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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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Pot S, Gstöttner C, Heinrich K, Hoelterhoff S, Grunert I, Leiss M, Bathke A, Domínguez-Vega E. Fast analysis of antibody-derived therapeutics by automated multidimensional liquid chromatography - Mass spectrometry. Anal Chim Acta 2021; 1184:339015. [PMID: 34625261 DOI: 10.1016/j.aca.2021.339015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 12/01/2022]
Abstract
Characterization of post-translational modifications (PTMs) of therapeutic antibodies is commonly performed by bottom-up approaches, involving sample preparation and peptide analysis by liquid chromatography-mass spectrometry (LC-MS). Conventional sample preparation requires extensive hands-on time and can increase the risk of inducing artificial modifications as many off-line steps - denaturation, disulfide-reduction, alkylation and tryptic digestion - are performed. In this study, we developed an on-line multidimensional (mD)-LC-MS bottom-up approach for fast sample preparation and analysis of (formulated) monoclonal antibodies and antibody-derived therapeutics. This approach allows on-column reduction, tryptic digestion and subsequent peptide analysis by RP-MS. Optimization of the 1D -and 2D flow and temperature improved the trapping of small polar peptides during on-line peptide mapping analysis. These adaptations increased the sequence coverage (95-98% versus 86-94% for off-line approaches) and allowed identification of various PTMs (i.e. deamidation of asparagine, methionine oxidation and lysine glycation) within a single analysis. This workflow enables a fast (<2 h) characterization of antibody heterogeneities within a single run and a low amount of protein (10 μg). Importantly, the new mD-LC-MS bottom-up method was able to detect the polar, fast-eluting peptides: Fc oxidation at Hc-Met-252 and the Fc N-glycosylation at Hc-Asn-297, which can be challenging using mD-LC-MS. Moreover, the method showed good comparability across the different measurements (RSD of retention time in the range of 0.2-1.8% for polar peptides). The LC system was controlled by only a standard commercial software package which makes implementation for fast characterization of quality attributes relatively easy.
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Affiliation(s)
- Sanne Pot
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christoph Gstöttner
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Katrin Heinrich
- Pharma Technical Development Europe, Roche Diagnostics GmbH, Penzberg, Germany
| | - Sina Hoelterhoff
- Pharma Technical Development Europe, Hoffmann-La Roche, Basel, Switzerland
| | - Ingrid Grunert
- Pharma Technical Development Europe, Roche Diagnostics GmbH, Penzberg, Germany
| | - Michael Leiss
- Pharma Technical Development Europe, Roche Diagnostics GmbH, Penzberg, Germany
| | - Anja Bathke
- Pharma Technical Development Europe, Hoffmann-La Roche, Basel, Switzerland
| | - Elena Domínguez-Vega
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
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Lee JS, Mitulović G, Panahipour L, Gruber R. Proteomic Analysis of Porcine-Derived Collagen Membrane and Matrix. MATERIALS 2020; 13:ma13225187. [PMID: 33212864 PMCID: PMC7698422 DOI: 10.3390/ma13225187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
Collagen membranes and matrices being widely used in guided bone regeneration and soft tissue augmentation have characteristic properties based on their composition. The respective proteomic signatures have not been identified. Here, we performed a high-resolution shotgun proteomic analysis on two porcine collagen-based biomaterials designed for guided bone regeneration and soft tissue augmentation. Three lots each of a porcine-derived collagen membrane and a matrix derived from peritoneum and/or skin were digested and separated by nano-reverse-phase high-performance liquid chromatography. The peptides were subjected to mass spectrometric detection and analysis. A total of 37 proteins identified by two peptides were present in all collagen membranes and matrices, with 11 and 16 proteins being exclusively present in the membrane and matrix, respectively. The common extracellular matrix proteins include fibrillar collagens (COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL5A3, COL11A2), non-fibrillar collagens (COL4A2, COL6A1, COL6A2, COL6A3, COL7A1, COL16A1, COL22A1), and leucine-rich repeat proteoglycans (DCN, LUM, BGN, PRELP, OGN). The structural proteins vimentin, actin-based microfilaments (ACTB), annexins (ANXA1, ANXA5), tubulins (TUBA1B, TUBB), and histones (H2A, H2B, H4) were also identified. Examples of membrane-only proteins are COL12A1 and COL14A1, and, of matrix only proteins, elastin (ELN). The proteomic signature thus revealed the similarities between but also some individual proteins of collagen membrane and matrix.
