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Foster SW, Parker D, Kurre S, Boughton J, Stoll DR, Grinias JP. A review of two-dimensional liquid chromatography approaches using parallel column arrays in the second dimension. Anal Chim Acta 2022; 1228:340300. [DOI: 10.1016/j.aca.2022.340300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/26/2022]
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Effects of first dimension eluent composition in two-dimensional liquid chromatography. J Chromatogr A 2011; 1218:2214-21. [PMID: 21411103 DOI: 10.1016/j.chroma.2011.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/31/2011] [Accepted: 02/09/2011] [Indexed: 12/25/2022]
Abstract
Comprehensive two-dimensional liquid chromatography (LC×LC) has received a great deal of attention during the past few years because of its extraordinary resolving power. The biggest advantage of this technique is that very high peak capacities can be generated in a relatively short time. Numerous approaches to maximize the peak capacity in LC×LC have been employed. In this work we investigate the impact of the first dimension mobile phase on selectivity. LC×LC has several potential advantages over one-dimensional LC (1DLC) in that unconventional solvents, at least in reversed-phase LC, can be used. For example, solvents which strongly adsorb in the UV in the first dimension are not problematic in LC×LC. This so because the UV detector is placed after the second dimensional column, as pulses of the first dimension eluent arrive at the second dimensional column, they elute well before the solutes of interest and therefore do not interfere at all with detection of solute peaks. So far, the most widely used solvents in reversed-phase 1DLC are methanol and acetonitrile. However, the "UV advantage" of 2DLC allows us to employ UV active solvents, such as acetone. We compare their differential selectivities to that of acetonitrile for the separation of 23 indole acetic acids of interest in plant biology. We also apply them to the separation of a maize seed extract, a very complex sample. In both sample sets, mobile phase composition can be an important parameter to increase the orthogonality of the two dimensions and thus, to increase the effective peak capacity of LC×LC.
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Mondello L, Donato P, Cacciola F, Fanali C, Dugo P. RP‐LC×RP‐LC analysis of a tryptic digest using a combination of totally porous and partially porous stationary phases. J Sep Sci 2010; 33:1454-61. [DOI: 10.1002/jssc.200900816] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Luigi Mondello
- Dipartimento Farmaco‐chimico, Facoltà di Farmacia, Università di Messina, Messina, Italy
- Campus‐Biomedico, Roma, Italy
| | - Paola Donato
- Dipartimento Farmaco‐chimico, Facoltà di Farmacia, Università di Messina, Messina, Italy
- Campus‐Biomedico, Roma, Italy
| | - Francesco Cacciola
- Dipartimento Farmaco‐chimico, Facoltà di Farmacia, Università di Messina, Messina, Italy
| | - Chiara Fanali
- Campus‐Biomedico, Roma, Italy
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Paola Dugo
- Dipartimento Farmaco‐chimico, Facoltà di Farmacia, Università di Messina, Messina, Italy
- Campus‐Biomedico, Roma, Italy
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François I, Cabooter D, Sandra K, Lynen F, Desmet G, Sandra P. Tryptic digest analysis by comprehensive reversed phase×two reversed phase liquid chromatography (RP-LC×2RP-LC) at different pH's. J Sep Sci 2009; 32:1137-44. [DOI: 10.1002/jssc.200800578] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Xia Q, Hendrickson EL, Wang T, Lamont RJ, Leigh JA, Hackett M. Protein abundance ratios for global studies of prokaryotes. Proteomics 2007; 7:2904-19. [PMID: 17639608 PMCID: PMC2660852 DOI: 10.1002/pmic.200700267] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The use of multidimensional capillary HPLC combined with MS/MS has allowed high qualitative and quantitative proteome coverage of prokaryotic organisms. The determination of protein abundance change between two or more conditions has matured to the point that false discovery rates can be very low and for smaller proteomes coverage is sufficiently high to explicitly consider false negative error. Selected aspects of using these methods for global protein abundance assessments are reviewed. These include instrumental issues that influence the reliability of abundance ratios; a comparison of sources of nonlinearity, errors, and data compression in proteomics and spotted cDNA arrays; strengths and weaknesses of spectral counting versus stable isotope metabolic labeling; and a survey of microbiological applications of global abundance analysis at the protein level. Proteomic results for two organisms that have been studied extensively using these methods are reviewed in greater detail. Spectral counting and metabolic labeling data are compared and the utility of proteomics for global gene regulation studies are discussed for the methanogenic Archaeon Methanococcus maripaludis. The oral pathogen Porphyromonas gingivalis is discussed as an example of an organism where a large percentage of the proteome differs in relative abundance between the intracellular and extracellular phenotype.
