In shotgun proteomics, multidimensional liquid chromatography (MDLC) is commonly used to reduce sample complexity and increase dynamic range of protein identification. Since reversed-phase chromatography is mostly used as the second-dimensional separation before mass spectrometric analysis, the improvement of MDLC primarily depends on the first dimension of separation. Here, we present a novel whole proteome analysis method that separates peptides based on ERLIC. Tryptic peptides were retained on a weak anion exchange column through ERLIC with a high organic mobile phase. They were then distributed into multiple fractions based on both pI and polarity through the simultaneous effect of electrostatic repulsion and hydrophilic interaction when eluted using a salt-free pH gradient of increasing water content. Applying this to rat kidney tissue, we identified 4821 proteins and 30 659 unique peptides with high confidence from two replicates using LTQ-FT. This was 36.2% and 64.3% higher, respectively, than was obtained with the widely used SCX separation mode. Notably, the identification of both highly hydrophobic and basic peptides increased over 120% using the ERLIC method. The results indicate that ERLIC is a promising alternative to SCX as the first dimension of MDLC. In total, 5499 proteins and 35 847 unique peptides of rat kidney tissue are characterized.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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61
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Wujcik CE, Tweed J, Kadar EP. Application of hydrophilic interaction chromatography retention coefficients for predicting peptide elution with TFA and methanesulfonic acid ion-pairing reagents. J Sep Sci 2010; 33:826-33. [PMID: 20087867 DOI: 10.1002/jssc.200900533] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Hydrophilic retention coefficients for 17 peptides were calculated based on retention coefficients previously published for TSKgel silica-60 and were compared with the experimental elution profile on a Waters Atlantis HILIC silica column using TFA and methanesulfonic acid (MSA) as ion-pairing reagents. Relative peptide retention could be accurately determined with both counter-ions. Peptide retention and chromatographic behavior were influenced by the percent acid modifier used with increases in both retention and peak symmetry observed at increasing modifier concentrations. The enhancement of net peptide polarity through MSA pairing shifted retention out by nearly five-fold for the earliest eluting peptide, compared with TFA. Despite improvements in retention and efficiency (N(eff)) for MSA over TFA, a consistent reduction in calculated selectivity (alpha) was observed. This result is believed to be attributed to the stronger polar contribution of MSA masking and diminishing the underlying influence of the amino acid residues of each associated peptide. Finally, post-column infusion of propionic acid and acetic acid was evaluated for their potential to recover signal intensity for TFA and MSA counter-ions for LC-ESI-MS applications. Acetic acid generally yielded more substantial signal improvements over propionic acid on the TFA system while minimal benefits and some further reductions were noted with MSA.
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62
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Phillips HL, Williamson JC, van Elburg KA, Snijders APL, Wright PC, Dickman MJ. Shotgun proteome analysis utilising mixed mode (reversed phase-anion exchange chromatography) in conjunction with reversed phase liquid chromatography mass spectrometry analysis. Proteomics 2010; 10:2950-60. [DOI: 10.1002/pmic.200900669] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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63
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Goucher E, Kicman A, Wolff K, Smith N, Jickells S. Hydrophilic stationary phases: A practical approach for the co-analysis of compounds with varying polarity in biological matrices. J Sep Sci 2010; 33:955-65. [DOI: 10.1002/jssc.200900727] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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64
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Fountain KJ, Xu J, Diehl DM, Morrison D. Influence of stationary phase chemistry and mobile-phase composition on retention, selectivity, and MS response in hydrophilic interaction chromatography. J Sep Sci 2010; 33:740-51. [DOI: 10.1002/jssc.200900660] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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65
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Zhao G, Dong XY, Sun Y. Ligands for mixed-mode protein chromatography: Principles, characteristics and design. J Biotechnol 2009; 144:3-11. [DOI: 10.1016/j.jbiotec.2009.04.009] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 04/10/2009] [Accepted: 04/23/2009] [Indexed: 11/24/2022]
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