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Blue LE, Franklin EG, Godinho JM, Grinias JP, Grinias KM, Lunn DB, Moore SM. Recent advances in capillary ultrahigh pressure liquid chromatography. J Chromatogr A 2017; 1523:17-39. [PMID: 28599863 DOI: 10.1016/j.chroma.2017.05.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 11/28/2022]
Abstract
In the twenty years since its initial demonstration, capillary ultrahigh pressure liquid chromatography (UHPLC) has proven to be one of most powerful separation techniques for the analysis of complex mixtures. This review focuses on the most recent advances made since 2010 towards increasing the performance of such separations. Improvements in capillary column preparation techniques that have led to columns with unprecedented performance are described. New stationary phases and phase supports that have been reported over the past decade are detailed, with a focus on their use in capillary formats. A discussion on the instrument developments that have been required to ensure that extra-column effects do not diminish the intrinsic efficiency of these columns during analysis is also included. Finally, the impact of these capillary UHPLC topics on the field of proteomics and ways in which capillary UHPLC may continue to be applied to the separation of complex samples are addressed.
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Affiliation(s)
- Laura E Blue
- Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | - Edward G Franklin
- HPLC Research & Development, Restek Corp., Bellefonte, PA 16823, USA
| | - Justin M Godinho
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James P Grinias
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA.
| | - Kaitlin M Grinias
- Department of Product Development & Supply, GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Daniel B Lunn
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Cai W, Tucholski T, Chen B, Alpert AJ, McIlwain S, Kohmoto T, Jin S, Ge Y. Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Anal Chem 2017; 89:5467-5475. [PMID: 28406609 DOI: 10.1021/acs.analchem.7b00380] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mass spectrometry (MS)-based top-down proteomics is a powerful method for the comprehensive analysis of proteoforms that arise from genetic variations and post-translational modifications (PTMs). However, top-down MS analysis of high molecular weight (MW) proteins remains challenging mainly due to the exponential decay of signal-to-noise ratio with increasing MW. Size exclusion chromatography (SEC) is a favored method for size-based separation of biomacromolecules but typically suffers from low resolution. Herein, we developed a serial size exclusion chromatography (sSEC) strategy to enable high-resolution size-based fractionation of intact proteins (10-223 kDa) from complex protein mixtures. The sSEC fractions could be further separated by reverse phase chromatography (RPC) coupled online with high-resolution MS. We have shown that two-dimensional (2D) sSEC-RPC allowed for the identification of 4044 more unique proteoforms and a 15-fold increase in the detection of proteins above 60 kDa, compared to one-dimensional (1D) RPC. Notably, effective sSEC-RPC separation of proteins significantly enhanced the detection of high MW proteins up to 223 kDa and also revealed low abundance proteoforms that are post-translationally modified. This sSEC method is MS-friendly, robust, and reproducible and, thus, can be applied to both high-efficiency protein purification and large-scale proteomics analysis of cell or tissue lysate for enhanced proteome coverage, particularly for low abundance and high MW proteoforms.
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Affiliation(s)
- Wenxuan Cai
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Andrew J Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,PolyLC Inc. , Columbia, Maryland 21045, United States
| | - Sean McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Takushi Kohmoto
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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3
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Moore S, Hess S, Jorgenson J. Characterization of an immobilized enzyme reactor for on-line protein digestion. J Chromatogr A 2016; 1476:1-8. [PMID: 27876348 PMCID: PMC5136339 DOI: 10.1016/j.chroma.2016.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/29/2016] [Accepted: 11/13/2016] [Indexed: 01/05/2023]
Abstract
Despite the developments for faster liquid chromatographic and mass spectral detection techniques, the standard in-solution protein digestion for proteomic analyses has remained relatively unchanged. The typical in-solution trypsin protein digestion is usually the slowest part of the workflow, albeit one of the most important. The development of a highly efficient immobilized enzyme reactor (IMER) with rapid performance for on-line protein digestion would greatly decrease the analysis time involved in a proteomic workflow. Presented here is the development of a silica based IMER for on-line protein digestion, which produced rapid digestions in the presence of organic mobile phase for both model proteins and a complex sample consisting of the insoluble portion of a yeast cell lysate. Protein sequence coverage and identifications evaluated between the IMER and in-solution digestions were comparable. Overall, for a yeast cell lysate with only a 10s volumetric residence time on-column, the IMER identified 507 proteins while the in-solution digestion identified 490. There were no significant differences observed based on identified protein's molecular weight or isoelectric point between the two digestion methods. Implementation of the IMER into the proteomic workflow provided similar protein identification results, automation for sample analysis, and reduced the analysis time by 15h.
