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Jadeja S, Kupcik R, Fabrik I, Sklenářová H, Lenčo J. A stationary phase with a positively charged surface allows for minimizing formic acid concentration in the mobile phase, enhancing electrospray ionization in LC-MS proteomic experiments. Analyst 2023; 148:5980-5990. [PMID: 37870390 DOI: 10.1039/d3an01508d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The default choice of mobile phase acidifier for bottom-up LC-MS proteomic analyses is 0.10% formic acid because of its decent acidity, decent ion pairing ability, and low suppression of electrospray ionization. In recent years, state-of-the-art columns have been designed specifically to provide efficient separation even when using an MS-friendly mobile phase of low ionic strength. Despite this, no attempts have been made to improve the sensitivity of the MS-based analytical methods by reducing the amount of formic acid in the mobile phase. In this study, we evaluated the effect of reduced formic acid concentration in the mobile phase on the chromatographic behavior and MS response of peptides when separated using columns packed with a C18 stationary phase with a positively charged surface. Using 0.01% formic acid in the mobile phase maintained excellent chromatographic performance and increased MS signal response compared to the standard of 0.10%. The enhanced MS response translated to about 50% improved peptide identifications depending on the complexity and amount of sample injected. The increased retention of peptides at a reduced formic acid concentration was directly proportional to the number of acidic residues in the peptide sequence. The study was carried out by covering a spectrum of protein samples with varied complexity using analytical flow, micro-, and nanoflow regimes to expand the applicability in routine practice.
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Affiliation(s)
- Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Rudolf Kupcik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
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2
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Gao H, Wang ST, Hu F, Shen BB, Sun MF, Wang H, Li L, Fang WJ. Investigation of an Uncommon Artifact during Reducing Capillary Electrophoresis-Sodium Dodecyl Sulfate Analysis of a Monoclonal Antibody with Dynamic Light Scattering and Reversed Phase High-Performance Liquid Chromatography. Pharm Res 2022; 39:1959-1968. [PMID: 35701679 DOI: 10.1007/s11095-022-03303-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
Abstract
PURPOSES In reducing capillary electrophoresis sodium dodecyl sulfate (CE-SDS) analysis of a monoclonal antibody (mAb-1), the peak area ratio of heavy chain (HC) to light chain (LC) was out of balance, while multiple artifact peaks were observed following the migration of HC. The main purposes of this study were to describe the techniques utilized to eliminate this artifact and clarify the root cause for this interesting phenomenon. METHODS We optimized the CE-SDS analysis of mAb-1 by a vairety of techniques including changing the concentration of protein or replacing SDS with a more hydrophobic surfactant (i.e., sodium hexadecyl sulfate (SHS) or sodium tetradecyl sulfate (STS) instead of SDS) in sample and/or the sieving gel buffer. Dynamic light scattering (DLS) and reversed phase high-performance liquid chromatography (RP-HPLC) were used to study the protein-surfactant complex. RESULTS The artifact could be partially mitigated by reducing the protein concentration and replacing SDS with SHS or STS in the sample and/or the sieving gel buffer solutions. Due to replacing a more hydrophobic surfactant, the HC-surfactant complex formed was more resistant to dissociation, preventing additional hydrophobic HC-HC interaction and aggregation, thus eliminating the artifact problem. CONCLUSIONS DLS and RP-HPLC are powerful supplementary techniques in characterizing the protein-surfactant complex, and hydrophobic surfactants such as SHS and STS could afford more normal electropherograms during the analysis of mAbs.
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Affiliation(s)
- Han Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Si-Tao Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Hu
- Zhejiang Bioray Biopharmaceutical Co., Taizhou, 317000, China
| | - Bin-Bin Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Min-Fei Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.,Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Haibin Wang
- Zhejiang Bioray Biopharmaceutical Co., Taizhou, 317000, China
| | - Lei Li
- Zhejiang Bioray Biopharmaceutical Co., Taizhou, 317000, China
| | - Wei-Jie Fang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China. .,Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310016, China.