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Affiliation(s)
- Qiangwei Xia
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Tiansong Wang
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Richard J. Lamont
- Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - John A. Leigh
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Murray Hackett
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
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6
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Stoll DR, Li X, Wang X, Carr PW, Porter SEG, Rutan SC. Fast, comprehensive two-dimensional liquid chromatography. J Chromatogr A 2007; 1168:3-43; discussion 2. [PMID: 17888443 PMCID: PMC3205947 DOI: 10.1016/j.chroma.2007.08.054] [Citation(s) in RCA: 307] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 07/09/2007] [Accepted: 08/10/2007] [Indexed: 11/21/2022]
Abstract
The absolute need to improve the separating power of liquid chromatography, especially for multi-constituent biological samples, is becoming increasingly evident. In response, over the past few years, there has been a great deal of interest in the development of two-dimensional liquid chromatography (2DLC). Just as 1DLC is preferred to 1DGC based on its compatibility with biological materials we believe that ultimately 2DLC will be preferred to the much more highly developed 2DGC for such samples. The huge advantage of 2D chromatographic techniques over 1D methods is inherent in the tremendous potential increase in peak capacity (resolving power). This is especially true of comprehensive 2D chromatography wherein it is possible, under ideal conditions, to obtain a total peak capacity equal to the product of the peak capacities of the first and second dimension separations. However, the very long timescale (typically several hours to tens of hours) of comprehensive 2DLC is clearly its chief drawback. Recent advances in the use of higher temperatures to speed up isocratic and gradient elution liquid chromatography have been used to decrease the time needed to do the second dimension LC separation of 2DLC to about 20s for a full gradient elution run. Thus, fast, high temperature LC is becoming a very promising technique. Peak capacities of over 2000 and rates of peak capacity production of nearly 1 peak/s have been achieved. In consequence, many real samples showing more than 200 peaks with signal to noise ratios of better than 10:1 have been run in total times of under 30 min. This report is not intended to be a comprehensive review of 2DLC, but is deliberately focused on the issues involved in doing fast 2DLC by means of elevating the column temperature; however, many issues of broader applicability will be discussed.
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Affiliation(s)
- Dwight R. Stoll
- University of Minnesota, Department of Chemistry, Smith and Kolthoff Halls, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Xiaoping Li
- University of Minnesota, Department of Chemistry, Smith and Kolthoff Halls, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Xiaoli Wang
- University of Minnesota, Department of Chemistry, Smith and Kolthoff Halls, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Peter W. Carr
- University of Minnesota, Department of Chemistry, Smith and Kolthoff Halls, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Sarah E. G. Porter
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284-2006, USA
| | - Sarah C. Rutan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284-2006, USA
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7
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Ryan D, Robards K. Analytical Chemistry Considerations in Plant Metabolomics. SEPARATION AND PURIFICATION REVIEWS 2006. [DOI: 10.1080/15422110601003523] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Evaluation of stationary phases for 2-dimensional HPLC of proteins Part 1. Validation of commercial RP-columns. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 844:204-12. [PMID: 16935574 DOI: 10.1016/j.jchromb.2006.07.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Revised: 06/29/2006] [Accepted: 07/09/2006] [Indexed: 11/17/2022]
Abstract
RP-separation with TFA-based water/acetonitrile eluents is widely used for peptides and small proteins but is well known difficult for large or membrane proteins. Especially in proteomics or other complex biological matrices reliable elution patterns are difficult to achieve. New commercial stationary phases are validated regarding long term stability, protein recovery, carry over, symmetry and selectivity using 10 different proteins with different molar weights, isoelectric points and glycosylation. It could be demonstrated that some stationary phases had poor protein elution performances. They did not elute a protein at all or with minor recovery, peak symmetries. Sometimes bad and formidable carry over effects for peak areas in the following run were observed. Selectivity in separation of different isomers or glycosylated proteins is also different. The results suggest that neither surface area nor pore diameter play an important role in the application of reversed phases for HPLC of proteins. The investigations leads one to suppose that the bonding chemistry seems to be an important aspect. Most critical fact is that some RP-phases did not elute a protein at all others only 20% of the injected protein mass, which makes the objective of an RP-chromatogram highly questionable.