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Affiliation(s)
- Stephanie Moore
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - Stephanie Hess
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States
| | - James Jorgenson
- Chemistry Department, University of North Carolina at Chapel Hill, NC 27599, United States.
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4
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Development of a 45kpsi ultrahigh pressure liquid chromatography instrument for gradient separations of peptides using long microcapillary columns and sub-2μm particles. J Chromatogr A 2016; 1469:60-67. [PMID: 27702615 DOI: 10.1016/j.chroma.2016.09.053] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 11/22/2022]
Abstract
Commercial chromatographic instrumentation for bottom-up proteomics is often inadequate to resolve the number of peptides in many samples. This has inspired a number of complex approaches to increase peak capacity, including various multidimensional approaches, and reliance on advancements in mass spectrometry. One-dimensional reversed phase separations are limited by the pressure capabilities of commercial instruments and prevent the realization of greater separation power in terms of speed and resolution inherent to smaller sorbents and ultrahigh pressure liquid chromatography. Many applications with complex samples could benefit from the increased separation performance of long capillary columns packed with sub-2μm sorbents. Here, we introduce a system that operates at a constant pressure and is capable of separations at pressures up to 45kpsi. The system consists of a commercially available capillary liquid chromatography instrument, for sample management and gradient creation, and is modified with a storage loop and isolated pneumatic amplifier pump for elevated separation pressure. The system's performance is assessed with a complex peptide mixture and a range of microcapillary columns packed with sub-2μm C18 particles.
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5
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Moore SM, Hess SM, Jorgenson JW. Extraction, Enrichment, Solubilization, and Digestion Techniques for Membrane Proteomics. J Proteome Res 2016; 15:1243-52. [PMID: 26979493 PMCID: PMC5488330 DOI: 10.1021/acs.jproteome.5b01122] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of membrane proteins in biological systems is indisputable; however, their amphipathic nature makes them difficult to analyze. In this study, the most popular techniques for extraction, enrichment, solubilization, and digestion are compared, resulting in an overall improved workflow for the insoluble portion of Saccharomyces cerevisiae cell lysate. Yeast cells were successfully lysed using a French press pressure cell at 20 000 psi, and resulting proteins were fractionated prior to digestion to reduce sample complexity. The proteins were best solubilized with the addition of ionic detergent sodium deoxycholate (1%) and through the application of high-frequency sonication prior to a tryptic digestion at 37 °C. Overall, the improved membrane proteomic workflow resulted in a 26% increase in membrane protein identifications for baker's yeast. In addition, more membrane protein identifications were unique to the improved protocol. When comparing membrane proteins that were identified in the improved protocol and the standard operating procedure (176 proteins), 93% of these proteins were present in greater abundance (higher intensity) when using the improved method.
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Affiliation(s)
- Stephanie M. Moore
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephanie M. Hess
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James W. Jorgenson
- Chemistry Department University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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6
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Huang Z, Yan G, Gao M, Zhang X. Array-Based Online Two Dimensional Liquid Chromatography System Applied to Effective Depletion of High-Abundance Proteins in Human Plasma. Anal Chem 2016; 88:2440-5. [DOI: 10.1021/acs.analchem.5b04553] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhi Huang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- Department
of Chemistry, Fudan University, Shanghai 200433, China
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mingxia Gao
- Department
of Chemistry, Fudan University, Shanghai 200433, China
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiangmin Zhang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
- Institutes
of Biomedical Sciences, Fudan University, Shanghai 200032, China
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7
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Chen B, Peng Y, Valeja SG, Xiu L, Alpert AJ, Ge Y. Online Hydrophobic Interaction Chromatography-Mass Spectrometry for Top-Down Proteomics. Anal Chem 2016; 88:1885-91. [PMID: 26729044 DOI: 10.1021/acs.analchem.5b04285] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent progress in top-down proteomics has led to a demand for mass spectrometry (MS)-compatible chromatography techniques to separate intact proteins using volatile mobile phases. Conventional hydrophobic interaction chromatography (HIC) provides high-resolution separation of proteins under nondenaturing conditions but requires high concentrations of nonvolatile salts. Herein, we introduce a series of more-hydrophobic HIC materials that can retain proteins using MS-compatible concentrations of ammonium acetate. The new HIC materials appear to function as a hybrid form of conventional HIC and reverse phase chromatography. The function of the salt seems to be preserving protein structure rather than promoting retention. Online HIC-MS is feasible for both qualitative and quantitative analysis. This is demonstrated with standard proteins and a complex cell lysate. The mass spectra of proteins from the online HIC-MS exhibit low charge-state distributions, consistent with those commonly observed in native MS. Furthermore, HIC-MS can chromatographically separate proteoforms differing by minor modifications. Hence, this new HIC-MS combination is promising for top-down proteomics.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Santosh G Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Lichen Xiu
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Andrew J Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States.,PolyLC, Inc., 9151 Rumsey Rd., Suite 180, Columbia, Maryland, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin, United States
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8
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Valeja SG, Xiu L, Gregorich ZR, Guner H, Jin S, Ge Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem 2015; 87:5363-5371. [PMID: 25867201 PMCID: PMC4575680 DOI: 10.1021/acs.analchem.5b00657] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To address the complexity of the proteome in mass spectrometry (MS)-based top-down proteomics, multidimensional liquid chromatography (MDLC) strategies that can effectively separate proteins with high resolution and automation are highly desirable. Although various MDLC methods that can effectively separate peptides from protein digests exist, very few MDLC strategies, primarily consisting of 2DLC, are available for intact protein separation, which is insufficient to address the complexity of the proteome. We recently demonstrated that hydrophobic interaction chromatography (HIC) utilizing a MS-compatible salt can provide high resolution separation of intact proteins for top-down proteomics. Herein, we have developed a novel 3DLC strategy by coupling HIC with ion exchange chromatography (IEC) and reverse phase chromatography (RPC) for intact protein separation. We demonstrated that a 3D (IEC-HIC-RPC) approach greatly outperformed the conventional 2D IEC-RPC approach. For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 nonredundant proteins) as compared to 47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications. Therefore, this novel 3DLC method has great potential for effective separation of intact proteins to achieve deep proteome coverage in top-down proteomics.