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3
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Field JK, Euerby MR, Haselmann KF, Petersson P. Investigation into reversed-phase chromatography peptide separation systems Part IV: Characterisation of mobile phase selectivity differences. J Chromatogr A 2021; 1641:461986. [PMID: 33631703 DOI: 10.1016/j.chroma.2021.461986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/25/2022]
Abstract
The differentiation of mobile phase compositions between sub-classes which exhibit distinct chromatographic selectivity (i.e. termed characterisation) towards a range of peptide probes with diverse functionality and hence the possibility for multi-modal retention mechanisms has been undertaken. Due to the complexity of peptide retention mechanisms in given mobile phase conditions, no attempt has been made to explain these, instead mobile phases have simply been classified into distinct groups with an aim of identifying those yielding differing selectivities for use in strategic method development roadmaps for the analysis of peptide mixtures. The selectivity differences between nine synthetic peptides (fragments of [Ile27]-Bovine GLP-2) were used to assess how fifty-one RPC mobile phase compositions of differing pH (range 1.8 - 7.8), salt types, ionic strengths, ion-pair reagents and chaotropic / kosmotropic additives affected chromatographic selectivity on a new generation C18 stationary phase (Ascentis Express C18). The mobile phase compositions consisted of commonly used and novel UV or MS compatible additives. The chemometric tool of Principal Component Analysis (PCA) was used to visualise the differences in selectivity generated between the various mobile phases evaluated. The results highlight the importance of screening numerous mobile phases of differing pH, ion-pair reagents and ionic strength in order to maximise the probability of achieving separation of all the peptides of interest within a complex mixture. PCA permitted a ranking of the relative importance of the various mobile phase parameters evaluated. The concept of using this approach was proven in the analysis of a sample of Bovine GLP-2 (1-15) containing synthesis related impurities. Mobile phases with high ionic strength were demonstrated to be crucial for the generation of symmetrical peaks. The observations made on the C18 phase were compared on three additional stationary phases (i.e. alkyl amide, fluorophenyl and biphenyl), which had previously been shown to possess large selectivity differences towards these peptides, on a limited sub-set of mobile phases. With the exception of the ion-pair reagent, similar trends were obtained for the C18, fluorophenyl and biphenyl phases intimating the applicability of these findings to the vast majority of RPC columns (i.e. neutral or weakly polar in character) which are suitable for the analysis of peptides. The conclusions were not relevant for columns with a more disparate nature (i.e. containing a high degree of positive charge).
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Affiliation(s)
- Jennifer K Field
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, United Kingdom
| | - Melvin R Euerby
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, United Kingdom; Shimadzu UK, Milton Keynes, Buckinghamshire, MK12 5RD, United Kingdom
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4
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Neubauer D, Jaśkiewicz M, Sikorska E, Bartoszewska S, Bauer M, Kapusta M, Narajczyk M, Kamysz W. Effect of Disulfide Cyclization of Ultrashort Cationic Lipopeptides on Antimicrobial Activity and Cytotoxicity. Int J Mol Sci 2020; 21:E7208. [PMID: 33003569 PMCID: PMC7582905 DOI: 10.3390/ijms21197208] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Ultrashort cationic lipopeptides (USCLs) are considered to be a promising class of antimicrobials with high activity against a broad-spectrum of microorganisms. However, the majority of these compounds are characterized by significant toxicity toward human cells, which hinders their potential application. To overcome those limitations, several approaches have been advanced. One of these is disulfide cyclization that has been shown to improve drug-like characteristics of peptides. In this article the effect of disulfide cyclization of the polar head of N-palmitoylated USCLs on in vitro biological activity has been studied. Lipopeptides used in this study consisted of three or four basic amino acids (lysine and arginine) and cystine in a cyclic peptide. In general, disulfide cyclization of the lipopeptides resulted in peptides with reduced cytotoxicity. Disulfide-cyclized USCLs exhibited improved selectivity between Candida sp., Gram-positive strains and normal cells in contrast to their linear counterparts. Interactions between selected USCLs and membranes were studied by molecular dynamics simulations using a coarse-grained force field. Moreover, membrane permeabilization properties and kinetics were examined. Fluorescence and transmission electron microscopy revealed damage to Candida cell membrane and organelles. Concluding, USCLs are strong membrane disruptors and disulfide cyclization of polar head can have a beneficial effect on its in vitro selectivity between Candida sp. and normal human cells.
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Affiliation(s)
- Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Maciej Jaśkiewicz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Emilia Sikorska
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Marta Bauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Magdalena Narajczyk
- Laboratory of Electron Microscopy, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland;
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland; (M.J.); (S.B.); (M.B.); (W.K.)