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Shellie RA, Haddad PR. Comprehensive two-dimensional liquid chromatography. Anal Bioanal Chem 2006; 386:405-15. [PMID: 16927069 DOI: 10.1007/s00216-006-0516-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 04/19/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
Having nearly exhausted the possibilities for generating peak capacity through improvements in column technology, chromatographers are increasingly looking to alternative ways of maximising chromatographic separation. In recent years there has been increasing activity in the field of comprehensive multidimensional separations to meet analysis demands. Comprehensive two-dimensional liquid chromatography (LCxLC) approaches offer high peak capacity which leads to significantly improved analytical performance over single-column liquid chromatography. There are several closely related avenues available for achieving an LCxLC separation and this review pays special attention to the different valve-based interfaces that have been used to comprehensively couple the first and second dimension columns in LCxLC systems. A brief discussion of column choices for selected applications and the conditions employed is also presented.
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Affiliation(s)
- Robert A Shellie
- Australian Centre for Research on Separation Science (ACROSS), School of Chemistry, University of Tasmania, Private Bag 75, Hobart, 7001, Australia.
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Stoll DR, Cohen JD, Carr PW. Fast, comprehensive online two-dimensional high performance liquid chromatography through the use of high temperature ultra-fast gradient elution reversed-phase liquid chromatography. J Chromatogr A 2006; 1122:123-37. [PMID: 16720027 DOI: 10.1016/j.chroma.2006.04.058] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Revised: 04/11/2006] [Accepted: 04/19/2006] [Indexed: 11/22/2022]
Abstract
A new approach to high speed, comprehensive online dual gradient elution 2DLC (LCxLC) based on the use of ultra-fast, high temperature gradient elution reversed phase chromatography is described. Entirely conventional gradient elution instrumentation and columns are assembled in a system which develops a total peak capacity of about 900 in 25 min; this is equivalent to roughly one peak/2 s. Each second dimension gradient is done in a cycle time of 21 s and the peak retention times measured for a set of twenty six indole-3-acetic acid (IAA) derivatives are reproducible to 0.2 s. Each peak eluting from the first dimension column is sampled at least twice across its width, as the corresponding peaks on the second dimension column appear in two or three consecutive second dimension chromatograms, clearly indicating that there is little loss in the resolution gained in the first dimension separation. Application to the separation of the low molecular weight components of wild-type and mutant maize seedlings indicates the presence of about 100 peaks on a timescale of 25 min. Compelling illustrations of the analytical potential of fast, high temperature 2DLC are evident in the clear presence of nine distinct peaks in a single second dimension chromatogram from a single quite narrow first dimension peak, and the great power of 2DLC to solve the "analytic dynamic range" problem inherent in the measurement of small peaks that are neighbors to a gigantic peak.
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Affiliation(s)
- Dwight R Stoll
- Department of Chemistry, University of Minnesota, Smith and Kolthoff Halls, 207 Pleasant Street SE, Minneapolis, MN 55455-0431, USA
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11
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Wang X, Barber WE, Carr PW. A practical approach to maximizing peak capacity by using long columns packed with pellicular stationary phases for proteomic research. J Chromatogr A 2006; 1107:139-51. [PMID: 16412451 DOI: 10.1016/j.chroma.2005.12.050] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/07/2005] [Accepted: 12/09/2005] [Indexed: 11/30/2022]
Abstract
Maximization of peak capacity is a very important step in developing one-dimensional separations of complex samples. In recent work, it was shown that the use of small particles in combination with the new technique of ultrahigh pressure liquid chromatography (UHPLC) was able to generate very high peak capacities. Here we show the ability of conventional HPLC instrumentation to give comparable peak capacities to those obtained in UHPLC for the important case of complex mixtures of peptides but at much lower pressures by using a 60 cm long set of columns packed with 5 microm pellicular (superficially porous) particles. We first show, in complete agreement with the well known results of the theory of isocratic separations that, when time is not limiting, the best peak capacities in gradient elution chromatography are obtained by using large particles and the longest column that can be operated at the pump's pressure limit. Two different types of 5 microm particles (superficially porous and totally porous) were compared for their efficiency in gradient chromatography of peptides. We find that the pellicular material gave about 50% higher peak capacity compared to the analogous porous material. A 60 cm column set packed with pellicular particles was made by connecting short columns in series; a peak capacity of about 460 was obtained in 4 h at room temperature. Increasing the column temperature to 70 degrees C reduced the analysis time to 2 h and further increased the peak capacity to more than 500. The number of peaks observed in the separation of bovine serum albumin tryptic peptides was greatly increased and the separation quality was significantly improved.
