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Jadeja S, Karsakov AA, Sklenářová H, Lenčo J. Evaluating C 18 stationary phases with a positively charged surface for proteomic LC-MS applications using mobile phase acidified with reduced formic acid concentration. J Chromatogr A 2024; 1730:465142. [PMID: 39002507 DOI: 10.1016/j.chroma.2024.465142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
We have recently demonstrated the ability of a C18 stationary phase with a positively charged surface (PCS-C18) to provide superior chromatographic separation of peptides using mobile phase acidified with a mere 0.01 % formic acid, significantly improving MS sensitivity. Here, we examined three columns packed with different PCS-C18 phases using the MS-favorable mobile phase acidified with low formic acid concentrations to establish the impact of separation performance and better MS sensitivity on peptide identifications. The surface charge interaction was evaluated using the retention of nitrate. The highest interaction was observed for the AdvanceBio Peptide Plus column. A surface charge-dependent shift in the retention time of peptides was confirmed with a change in formic acid concentration in the mobile phase. The separation performance of the columns with MS-favorable mobile phase acidified with low concentrations of formic acid was evaluated using well-characterized peptides. The loading capacity was assessed using a basic peptide with three lysine residues. Good chromatographic peak shapes and high loading capacity were observed for the Acquity Premier CSH C18 column, even when using a mobile phase acidified with 0.01 % formic acid. The extent of improvement in peptide identification when using reduced formic acid concentration was evaluated by analyzing the tryptic digest of trastuzumab and tryptic digest of whole bacteria cell lysate. Each column provided improved MS signal intensity and peptide identification when using the mobile phase with 0.01 % formic acid. The ability of the Acquity Premier CSH C18 column to provide better separation of peptides, even with a reduced formic acid concentration in the mobile phase, boosted MS signal intensity by 65 % and increased the number of identified peptides from the bacterial sample by 19 %. Our study confirms that significant improvement in the proteomic outputs can be achieved without additional costs only by tailoring the chemistry of the stationary phase to the composition of the mobile phase. Our results can help researchers understand the retention mechanism of peptides on the PCS-C18 stationary phases using low-ionic strength mobile phases and, more importantly, select the best-suited stationary phases for their LC-MS proteomic applications.
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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
| | - Aleksandr A Karsakov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 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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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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Lenčo J, Jadeja S, Naplekov DK, Krokhin OV, Khalikova MA, Chocholouš P, Urban J, Broeckhoven K, Nováková L, Švec F. Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial. J Proteome Res 2022; 21:2846-2892. [PMID: 36355445 DOI: 10.1021/acs.jproteome.2c00407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Denis K Naplekov
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Oleg V Krokhin
- Department of Internal Medicine, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, WinnipegR3E 3P4, Manitoba, Canada
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Petr Chocholouš
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - Jiří Urban
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Ken Broeckhoven
- Department of Chemical Engineering (CHIS), Faculty of Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050Brussel, Belgium
| | - Lucie Nováková
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05Hradec Králové, Czech Republic
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Abstract
INTRODUCTION Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples. AREAS COVERED This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications. EXPERT OPINION Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.
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Affiliation(s)
- Yangyang Bian
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Chunli Gao
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
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Fahrner M, Föll MC, Grüning BA, Bernt M, Röst H, Schilling O. Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. Gigascience 2022; 11:giac005. [PMID: 35166338 PMCID: PMC8848309 DOI: 10.1093/gigascience/giac005] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/26/2021] [Accepted: 01/12/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Data-independent acquisition (DIA) has become an important approach in global, mass spectrometric proteomic studies because it provides in-depth insights into the molecular variety of biological systems. However, DIA data analysis remains challenging owing to the high complexity and large data and sample size, which require specialized software and vast computing infrastructures. Most available open-source DIA software necessitates basic programming skills and covers only a fraction of a complete DIA data analysis. In consequence, DIA data analysis often requires usage of multiple software tools and compatibility thereof, severely limiting the usability and reproducibility. FINDINGS To overcome this hurdle, we have integrated a suite of open-source DIA tools in the Galaxy framework for reproducible and version-controlled data processing. The DIA suite includes OpenSwath, PyProphet, diapysef, and swath2stats. We have compiled functional Galaxy pipelines for DIA processing, which provide a web-based graphical user interface to these pre-installed and pre-configured tools for their use on freely accessible, powerful computational resources of the Galaxy framework. This approach also enables seamless sharing workflows with full configuration in addition to sharing raw data and results. We demonstrate the usability of an all-in-one DIA pipeline in Galaxy by the analysis of a spike-in case study dataset. Additionally, extensive training material is provided to further increase access for the proteomics community. CONCLUSION The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework in combination with extensive training material empowers a broad community of researches to perform reproducible and transparent DIA data analysis.