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5
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Mao Y, Kleinberg A, Zhao Y, Raidas S, Li N. Simple Addition of Glycine in Trifluoroacetic Acid-Containing Mobile Phases Enhances the Sensitivity of Electrospray Ionization Mass Spectrometry for Biopharmaceutical Characterization. Anal Chem 2020; 92:8691-8696. [DOI: 10.1021/acs.analchem.0c01319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuan Mao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Andrew Kleinberg
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Yunlong Zhao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Shivkumar Raidas
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
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6
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Larsen DN, Mikkelsen CE, Kierkegaard M, Bereta GP, Nowakowska Z, Kaczmarek JZ, Potempa J, Højrup P. Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated Peptides. Mol Cell Proteomics 2020; 19:167-180. [PMID: 31754044 PMCID: PMC6944236 DOI: 10.1074/mcp.ra119.001700] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/12/2019] [Indexed: 12/20/2022] Open
Abstract
Porphyromonas gingivalis is a key pathogen in chronic periodontitis and has recently been mechanistically linked to the development of rheumatoid arthritis via the activity of peptidyl arginine deiminase generating citrullinated epitopes in the periodontium. In this project the outer membrane vesicles (OMV) from P. gingivalis W83 wild-type (WT), a W83 knock-out mutant of peptidyl arginine deiminase (ΔPPAD), and a mutant strain expressing PPAD with the active site cysteine mutated to alanine (C351A), have been analyzed using a two-dimensional HFBA-based separation system combined with LC-MS. For optimal and positive identification and validation of citrullinated peptides and proteins, high resolution mass spectrometers and strict MS search criteria were utilized. This may have compromised the total number of identified citrullinations but increased the confidence of the validation. A new two-dimensional separation system proved to increase the strength of validation, and along with the use of an in-house build program, Citrullia, we establish a fast and easy semi-automatic (manual) validation of citrullinated peptides. For the WT OMV we identified 78 citrullinated proteins having a total of 161 citrullination sites. Notably, in keeping with the mechanism of OMV formation, the majority (51 out of 78) of citrullinated proteins were predicted to be exported via the inner membrane and to reside in the periplasm or being translocated to the bacterial surface. Citrullinated surface proteins may contribute to the pathogenesis of rheumatoid arthritis. For the C351A-OMV a single citrullination site was found and no citrullinations were identified for the ΔPPAD-OMV, thus validating the unbiased character of our method of citrullinated peptide identification.
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Affiliation(s)
| | | | | | - Grzegorz P Bereta
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Zuzanna Nowakowska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Malopolska Center of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jakub Z Kaczmarek
- Research and Development Department, Ovodan Biotech A/S, 5000 Odense, Denmark
| | - Jan Potempa
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 S. Preston St., Louisville, Kentucky
| | - Peter Højrup
- University of Southern Denmark, Campusvej 55, Odense M, Denmark.
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7
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Abstract
In bottom-up proteomics, proteins are typically identified by enzymatic digestion into peptides, tandem mass spectrometry and comparison of the tandem mass spectra with those predicted from a sequence database for peptides within measurement uncertainty from the experimentally obtained mass. Although now decreasingly common, isolated proteins or simple protein mixtures can also be identified by measuring only the masses of the peptides resulting from the enzymatic digest, without any further fragmentation. Separation methods such as liquid chromatography and electrophoresis are often used to fractionate complex protein or peptide mixtures prior to analysis by mass spectrometry. Although the primary reason for this is to avoid ion suppression and improve data quality, these separations are based on physical and chemical properties of the peptides or proteins and therefore also provide information about them. Depending on the separation method, this could be protein molecular weight (SDS-PAGE), isoelectric point (IEF), charge at a known pH (ion exchange chromatography), or hydrophobicity (reversed phase chromatography). These separations produce approximate measurements on properties that to some extent can be predicted from amino acid sequences. In the case of molecular weight of proteins without posttranslational modifications this is straightforward: simply add the molecular weights of the amino acid residues in the protein. For IEF, charge and hydrophobicity, the order of the amino acids, and folding state of the peptide or protein also matter, but it is nevertheless possible to predict the behavior of peptides and proteins in these separation methods to a degree which renders such predictions useful. This chapter reviews the topic of using data from separation methods for identification and validation in proteomics, with special emphasis on predicting retention times of tryptic peptides in reversed-phase chromatography under acidic conditions, as this is one of the most commonly used separation methods in bottom-up proteomics.
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8
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Moruz L, Käll L. Peptide retention time prediction. MASS SPECTROMETRY REVIEWS 2017; 36:615-623. [PMID: 26799864 DOI: 10.1002/mas.21488] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 11/12/2015] [Indexed: 06/05/2023]
Abstract
Most methods for interpreting data from shotgun proteomics experiments are to large degree dependent on being able to predict properties of peptide-ions. Often such predicted properties are limited to molecular mass and fragment spectra, but here we put focus on a perhaps underutilized property, a peptide's chromatographic retention time. We review a couple of different principles of retention time prediction,and their applications within computational proteomics. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:615-623, 2017.