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Affiliation(s)
- Jung-Seok Lee
- Department of Oral Biology, School of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (J.-S.L.); (L.P.)
- Department of Periodontology, Research Institute for Periodontal Regeneration, College of Dentistry, Yonsei University, Seoul 03722, Korea
| | - Goran Mitulović
- Proteomics Core Facility, Clinical Institute of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
| | - Layla Panahipour
- Department of Oral Biology, School of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (J.-S.L.); (L.P.)
| | - Reinhard Gruber
- Department of Oral Biology, School of Dentistry, Medical University of Vienna, 1090 Vienna, Austria; (J.-S.L.); (L.P.)
- Proteomics Core Facility, Clinical Institute of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria;
- Department of Periodontology, School of Dental Medicine, University of Bern, 3010 Bern, Switzerland
- Correspondence:
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Bekes K, Mitulović G, Meißner N, Resch U, Gruber R. Saliva proteomic patterns in patients with molar incisor hypomineralization. Sci Rep 2020; 10:7560. [PMID: 32371984 PMCID: PMC7200701 DOI: 10.1038/s41598-020-64614-z] [Citation(s) in RCA: 8] [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: 11/13/2019] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Molar incisor hypomineralization (MIH) is an endemic pediatric disease with an unclear pathogenesis. Considering that saliva controls enamel remineralization and that MIH is associated with higher saliva flow rate, we hypothesized that the protein composition of saliva is linked to disease. To test this, we enrolled 5 children aged 6-14 years with MIH showing at least one hypersensitive molar and 5 caries-free children without hypomineralization. Saliva samples were subjected to proteomic analysis followed by protein classification in to biological pathways. Among 618 salivary proteins identified with high confidence, 88 proteins were identified exclusively in MIH patients and 16 proteins in healthy controls only. Biological pathway analysis classified these 88 patient-only proteins to neutrophil-mediated adaptive immunity, the activation of the classical pathway of complement activation, extracellular matrix degradation, heme scavenging as well as glutathione -and drug metabolism. The 16 controls-only proteins were associated with adaptive immunity related to platelet degranulation and the lysosome. This report suggests that the proteaneous composition of saliva is affected in MIH patients, reflecting a catabolic environment which is linked to inflammation.
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Affiliation(s)
- K Bekes
- Department of Paediatric Dentistry, School of Dentistry, Medical University of Vienna, Vienna, Austria.
| | - G Mitulović
- Proteomics Core Facility, Clinical Institute of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - U Resch
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - R Gruber
- Department of Oral Biology, School of Dentistry, Medical University of Vienna, Vienna, Austria
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
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Pillar array columns for peptide separations in nanoscale reversed-phase chromatography. J Chromatogr A 2019; 1603:426-432. [DOI: 10.1016/j.chroma.2019.06.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 06/13/2019] [Accepted: 06/30/2019] [Indexed: 12/21/2022]
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Abstract
Nano liquid chromatography (nanoLC), with columns having an inner diameter (ID) of ≤100 μm, can provide enhanced sensitivity and enable analysis of limited samples.
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Affiliation(s)
- Steven Ray Wilson
- Department of Chemistry
- University of Oslo
- Oslo
- Norway
- Hybrid Technology Hub-Centre of Excellence
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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Young C, Podtelejnikov AV, Nielsen ML. Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature. J Proteome Res 2017; 16:2307-2317. [DOI: 10.1021/acs.jproteome.6b01055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Clifford Young
- The
Novo Nordisk Foundation Center for Protein Research, Proteomics Program,
Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | | | - Michael L. Nielsen
- The
Novo Nordisk Foundation Center for Protein Research, Proteomics Program,
Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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