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Affiliation(s)
- Matthias Fahrner
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 115a, D-79106 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, D-79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19A, D-79104, Germany
| | - Melanie Christine Föll
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 115a, D-79106 Freiburg, Germany
- Khoury College of Computer Sciences, Northeastern University, 440 Huntington Ave, Boston, MA 02115, USA
| | - Björn Andreas Grüning
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Matthias Bernt
- Young Investigators Group Bioinformatics and Transcriptomics, Helmholtz Centre for Environmental Research–UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hannes Röst
- Donnelly Centre, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Straße 115a, D-79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Hugstetter Straße 55, D-79106 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schänzlestraße 18, D-79104 Freiburg, Germany
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6
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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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7
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Uçaktürk E, Başaran AA, Demirel AH. Effect of the Mobile Phase Compositions on the Confirmation Analysis of Some Prohibited Substances in Sport by LC–ESI–MS/MS. Chromatographia 2020. [DOI: 10.1007/s10337-020-03957-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Bollmann UE, Bester K. High-performance liquid chromatography-tandem mass spectrometry with post-column pH modification: Independent pH optimization for chromatographic separation and electrospray ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8844. [PMID: 32458511 DOI: 10.1002/rcm.8844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE In recent environmental research, multi-methods using high-performance liquid chromatography-mass spectrometry (HPLC/MS/MS) have become more and more important for the analysis of organic micropollutants in environmental matrices. As the targeted compounds usually have different physicochemical properties, the optimization of these methods is challenging. METHODS The pH in the electrospray of the mass spectrometer ion source was modified independently of the one used for the HPLC separation, using a post-column HPLC flow to make the spray acidic or alkaline. The method development was carried out manually in a systematic multistep way. RESULTS The method used for the analysis of organic biocides (e.g., terbutryn, propiconazole, and isothiazolinones) was optimized. It was shown that the use of a neutral as well as an acidified gradient could not be optimized for all target compounds, whereas a neutral gradient with post-column acidification was optimum for all target compounds. CONCLUSIONS Acidic or alkaline post-column infusion allows pH optimization for ionization conditions, independent of the pH optimization for chromatographic separation. The introduction of an additional modifier might also allow the minimization of matrix effects or directed formation of sodium adducts, without affecting the chromatographic separation.
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Affiliation(s)
- Ulla E Bollmann
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Kai Bester
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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9
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Gangnus T, Burckhardt BB. Improving sensitivity for the targeted LC-MS/MS analysis of the peptide bradykinin using a design of experiments approach. Talanta 2020; 218:121134. [PMID: 32797891 DOI: 10.1016/j.talanta.2020.121134] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
The nonapeptide bradykinin is endogenously present only in low picomolar plasma concentrations, subsequently making reliable detection using liquid chromatography coupled to mass spectrometry (LC-MS/MS) challenging. Furthermore, non-specific adsorption during sample preparation and storage can lead to unpredictable peptide losses. To overcome these issues, a design of experiments (DoE) approach was applied, which consisted of a screening to identify impacting factors, optimisation and confirmation runs. On the one hand, different injection solvent compositions and sample collection materials were investigated in order to decrease non-specific adsorption. On the other hand, the addition of modifiers, which are known to enhance the signal intensity in LC-MS/MS, to the chromatographic mobile phase was examined. Polypropylene was the most suitable material among those investigated and resulted in a factor increase of 12.0 compared to LC-MS glass. The advantages of protein low-binding polypropylene versus standard polypropylene were fully compensated by the optimisation of the injection solvent. The latter substantially contributed to a decrease of non-specific adsorption of bradykinin. In this regard, bradykinin further benefitted from an organic fraction and a high amount of formic acid. Based on the DoE results, the final optimised injection solvent-consisting of 8.7% formic acid in 49.4/5.3/36.6 water/methanol/dimethyl sulfoxide (v/v/v)-was established. Furthermore, optimisation of the mobile phase composition yielded a signal intensity increase by a factor of 7.7. The transferability of the optimisation results conducted in neat solutions were successfully confirmed in human plasma. The applicability of this approach was further supported by the successful determination of low-abundance endogenous bradykinin levels in human plasma using LC-MS/MS.
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Affiliation(s)
- Tanja Gangnus
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University Dusseldorf, Universitaetsstr. 1, 40225, Dusseldorf, Germany.
| | - Bjoern B Burckhardt
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University Dusseldorf, Universitaetsstr. 1, 40225, Dusseldorf, Germany.
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10
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Distler U, Łącki MK, Schumann S, Wanninger M, Tenzer S. Enhancing Sensitivity of Microflow-Based Bottom-Up Proteomics through Postcolumn Solvent Addition. Anal Chem 2019; 91:7510-7515. [PMID: 31117400 DOI: 10.1021/acs.analchem.9b00118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The introduction of more sensitive mass spectrometers allows researchers to adapt front-end liquid chromatography (LC) to individual needs for the analysis of complex proteomes. Where absolute sensitivity is not paramount, it is advantageous to switch from a highly sensitive nanoflow-LC setup, the de facto standard platform in mass-spectrometry (MS)-based discovery proteomics, to a more robust, high-throughput-compatible microflow or conventional-flow setup. To enhance the microflow-LC-MS electrospray process of complex proteomic samples, we tested the effects of different solvents, including 2-propanol, methanol, and acetonitrile, pure or as mixture with dimethyl sulfoxide, which were added postcolumn to the eluting sample. Postcolumn addition of organic solvents strongly enhanced the electrospray efficiency in microflow-LC-MS experiments and improved the sensitivity across the entire gradient and for early eluting peptides by up to 10-fold. Postcolumn solvent addition did not negatively affect chromatographic performance and resulted in an overall 28-36% increase in identifications at both the protein and peptide levels. The presented microflow-LC-MS workflow, including postcolumn solvent addition, can be easily adopted on any LC-MS/MS platform.