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Affiliation(s)
- Luminita Moruz
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology - KTH, Stockholm, Sweden
| | - Lukas Käll
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology - KTH, Stockholm, Sweden
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9
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Furuki K, Toyo'oka T. Retention of glycopeptides analyzed using hydrophilic interaction chromatography is influenced by charge and carbon chain length of ion-pairing reagent for mobile phase. Biomed Chromatogr 2017; 31. [DOI: 10.1002/bmc.3988] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/15/2017] [Accepted: 04/06/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Kenichiro Furuki
- Process Lab II, Biotechnology Labs, Astellas Pharma Inc; Ibaraki Japan
- School of Pharmaceutical Sciences; University of Shizuoka; Shizuoka Japan
| | - Toshimasa Toyo'oka
- School of Pharmaceutical Sciences; University of Shizuoka; Shizuoka Japan
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10
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Maes E, Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Hooyberghs J, Mertens I, Baggerman G, Ramon J, Laukens K, Martens L, Valkenborg D. Designing biomedical proteomics experiments: state-of-the-art and future perspectives. Expert Rev Proteomics 2016; 13:495-511. [PMID: 27031651 DOI: 10.1586/14789450.2016.1172967] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.
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Affiliation(s)
- Evelyne Maes
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium
| | - Pieter Kelchtermans
- b CFP , University of Antwerp , Antwerp , Belgium.,c Medical Biotechnology Center , VIB , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium
| | - Wout Bittremieux
- f Department of Mathematics and Computer Science , University of Antwerp , Antwerp , Belgium.,g Biomedical Informatics Research Center Antwerp (biomina) , University of Antwerp/Antwerp University Hospital , Antwerp , Belgium
| | - Kurt De Grave
- h Department of Computer Science , KU Leuven , Leuven , Belgium
| | - Sven Degroeve
- c Medical Biotechnology Center , VIB , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium
| | - Jef Hooyberghs
- a Applied Bio & molecular systems , VITO , Mol , Belgium
| | - Inge Mertens
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium
| | - Geert Baggerman
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium
| | - Jan Ramon
- h Department of Computer Science , KU Leuven , Leuven , Belgium.,i INRIA , Lille , France
| | - Kris Laukens
- f Department of Mathematics and Computer Science , University of Antwerp , Antwerp , Belgium.,g Biomedical Informatics Research Center Antwerp (biomina) , University of Antwerp/Antwerp University Hospital , Antwerp , Belgium
| | - Lennart Martens
- c Medical Biotechnology Center , VIB , Ghent , Belgium.,d Department of Biochemistry , Ghent University , Ghent , Belgium.,e Bioinformatics Institute Ghent , Ghent University , Ghent , Belgium
| | - Dirk Valkenborg
- a Applied Bio & molecular systems , VITO , Mol , Belgium.,b CFP , University of Antwerp , Antwerp , Belgium.,j Interuniversity Institute for Biostatistics and statistical Bioinformatics , Hasselt University , Hasselt , Belgium
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11
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Comparative studies of peak intensities and chromatographic separation of proteolytic digests, PTMs, and intact proteins obtained by nanoLC-ESI MS analysis at room and elevated temperatures. Anal Bioanal Chem 2016; 408:3953-68. [DOI: 10.1007/s00216-016-9386-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 12/26/2022]
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12
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Ravipati AS, Henriques ST, Poth AG, Kaas Q, Wang CK, Colgrave ML, Craik DJ. Lysine-rich Cyclotides: A New Subclass of Circular Knotted Proteins from Violaceae. ACS Chem Biol 2015; 10:2491-500. [PMID: 26322745 DOI: 10.1021/acschembio.5b00454] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclotides are macrocyclic proteins produced by plants for host defense. Although they occur sparsely in other plant families, cyclotides have been detected in every Violaceae plant species so far screened. Many of the Violaceae species examined until now have been from closely related geographical regions or habitats. To test the hypothesis that cyclotides are ubiquitous in this family, two geographically isolated (and critically endangered) species of Australasian Violaceae, namely Melicytus chathamicus and M. latifolius, were examined. Surprisingly, we discovered a suite of cyclotides possessing novel sequence features, including a lysine-rich nature, distinguishing them from "conventional" cyclotides and suggesting that they might have different physiological activities in plants to those reported to date. The newly discovered cyclotides were found to bind to lipid membranes and were cytotoxic against cancer cell lines but had low toxicity against red blood cells, which is advantageous for potential therapeutic applications. This suite of novel Lys-rich cyclotides emphasizes the broad diversity of cyclotides in Violaceae species.