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Affiliation(s)
- Xiaoli Wang
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
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13
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Fraga CG, Corley CA. The chemometric resolution and quantification of overlapped peaks form comprehensive two-dimensional liquid chromatography. J Chromatogr A 2005; 1096:40-9. [PMID: 16301068 DOI: 10.1016/j.chroma.2005.03.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 03/25/2005] [Accepted: 03/30/2005] [Indexed: 11/17/2022]
Abstract
The chemometric resolution and quantification of overlapped peaks from comprehensive two-dimensional (2D) liquid chromatography (LCxLC) data are demonstrated. The LCxLC data is produced from an in-house LCxLC analyzer that couples an anion-exchange column via a multi-port valve with a reversed-phase column connected to a UV absorbance detector. Three test mixtures, each containing a target analyte, are subjected to partial LCxLC separations to simulate likely cases of signal overlap. The resulting unresolved target-analyte signals are then analyzed by the standard-addition method and two chemometric methods. The LCxLC analyses of a test mixture and its corresponding standard-addition mixture results in two data matrices, one for each mixture. The stacking of these two data matrices produces a data structure that can then be analyzed by trilinear chemometric methods. One method, the generalized rank annihilation method (GRAM), uses a non-iterative eigenvalue-based approach to mathematically resolve overlapped trilinear signals. The other method, parallel factor analysis (PARAFAC), uses an iterative approach to resolve trilinear signals by the optimization of initial estimates using alternating least squares and signal constraints. In this paper, GRAM followed by PARAFAC analysis is shown to produce better qualitative and quantitative results than using each method separately. For instance, for all three test mixtures, the GRAM-PARAFAC approach improved quantitative accuracy by at least a factor of 4 and quantitative precision by more than 2 when compared to GRAM alone. This paper also introduces a new means of correcting run-to-run retention time shifts in comprehensive 2D chromatographic data.
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Affiliation(s)
- Carlos G Fraga
- Department of Chemistry, 2355 Fairchild Dr., Suite 2N225, United States Air Force Academy, CO 80840-6230, USA.
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14
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Stoll DR, Carr PW. Fast, Comprehensive Two-Dimensional HPLC Separation of Tryptic Peptides Based on High-Temperature HPLC. J Am Chem Soc 2005; 127:5034-5. [PMID: 15810834 DOI: 10.1021/ja050145b] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two-dimensional HPLC (2D-LC) has recently received considerable attention, and is being used as an alternative to 2D gel electrophoresis in proteomics research. The greatest impediment to the widespread use of 2D-LC is the long analysis time ranging up to days per analysis, making the technique impractical for many jobs. Here we focus on improving the speed of gradient separations since these are typically used as the second dimension in peptide separations by 2D-LC. Specifically we describe high-temperature, ultrafast HPLC conditions, along with the instrument modifications needed to reduce the analysis time of each complete second-dimension gradient separation to tens of seconds. Most importantly, this system is capable of generating a high peak capacity (1350) characteristic of comprehensive 2D-LC in a relatively shorter analysis time (20 min) with a sampling rate sufficient to minimize information loss with simpler instrumentation than currently used; this is equivalent to one unit of peak capacity per second.