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Affiliation(s)
- Ute Distler
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany.,Focus Program Translational Neuroscience (FTN) , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
| | - Mateusz Krzysztof Łącki
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
| | - Sven Schumann
- Institute of Anatomy , Otto von Guericke University Magdeburg , Magdeburg 39120 , Germany
| | - Markus Wanninger
- Waters Corporation , Milford , Massachusetts 01757 , United States
| | - Stefan Tenzer
- Institute of Immunology , University Medical Center of the Johannes-Gutenberg University Mainz , Mainz 55131 , Germany
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11
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Judák P, Van Eenoo P, Deventer K. Urinary matrix effects in electrospray ionization mass spectrometry in the presence of DMSO. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1018-1021. [PMID: 29952038 DOI: 10.1002/jms.4255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Péter Judák
- Department of Clinical Chemistry, Microbiology and Immunology, Doping Control Laboratory, Ghent University, Zwijnaarde, Belgium
| | - Peter Van Eenoo
- Department of Clinical Chemistry, Microbiology and Immunology, Doping Control Laboratory, Ghent University, Zwijnaarde, Belgium
| | - Koen Deventer
- Department of Clinical Chemistry, Microbiology and Immunology, Doping Control Laboratory, Ghent University, Zwijnaarde, Belgium
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12
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Ammonium hydroxide enhancing electrospray response and boosting sensitivity of bisphenol A and its analogs. Talanta 2018; 182:590-594. [DOI: 10.1016/j.talanta.2018.02.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/05/2018] [Accepted: 02/07/2018] [Indexed: 11/23/2022]
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13
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Kelstrup CD, Bekker-Jensen DB, Arrey TN, Hogrebe A, Harder A, Olsen JV. Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics. J Proteome Res 2017; 17:727-738. [DOI: 10.1021/acs.jproteome.7b00602] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian D. Kelstrup
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
| | - Dorte B. Bekker-Jensen
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
| | - Tabiwang N. Arrey
- Thermo Fisher Scientific, Hanna-Kunath-Straße
11, Bremen 28199, Germany
| | - Alexander Hogrebe
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
| | - Alexander Harder
- Thermo Fisher Scientific, Hanna-Kunath-Straße
11, Bremen 28199, Germany
| | - Jesper V. Olsen
- The
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen 2200, Denmark
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14
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Hermans J, Ongay S, Markov V, Bischoff R. Physicochemical Parameters Affecting the Electrospray Ionization Efficiency of Amino Acids after Acylation. Anal Chem 2017; 89:9159-9166. [PMID: 28737384 PMCID: PMC5588090 DOI: 10.1021/acs.analchem.7b01899] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Electrospray
ionization (ESI) is widely used in liquid chromatography
coupled to mass spectrometry (LC–MS) for the analysis of biomolecules.
However, the ESI process is still not completely understood, and it
is often a matter of trial and error to enhance ESI efficiency and,
hence, the response of a given set of compounds. In this work we performed
a systematic study of the ESI response of 14 amino acids that were
acylated with organic acid anhydrides of increasing chain length and
with poly(ethylene glycol) (PEG) changing certain physicochemical
properties in a predictable manner. By comparing the ESI response
of 70 derivatives, we found that there was a strong correlation between
the calculated molecular volume and the ESI response, while correlation
with hydrophobicity (log P values), pKa, and the inverse calculated surface tension was significantly
lower although still present, especially for individual derivatized
amino acids with increasing acyl chain lengths. Acylation with PEG
containing five ethylene glycol units led to the largest gain in ESI
response. This response was maximal independent of the calculated
physicochemical properties or the type of amino acid. Since no actual
physicochemical data is available for most derivatized compounds,
the responses were also used as input for a quantitative structure–property
relationship (QSPR) model to find the best physicochemical descriptors
relating to the ESI response from molecular structures using the amino
acids and their derivatives as a reference set. A topological descriptor
related to molecular size (SPAN) was isolated next to a descriptor
related to the atomic composition and structural groups (BIC0). The
validity of the model was checked with a test set of 43 additional
compounds that were unrelated to amino acids. While prediction was
generally good (R2 > 0.9), compounds
containing
halogen atoms or nitro groups gave a lower predicted ESI response.
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Affiliation(s)
- Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Sara Ongay
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Vadym Markov
- Department of Chemical Metrology, Kharkov V. N. Karazin National University , Svoboda Square 4, 61022 Kharkov, Ukraine
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
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