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Affiliation(s)
- Anjaneya S. Ravipati
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Aaron G. Poth
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Michelle L. Colgrave
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St. Lucia, Queensland 4067, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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13
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Comparison of retention behavior of oligolysine and oligoarginine in ion-pairing chromatography using heptafluorobutyric acid. Anal Bioanal Chem 2013; 405:9739-46. [DOI: 10.1007/s00216-013-7397-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/21/2013] [Accepted: 09/23/2013] [Indexed: 12/01/2022]
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14
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Reversed phase ion-pairing chromatography of an oligolysine mixture in different mobile phases: effort of searching critical chromatography conditions. J Chromatogr A 2013; 1304:127-32. [PMID: 23876768 DOI: 10.1016/j.chroma.2013.06.078] [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: 03/07/2013] [Revised: 06/28/2013] [Accepted: 06/28/2013] [Indexed: 11/23/2022]
Abstract
Our earlier study [J. Chromatogr. A 1218 (2011) 7765] on separation of an oligolysine mixture consisting of chains with 2-8 lysine residues (number of lysine residues, dp=2-8) by ion-pairing reversed-phase chromatography using heptafluorobutyric acid (HFBA) as an ion pairing reagent at fixed mobile phase acetonitrile (ACN) content was extended to isocratic elution conditions with different ACN percentages. The present work explored how manipulating the mobile phase HFBA concentration ([HFBA]) and %-ACN content influences separations of the oligolysine mixture. The closed pairing model was used to analyze variation of the retention factor as a function of [HFBA]. The partition coefficient of the paired peptide decreased with increasing %-ACN. Pairing of HFBA to oligolysine was cooperative, and the effect increased when %-ACN in the mobile phase was lowered. A plot of the partition coefficient as a function of %-ACN for oligolysines varying in dp converged at one ACN content, indicating a critical condition in which components of different dp co-elute.
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15
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Abstract
In bottom-up proteomics, proteins are typically identified by enzymatic digestion into peptides, tandem mass spectrometry and comparison of the tandem mass spectra with those predicted from a sequence database for peptides within measurement uncertainty from the experimentally obtained mass. Although now decreasingly common, isolated proteins or simple protein mixtures can also be identified by measuring only the masses of the peptides resulting from the enzymatic digest, without any further fragmentation. Separation methods such as liquid chromatography and electrophoresis are often used to fractionate complex protein or peptide mixtures prior to analysis by mass spectrometry. Although the primary reason for this is to avoid ion suppression and improve data quality, these separations are based on physical and chemical properties of the peptides or proteins and therefore also provide information about them. Depending on the separation method, this could be protein molecular weight (SDS-PAGE), isoelectric point (IEF), charge at a known pH (ion exchange chromatography), or hydrophobicity (reversed phase chromatography). These separations produce approximate measurements on properties that to some extent can be predicted from amino acid sequences. In the case of molecular weight of proteins without posttranslational modifications this is straightforward: simply add the molecular weights of the amino acid residues in the protein. For IEF, charge and hydrophobicity, the order of the amino acids, and folding state of the peptide or protein also matter, but it is nevertheless possible to predict the behavior of peptides and proteins in these separation methods to a degree which renders such predictions useful. This chapter reviews the topic of using data from separation methods for identification and validation in proteomics, with special emphasis on predicting retention times of tryptic peptides in reversed-phase chromatography under acidic conditions, as this is one of the most commonly used separation methods in proteomics.
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Affiliation(s)
- Alex A Henneman
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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Xie W, Qin X, Teraoka I, Gross RA. Cooperative effect in ion pairing of oligolysine with heptafluorobutyric acid in reversed-phase chromatography. J Chromatogr A 2011; 1218:7765-70. [DOI: 10.1016/j.chroma.2011.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/02/2011] [Accepted: 08/03/2011] [Indexed: 11/26/2022]
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Cao W, Ma D, Kapur A, Patankar MS, Ma Y, Li L. RT-SVR+q: a strategy for post-Mascot analysis using retention time and q value metric to improve peptide and protein identifications. J Proteomics 2011; 75:480-90. [PMID: 21888997 DOI: 10.1016/j.jprot.2011.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 07/31/2011] [Accepted: 08/17/2011] [Indexed: 10/17/2022]
Abstract
Shotgun proteomics commonly utilizes database search like Mascot to identify proteins from tandem MS/MS spectra. False discovery rate (FDR) is often used to assess the confidence of peptide identifications. However, a widely accepted FDR of 1% sacrifices the sensitivity of peptide identification while improving the accuracy. This article details a machine learning approach combining retention time based support vector regressor (RT-SVR) with q value based statistical analysis to improve peptide and protein identifications with high sensitivity and accuracy. The use of confident peptide identifications as training examples and careful feature selection ensures high R values (>0.900) for all models. The application of RT-SVR model on Mascot results (p=0.10) increases the sensitivity of peptide identifications. q Value, as a function of deviation between predicted and experimental RTs (ΔRT), is used to assess the significance of peptide identifications. We demonstrate that the peptide and protein identifications increase by up to 89.4% and 83.5%, respectively, for a specified q value of 0.01 when applying the method to proteomic analysis of the natural killer leukemia cell line (NKL). This study establishes an effective methodology and provides a platform for profiling confident proteomes in more relevant species as well as a future investigation of accurate protein quantification.