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Affiliation(s)
- Santosh G. Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lichen Xiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Wisconsin, USA
| | - Huseyin Guner
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Mohr W, Tang T, Sattin SR, Bovee RJ, Pearson A. Protein Stable Isotope Fingerprinting: Multidimensional Protein Chromatography Coupled to Stable Isotope-Ratio Mass Spectrometry. Anal Chem 2014; 86:8514-20. [DOI: 10.1021/ac502494b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wiebke Mohr
- Department of Earth and Planetary
Sciences, Harvard University, 20 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Tiantian Tang
- Department of Earth and Planetary
Sciences, Harvard University, 20 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Sarah R. Sattin
- Department of Earth and Planetary
Sciences, Harvard University, 20 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Roderick J. Bovee
- Department of Earth and Planetary
Sciences, Harvard University, 20 Oxford St., Cambridge, Massachusetts 02138, United States
| | - Ann Pearson
- Department of Earth and Planetary
Sciences, Harvard University, 20 Oxford St., Cambridge, Massachusetts 02138, United States
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10
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Ye X, Li L. Macroporous reversed-phase separation of proteins combined with reversed-phase separation of phosphopeptides and tandem mass spectrometry for profiling the phosphoproteome of MDA-MB-231 cells. Electrophoresis 2014; 35:3479-86. [PMID: 24888630 DOI: 10.1002/elps.201300586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 12/13/2022]
Abstract
A new method of combining macroporous RP (mRP) protein fractionation with RPLC peptide separation MS/MS is reported for profiling the phosphoproteome of a complex sample. In this method, an mRP-C18 column was used to fractionate the proteins from a whole cell lysate of a breast cancer cell line, MDA-MB-231, into 38 fractions. Each fraction was subjected to tryptic digestion, sequential phosphopeptide enrichment by immobilized metal ion affinity chromatography and titanium dioxide (TiO2 ), followed by capillary RPLC-MS/MS analysis. For comparison, the conventional method of using strong cation exchange RPLC separation of peptides combined with MS/MS was also used for analyzing the phosphoproteome. Replicate experiments by the mRP-RPLC method identified 1585 distinct phosphoproteins with 4519 phosphopeptides, compared to 1585 phosphoproteins with 4297 phosphopeptides by strong cation exchange RPLC, with a total of 1947 phosphoproteins and 6278 phosphopeptides identified from the combined results. While the two methods have similar ability in the identification of the phosphoproteome, they produce complementary information. The phosphoproteins identified in this study, including 67 novel phosphorylation sites from 56 breast cancer related proteins, can serve as the entry point for future validation with biological implications in breast cancer. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000948 and DOI 10.6019/PXD000948.
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Affiliation(s)
- Xiaoxia Ye
- Department of Chemistry, University of Alberta, Edmonton, Canada
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11
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Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2014; 10:551-66. [PMID: 24206228 DOI: 10.1586/14789450.2013.858022] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS(E), all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.
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Affiliation(s)
- Kai Pong Law
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, Level 1, 14 Medical Drive, 117599, Singapore
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12
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Decrease of dynamic range of proteins in human plasma by ampholine immobilized polymer microspheres. Anal Chim Acta 2014; 826:43-50. [DOI: 10.1016/j.aca.2014.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/28/2014] [Accepted: 04/03/2014] [Indexed: 12/25/2022]
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