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Affiliation(s)
- Dwight R Stoll
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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15
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Winther B, Reubsaet JLE. Application of supplementary flow in comprehensive 2D liquid chromatography combining SEC and RPC. J Sep Sci 2005; 28:477-82. [PMID: 15835736 DOI: 10.1002/jssc.200400004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A comprehensive two-dimensional HPLC system (SEC x RPC) was evaluated. Various model compounds with differing hydrophobicity (log D: -0.08 to 2.22) and size (MW: 194 to 66.0 x 10(3)) were used. In order to reduce the run time of the second dimension, and thereby optimize the number of runs per unit volume from the first dimension, short RPC columns were used (7.5 mm). This column size demanded a low concentration of methanol in the mobile phase from the first dimension, in order to avoid severe band broadening and solute loss. Secondary interactions on SEC make a high methanol concentration in the mobile phase a necessity. Up to 40% methanol was required to diminish non-ideal SEC behavior. These conditions were non-compatible with trapping of hydrophilic compounds on RPC. The use of a supplementary flow (0.1% TFA) mixed after the first dimension led to better peak shape and trapping of hydrophilic compounds in the second dimension. This demanded flow adjustment in SEC, which in turn caused performance improvement and an increase in analysis time, making more RPC separations possible. These factors contributed to a larger peak capacity.
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Affiliation(s)
- Bjørn Winther
- Department of Pharmaceutical Analysis, School of Pharmacy, University of Oslo, PO Box 1068, N-0316 Blindern, Oslo, Norway
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16
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Toriumi C, Imai K. An identification method for altered proteins in tissues utilizing fluorescence derivatization, liquid chromatography, tandem mass spectrometry, and a database-searching algorithm. Anal Chem 2004; 75:3725-30. [PMID: 14572036 DOI: 10.1021/ac020693x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is now widely used as a tool for proteomic studies. For the sensitive determination of proteins in 2D-PAGE, fluorescence derivatization of primary amino moieties of proteins with cyanine dyes was recently developed. However, precipitation of the proteins could occur if completely derivatized because of the lower solubility of the resultant derivatives owing to the hydrophobicity of the reagents and the loss of the hydrophilic primary amino moieties. Thus, in this paper, a water-soluble and thiol-specific fluorogenic reagent, ammonium 7-fluoro-2,1,3-benzoxadiazole-4-sulfonate, was adopted for the derivatization of proteins in tissues either with and without stimulation. Then, the method follows a separation of the derivatives by liquid chromatography with fluorescence detection, an isolation of only the altered proteins, an enzymatic digestion of the isolated proteins, and an identification of the proteins by liquid chromatography/MS/MS with the database-searching algorithm. By using this method, we identified the altered expressions of five increased proteins (e.g., pancreatic polypeptide) as well as three decreased proteins (e.g., insulin 2) in the islets of Langerhans in Wistar rats 2 days after they were subcutaneously administered with dexamethasone.
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Affiliation(s)
- Chifuyu Toriumi
- Laboratory of Bio-Analytical Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Wagner Y, Sickmann A, Meyer HE, Daum G. Multidimensional nano-HPLC for analysis of protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1003-1011. [PMID: 12954168 DOI: 10.1016/s1044-0305(03)00399-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The analysis of macromolecular protein complexes is an important factor in understanding most cellular processes, e.g., protein transport into cell organells, signal transduction via biological membranes, apoptosis, energy metabolism, directed motion of cells, and cell division. These complexes are not only built of various numbers of different proteins but also of prosthetic groups and RNA molecules. To understand the role each protein plays in a complex, a complete analysis of all protein compounds is necessary. Therefore, several separation steps have to be coupled to mass spectrometry to identify the proteins. In this work, we describe the application of multidimensional liquid chromatography, SCX-RP-LC as well as SAX-RP-LC, coupled to electrospray ion trap mass spectrometry. Tryptic digested ribosomes were separated by ion exchange chromatography manually collected and prepared for reversed phase chromatography to analyze the peptides via nano-ESI mass spectrometry. The total numbers of identified proteins are compared in consideration of the separation method (SCX-RP versus SAX-RP).
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Affiliation(s)
- Yvonne Wagner
- Rudolf Virchow-Zentrum, Julius Maximilians University Wuerzberg, Wuerzburg, Germany
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18
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Haefliger OP. Universal two-dimensional HPLC technique for the chemical analysis of complex surfactant mixtures. Anal Chem 2003; 75:371-8. [PMID: 12585460 DOI: 10.1021/ac020534d] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two-dimensional HPLC was applied for the first time to the analysis of complex surfactant mixtures. In the first dimension, ion chromatographic-type separations were performed on a diol column eluted by an acetonitrile-water (0.1% trifluoroacetic acid) gradient. Using this new technique, cationic and amphoteric surfactants were not retained at all, nonionic surfactants exhibited a weak and essentially unspecific retention, and anionic surfactants were retained mainly according to their functional group. Rather than detecting the analytes immediately after this first separation, successive fractions were automatically and quantitatively transferred to parallel C2 (dimethyl) and C4 (butyl) reversed-phase columns using an innovative setup. The second dimension of the separation then took place, by which the analytes were separated according to their hydrophobicity. Surfactants from all four classes, cationic, amphoteric, nonionic, and anionic, were separated simultaneously in single 54-min two-dimensional HPLC runs. The suitability of the method for quantitative measurements was demonstrated.