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Affiliation(s)
- Weifeng Cao
- Department of Chemistry, University of Wisconsin-Madison, 777 Highland Ave., Madison, WI 53705, USA.
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Schubert B, Oberacher H. Impact of solvent conditions on separation and detection of basic drugs by micro liquid chromatography–mass spectrometry under overloading conditions. J Chromatogr A 2011; 1218:3413-22. [DOI: 10.1016/j.chroma.2011.03.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 03/11/2011] [Accepted: 03/18/2011] [Indexed: 10/18/2022]
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Cecchi T. Retention Mechanism for Ion-Pair Chromatography with Chaotropic Reagents. ADVANCES IN CHROMATOGRAPHY 2011; 49:1-35. [DOI: 10.1201/b10721-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Azarova IN, Kuchkina AY, Baram GI, Goldberg EL. Prediction of peptide retention volumes in gradient reversed phase HPLC. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 34:171-6. [DOI: 10.1134/s1068162008020039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Delporte C, Van Antwerpen P, Zouaoui Boudjeltia K, Noyon C, Abts F, Métral F, Vanhamme L, Reyé F, Rousseau A, Vanhaeverbeek M, Ducobu J, Nève J. Optimization of apolipoprotein-B-100 sequence coverage by liquid chromatography-tandem mass spectrometry for the future study of its posttranslational modifications. Anal Biochem 2010; 411:129-38. [PMID: 21129357 DOI: 10.1016/j.ab.2010.11.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/24/2010] [Accepted: 11/24/2010] [Indexed: 11/18/2022]
Abstract
Proteomic applications have been increasingly used to study posttranslational modifications of proteins (PTMs). For the purpose of identifying and localizing specific but unknown PTMs on huge proteins, improving their sequence coverage is fundamental. Using liquid chromatography coupled to mass spectrometry (LC-MS/MS), peptide mapping of the native apolipoprotein-B-100 was performed to further document the effects of oxidation. Apolipoprotein-B-100 is the main protein of low-density lipoprotein particles and its oxidation could play a role in atherogenesis. Because it is one of the largest human proteins, the sequence recovery rate of apolipoprotein-B-100 only reached 1% when conventional analysis parameters were used. The different steps of the peptide mapping process-from protein treatment to data analysis-were therefore reappraised and optimized. These optimizations allowed a protein sequence recovery rate of 79%, a rate which has never been achieved previously for such a large human protein. The key points for improving peptide mapping were optimization of the data analysis software; peptide separation by LC; sample preparation; and MS acquisition. The new protocol has allowed us to increase by a factor of 4 the detection of modified peptides in apolipoprotein-B-100. This approach could easily be transferred to any study of PTMs using LC-MS/MS.
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Liu C, Wang H, Fu Y, Yuan Z, Chi H, Wang L, Sun R, He S. [Prediction of peptide retention time in reversed-phase liquid chromatography and its application in protein identification]. Se Pu 2010; 28:529-34. [PMID: 20873570 DOI: 10.3724/sp.j.1123.2010.00529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is the mainstream of high throughput protein identification technology. Peptide retention time in reversed-phase liquid chromatography (RPLC) is mainly determined by the physicochemical properties of the peptide and the LC conditions (stationary phase and mobile phase). Retention time can be predicted by analyzing these properties and quantifying their effects on peptide chromatographic behavior. Prediction of peptide retention time in LC can be used to improve identification of peptides and post translational modifications (PTM). There are mainly two methods to predict retention time: i.e., retention coefficients and machine learning. The coefficient of determination between observed and predicted retention times can reach 0.93. With the development of LC-MS technology, retention time prediction will become an important tool to facilitate protein identification.
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Affiliation(s)
- Chao Liu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
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The role of ion-pairing in peak deformations in overloaded reversed-phase chromatography of peptides. J Chromatogr A 2010; 1217:7065-73. [PMID: 20875642 DOI: 10.1016/j.chroma.2010.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 07/07/2010] [Accepted: 09/03/2010] [Indexed: 11/20/2022]
Abstract
The paper reports a study on the role of ion-pairing behind peak deformations, e.g. peak splitting and even peak disappearance, during the elution of a peptide at highly overloaded conditions in reversed-phase chromatography. Deformation of component peaks is not uncommon in chromatography. There are reports which discuss their occurrence, but mostly at analytical scale, while their occurrence is quite common also in the preparative scale, as in the case discussed in this work. This paper first describes the conditions leading to peak splitting and peak disappearance of an industrial peptide, then explains the plausible reasons behind such behaviour, and finally with experimental analysis demonstrates the role of ion-pairing in causing such behaviour.