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Affiliation(s)
- Olivier P Haefliger
- Firmenich SA, Corporate R&D Division, P.O. Box 239, CH- 1211 Geneva 8, Switzerland.
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Vissers JPC, Blackburn RK, Moseley MA. A novel interface for variable flow nanoscale LC/MS/MS for improved proteome coverage. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:760-771. [PMID: 12148801 DOI: 10.1016/s1044-0305(02)00418-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A variable flow "peak trapping" liquid chromatography (LC) interface has been developed for the coupling of nanoscale LC to electrospray ionization mass spectrometry (ESI-MS). The presented peak trapping LC interface allows for the extended analysis time of co-eluting compounds and has been employed for the identification of proteins via tandem mass spectrometry (MS/MS). The variable flow process can be controlled either manually or in a completely automated manner where the mass spectrometer status determines the status of the variable flow interface. When the mass spectrometer operates in MS survey mode, the interface is operated in a so-called "high-flow" mode. Alternatively, the interface is operated in a "low-flow" mode during MS/MS analysis. In the "high-flow" mode of the variable flow process the column flow rate is typically around 200 nL/min, whereas in the "low-flow" mode the column effluent is introduced into the source of the mass spectrometer at 25 nL/min. In addition to the flow reduction during MS/MS analysis, the gradient is paused to preserve the peptide separation on the analytical nanoscale LC column. The performance of the variable flow nanoscale LC/MS/MS interface is demonstrated by the automated analysis of standard peptide mixtures and protein digests utilizing variable flow, data-dependent scanning MS/MS techniques, and automated database searching.
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Abstract
Isotopically coded tag methodology holds significant promise for differential expression proteomic experiments. This methodology has the potential for high sensitivity, high coverage, and high throughput. Although significant technical advances have been made in the past year, this approach must be viewed as an emerging technique. Advances in sample fractionation, both at the protein and peptide level, and improved data acquisition schemes, will all be required before the full potential of the method is realized.
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Affiliation(s)
- M A Moseley
- GlaxoSmithKline, Triangle Park, NC 27709, USA.
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22
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Zhang X, Hu HL, Xu S, Yang X, Zhang J. Comprehensive two-dimensional capillary LC and CE for resolution of neutral components in traditional Chinese medicines. J Sep Sci 2001. [DOI: 10.1002/1615-9314(20010501)24:5<385::aid-jssc385>3.0.co;2-u] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Davis MT, Beierle J, Bures ET, McGinley MD, Mort J, Robinson JH, Spahr CS, Yu W, Luethy R, Patterson SD. Automated LC-LC-MS-MS platform using binary ion-exchange and gradient reversed-phase chromatography for improved proteomic analyses. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 752:281-91. [PMID: 11270867 DOI: 10.1016/s0378-4347(00)00547-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A simple multidimensional liquid chromatography system utilizing an isocratic pump and a HPLC system is described for the comprehensive proteomic analysis of complex peptide digest mixtures by coupled LC-LC-MS-MS techniques. A binary ion-exchange separation was achieved through the use of a strong cation-exchange column followed by a reversed-phase column for data-dependent LC-MS-MS analysis of the unbound analytes, and following salt elution (and concomitant column reequilibration), the bound analytes. Off-line validation of the platform showed near quantitative recovery of fractionated peptides and essentially complete ion-exchange partitioning. In comparative analyses of a highly complex peptide digest mixture a >40% increase in the number of peptide and protein identifications was achieved using this multidimensional platform compared to an unfractionated control.
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Affiliation(s)
- M T Davis
- Department of Biochemistry, Amgen, Inc., Thousand Oaks, CA 91320, USA
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Affiliation(s)
- K B Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institute of Health, P.O. Box 12233, Research Triangle Park, North Carolina 27709, USA
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25
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Comprehensive two-dimensional gas chromatography and chemometrics for the high-speed quantitative analysis of aromatic isomers in a jet fuel using the standard addition method and an objective retention time alignment algorithm. Anal Chem 2000; 72:4154-62. [PMID: 10994978 DOI: 10.1021/ac000303b] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A high-speed quantitative analysis of aromatic isomers in a jet fuel sample is performed using comprehensive two-dimensional gas chromatography (GC x GC) and chemometrics. A GC x GC separation time of 2.8 min is achieved for three aromatic isomers in jet fuel, which is 5 times faster than a reference method in which a singlecolumn separation resolves two of the three isomers of interest. The high-speed GC x GC separation is more than 10 times faster than a recent GC x GC separation that fully resolves the three components of interest in gasoline. The high-speed GC x GC analysis of jet fuel is accomplished through short GC columns, high gas velocities, and partial chromatographic peak resolution followed by chemometric resolution of overlapped peaks. The standard addition method and an objective retention time alignment algorithm are used to correct for retention time variations prior to the chemometric data analysis. The standard addition method corrects for chemical matrix effects that cause analytes in complex samples to have peak shapes, widths, and retention times that differ considerably from those of calibration standards in pure solvents. The retention time alignment algorithm corrects for the relatively small retention time variations caused by fluctuating instrumental parameters such as flow rate and temperature. The use of data point interpolation in the retention time alignment algorithm results in a more accurate retention time correction then previously achieved. The generalized rank annihilation method (GRAM) is the chemometric technique used to resolve the overlapped GC x GC peaks. The correction of retention time variations allows for successful GRAM signal deconvolution. Using the retention time alignment algorithm, GRAM quantification accuracy and precision are improved by a factor of 4. The methodology used in this paper should be applicable to other comprehensive separation methods, such as two-dimensional liquid chromatography, liquid chromatography coupled with capillary electrophoresis, and liquid chromatography coupled with gas chromatography.
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Fraga CG, Prazen BJ, Synovec RE. Enhancing the Limit of Detection for Comprehensive Two-Dimensional Gas Chromatography (GC×GC) using Bilinear Chemometric Analysis. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/(sici)1521-4168(20000301)23:3<215::aid-jhrc215>3.0.co;2-q] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Figeys D, Corthals GL, Gallis B, Goodlett DR, Ducret A, Corson MA, Aebersold R. Data-dependent modulation of solid-phase extraction capillary electrophoresis for the analysis of complex peptide and phosphopeptide mixtures by tandem mass spectrometry: application to endothelial nitric oxide synthase. Anal Chem 1999; 71:2279-87. [PMID: 10405598 DOI: 10.1021/ac9813991] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) of peptides in conjunction with automated sequence database searching of the resulting collision-induced dissociation (CID) spectra has become a powerful method for the identification of purified proteins or the components of protein mixtures. The success of the method is critically dependent on the manner by which the peptides are introduced into the mass spectrometer. In this report, we describe a capillary electrophoresis-based system for the automated, sensitive analysis of complex peptide mixtures. The system consists of an ESI-MS/MS instrument, a solid-phase extraction (SPE)-capillary zone electrophoresis (CZE) device for peptide concentration and separation, and an algorithm written in Instrument Control Language (ICL) which modulates the electrophoretic conditions in a data-dependent manner to optimize available time for the generation of high-quality CID spectra of peptides in complex samples. We demonstrate that the data-dependent modulation of the electric field significantly expands the analytical window for each peptide analyzed and that the sensitivity of the SPE-CZE technique is not noticeably altered by the procedure. By applying the technique to the analysis of in vivo phosphorylation sites of endothelial nitric oxide synthase (eNOS), we demonstrate the power of this system for the MS/MS analysis of minor peptide species in complex samples such as phosphopeptides generated by the proteolytic digestion of a large protein, eNOS, phosphorylated at low stoichiometry.
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Affiliation(s)
- D Figeys
- Department of Molecular Biotechnology, University of Washington, Seattle 98195-7730, USA
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28
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Larive CK, Lunte SM, Zhong M, Perkins MD, Wilson GS, Gokulrangan G, Williams T, Afroz F, Schöneich C, Derrick TS, Middaugh CR, Bogdanowich-Knipp S. Separation and analysis of peptides and proteins. Anal Chem 1999; 71:389R-423R. [PMID: 10409086 DOI: 10.1021/a1990013o] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C K Larive
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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