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Babushok VI, Zenkevich IG. Retention Characteristics of Peptides in RP-LC: Peptide Retention Prediction. Chromatographia 2010. [DOI: 10.1365/s10337-010-1721-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Application of perfluorinated acids as ion-pairing reagents for reversed-phase chromatography and retention-hydrophobicity relationships studies of selected β-blockers. J Chromatogr A 2010; 1217:540-9. [DOI: 10.1016/j.chroma.2009.11.083] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 11/25/2009] [Accepted: 11/26/2009] [Indexed: 11/23/2022]
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Gilar M, Xie H, Jaworski A. Utility of Retention Prediction Model for Investigation of Peptide Separation Selectivity in Reversed-Phase Liquid Chromatography: Impact of Concentration of Trifluoroacetic Acid, Column Temperature, Gradient Slope and Type of Stationary Phase. Anal Chem 2009; 82:265-75. [DOI: 10.1021/ac901931c] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, and 51 Palomino Drive, Franklin, Massachusetts 02038
| | - Hongwei Xie
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, and 51 Palomino Drive, Franklin, Massachusetts 02038
| | - Aleksander Jaworski
- Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, and 51 Palomino Drive, Franklin, Massachusetts 02038
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Chitta KR, Van Meter DS, Stalcup AM. Separation of peptides by HPLC using a surface-confined ionic liquid stationary phase. Anal Bioanal Chem 2009; 396:775-81. [PMID: 19876619 DOI: 10.1007/s00216-009-3228-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 10/05/2009] [Accepted: 10/10/2009] [Indexed: 10/20/2022]
Abstract
A butylimidazolium bromide surface-confined ionic liquid stationary phase was synthesized in-house. The synthesized phase was investigated for the separation of five peptides (Gly-Tyr, Val-Tyr-Val, leucine enkephalin, methionine enkephalin, and angiotensin-II). The peptides were successfully separated in less than 5 min. The effect of trifluoroacetic acid (TFA) on the separation of peptides was evaluated with results confirming that TFA was not acting as ion-pairing agent in separation of peptides on this phase.
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Affiliation(s)
- K R Chitta
- Department of Chemistry, P. O. Box 210172, Cincinnati, OH 45221-0172, USA
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Loeser E, Babiak S. Duplicating the Retention of Cationic Analytes Obtained with Ammonium Formate Mobile Phases when Switching to UV Transparent Mobile Phase Additives in RP-LC. Chromatographia 2009. [DOI: 10.1365/s10337-009-1326-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Retention mechanism for ion-pair chromatography with chaotropic reagents. J Chromatogr A 2009; 1216:1789-97. [DOI: 10.1016/j.chroma.2008.10.031] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/08/2008] [Accepted: 10/10/2008] [Indexed: 11/18/2022]
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Bączek T, Kaliszan R. Predictions of peptides' retention times in reversed-phase liquid chromatography as a new supportive tool to improve protein identification in proteomics. Proteomics 2009; 9:835-47. [DOI: 10.1002/pmic.200800544] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Liu H, Xu B, Ray MK, Shahrokh Z. Peptide mapping with liquid chromatography using a basic mobile phase. J Chromatogr A 2008; 1210:76-83. [DOI: 10.1016/j.chroma.2008.09.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 09/08/2008] [Accepted: 09/11/2008] [Indexed: 10/21/2022]
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Zanella-Cleon I, Becchi M, Lacan P, Giordano PC, Wajcman H, Francina A. Detection of a thalassemic alpha-chain variant (Hemoglobin Groene Hart) by reversed-phase liquid chromatography. Clin Chem 2008; 54:1053-9. [PMID: 18420733 DOI: 10.1373/clinchem.2007.097857] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Hemoglobin (Hb) Groene Hart [alpha119 (H2)Pro-->Ser (alpha1)], also known as Hb Bernalda, is a nondeletional alpha-thalassemic Hb variant that is frequent in southern Italy and North Africa. This variant is not supposed to be produced in the erythrocytes of carriers. The alpha-thalassemic behavior of this variant has been explained as an impaired interaction between the alpha-globin chain and the alpha-Hb-stabilizing protein. METHODS To separate globin chains, we developed a modified reversed-phase liquid chromatography (RPLC) procedure that uses acetonitrile-water solvents containing up to 3 mL/L trifluoroacetic acid. After RPLC, we characterized the isolated globin chains by electrospray ionization (ESI) mass spectrometry (MS) and analyzed their tryptic peptides with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and nano-LC-ESI-MS/MS. RESULTS RPLC detected an abnormal peak with a retention time substantially greater than that of the wild-type alpha(A)-globin chain. We identified this variant as Hb Groene Hart and found it in the hemolysates of 11 unrelated patients (1 homozygote, 9 heterozygotes, and 1 heterozygote associated with the -alpha(3.7) deletion). These patients possessed abnormal hematologic features suggesting an alpha-thalassemia phenotype. Molecular modeling suggested that the increase in hydrophobicity was due to opening of the GH interhelical segment following replacement of amino acid residue 119 with a nonhelix breaker residue. CONCLUSIONS This method allows the detection of Hb variants at low concentrations, and adjusting the composition of the organic solvents enables the method to identify Hb variants with large changes in hydrophobicity.
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Affiliation(s)
- Isabelle Zanella-Cleon
- Institut de Biologie et de Biochimie des Protéines, IFR128, Université Claude Bernard-Lyon I, Lyon, France
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Kim J, Petritis K, Shen Y, Camp DG, Moore RJ, Smith RD. Phosphopeptide elution times in reversed-phase liquid chromatography. J Chromatogr A 2007; 1172:9-18. [PMID: 17935722 PMCID: PMC2096734 DOI: 10.1016/j.chroma.2007.09.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 09/10/2007] [Accepted: 09/14/2007] [Indexed: 11/16/2022]
Abstract
Elution time shifts between 33 different peptides and their corresponding phosphopeptides ranging from 4 amino acid residues to 35 amino acids in length were systematically investigated using high-resolution reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) analysis with trifluoroacetic acid as the ion pairing agent. Observed peptide elution time shifts for a single phosphorylation ranged from -5.28 min (for pYVPML) to +0.59 min (for HRDpSGLLDSLGR). Peptides containing a phosphotyrosine residue displayed a significant decrease in elution time following phosphorylation compared to their similar-sized peptides with phosphoserine or phosphothreonine residues. While peptide phosphorylation generally led to a decrease in the observed elution time, five peptides displayed increased elution times as a result of phosphorylation. For large peptides (> or =18 amino acids), the elution time shifts due to single phosphorylation were limited (ranging between -0.48 and +0.03 min), while the elution time shifts for small peptides (<18 amino acids) were characterized by a larger deviation (ranging between -5.28 and +0.59 min). The predictive capability for the observed RPLC elution time change due to phosphorylation has been suggested, which will aid in assigning confident phosphopeptide identifications and their subsequent confirmation.
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Affiliation(s)
- Jeongkwon Kim
- Environmental Molecular Science Laboratory, MSIN K8-98, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
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Popa TV, Mant CT, Hodges RS. Ion-interaction CZE: the presence of high concentrations of ion-pairing reagents demonstrates the complex mechanisms involved in peptide separations. Electrophoresis 2007; 28:2181-90. [PMID: 17557361 PMCID: PMC2763530 DOI: 10.1002/elps.200600729] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have furthered our understanding of the separative mechanism of a novel CE approach, termed ion-interaction CZE (II-CZE), developed in our laboratory for the resolution of mixtures of cationic peptides. Thus, II-CZE and RP-HPLC were applied to the separation of peptides differing by a single amino acid substitution in 10- and 12-residue synthetic model peptide sequences. Substitutions differed by a wide range of properties or side-chain type (e.g., alkyl side-chains, polar side-chains, etc.) at the substitution site. When carried out in high concentrations (400 mM) of pentafluoropropionic acid (PFPA), II-CZE separated peptides in order of increasing hydrophobicity when the substituted side-chains were of a similar type; when II-CZE was applied to the mixtures of peptides with substitutions of side-chains that differed in the type of functional group, there was no longer a correlation of electrophoretic mobility in II-CZE with relative peptide hydrophobicity, suggesting that a third factor is involved in the separative mechanism beyond charge and hydrophobicity. Interestingly, the hydrophobic PFPA- anion is best for separating peptides that differ in hydrophobicity with hydrophobic side-chains but high concentrations of the hydrophilic H2PO4- anion are best when separating peptides that differ in polar side-chains relative to hydrophobic side-chains. We speculate that differential hydration/dehydration properties of various side-chains in the peptide and the hydration/dehydration properties of the hydrophilic/hydrophobic anions as well as the electrostatic attractions between the peptide and the anions in solution all play a critical role in these solution-based effects.
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Affiliation(s)
- Traian V Popa
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA
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