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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Naplekov DK, Bárta P, Trejtnar F, Sklenářová H, Lenčo J. Implementing reversed-phase and hydrophilic interaction liquid chromatography into the characterization of DTPA-ramucirumab conjugate before radiolabeling. J Pharm Biomed Anal 2023; 235:115615. [PMID: 37566949 DOI: 10.1016/j.jpba.2023.115615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023]
Abstract
Radioimmunoconjugates represent a promising class of therapeutics and diagnostics. The characterization of intermediate chelator-antibody products, i.e., without the radionuclide, is frequently omitted, bringing significant uncertainty in the radioimmunoconjugate preparation. In the present study, we explored the utility of reversed-phase (RPLC) and hydrophilic interaction (HILIC) liquid chromatography with UV detection to characterize ramucirumab stochastically conjugated with p-SCN-Bn-CHX-A"-DTPA chelator (shortly DTPA). The conjugation was well reflected in RPLC chromatograms, while chromatograms from HILIC were significantly less informative. RPLC analyses at the intact level confirmed that the conjugation resulted in a heterogeneous mixture of modified ramucirumab. Moreover, the RPLC of DTPA-ramucirumab confirmed heterogeneous conjugation of all subunits. The peptide mapping did not reveal substantial changes after the conjugation, indicating that most parts of ramucirumab molecules remained unmodified and that the DTPA chelator was bound to various sites. Eventually, the RPLC method for analysis of intact ramucirumab was successfully applied to online monitoring of conjugation reaction in 1 h intervals for a total of 24 h synthesis, which readily reflected the structural changes of ramucirumab in the form of retention time shift by 0.21 min and increase in peak width by 0.22 min. The results were obtained in real-time, practically under 10 min per monitoring cycle. To the best of our knowledge, our study represents the first evaluation of RPLC and HILIC to assess the quality of intermediates during the on-site preparation of radioimmunoconjugates prior to radiolabeling.
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Affiliation(s)
- Denis K Naplekov
- Charles University, Faculty of Pharmacy in Hradec Kralove, Department of Analytical Chemistry, Akademika Heyrovskeho 1203/8, 500 05 Hradec Kralove, Czech Republic
| | - Pavel Bárta
- Charles University, Faculty of Pharmacy in Hradec Kralove, Department of Biophysics and Physical Chemistry, Akademika Heyrovskeho 1203/8, 500 05 Hradec Kralove, Czech Republic
| | - František Trejtnar
- Charles University, Faculty of Pharmacy in Hradec Kralove, Department of Pharmacology and Toxicology, Akademika Heyrovskeho 1203/8, 500 05 Hradec Kralove, Czech Republic
| | - Hana Sklenářová
- Charles University, Faculty of Pharmacy in Hradec Kralove, Department of Analytical Chemistry, Akademika Heyrovskeho 1203/8, 500 05 Hradec Kralove, Czech Republic
| | - Juraj Lenčo
- Charles University, Faculty of Pharmacy in Hradec Kralove, Department of Analytical Chemistry, Akademika Heyrovskeho 1203/8, 500 05 Hradec Kralove, Czech Republic.
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Naplekov D, Jadeja S, Fučíková AM, Švec F, Sklenářová H, Lenčo J. Easy, Robust, and Repeatable Online Acid Cleavage of Proteins in Mobile Phase for Fast Quantitative LC-MS Bottom-Up Protein Analysis─Application for Ricin Detection. Anal Chem 2023; 95:12339-12348. [PMID: 37565982 PMCID: PMC10448442 DOI: 10.1021/acs.analchem.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Sample preparation involving the cleavage of proteins into peptides is the first critical step for successful bottom-up proteomics and protein analyses. Time- and labor-intensiveness are among the bottlenecks of the commonly used methods for protein sample preparation. Here, we report a fast online method for postinjection acid cleavage of proteins directly in the mobile phase typically used for LC-MS analyses in proteomics. The chemical cleavage is achieved in 0.1% formic acid within 35 s in a capillary heated to 195 °C installed upstream of the analytical column, enabling the generated peptides to be separated. The peptides generated by the optimized method covered the entire sequence except for one amino acid of trastuzumab used for the method development. The qualitative results are extraordinarily stable, even over a long period of time. Moreover, the method is also suitable for accurate and repeatable quantification. The procedure requires only one manual step, significantly decreasing sample transfer losses. To demonstrate its practical utility, we tested the method for the fast detection of ricin. Ricin can be unambiguously identified from an injection of 10 ng, and the results can be obtained within 7-8 min after receiving a suspicious sample. Because no sophisticated accessories and no additional reagents are needed, the method can be seamlessly transferred to any laboratory for high-throughput proteomic workflows.
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Affiliation(s)
- Denis
K. Naplekov
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Siddharth Jadeja
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Alena Myslivcová Fučíková
- Department
of Biology, Faculty of Science, University
of Hradec Králové, Hradecká 1285, 500 03 Hradec Králové, Czech Republic
| | - František Švec
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Juraj Lenčo
- Department
of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Lenčo J, Šemlej T, Khalikova MA, Fabrik I, Švec F. Sense and Nonsense of Elevated Column Temperature in Proteomic Bottom-up LC-MS Analyses. J Proteome Res 2020; 20:420-432. [PMID: 33085896 DOI: 10.1021/acs.jproteome.0c00479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Elevated column temperature represents a simple means for improving chromatographic separation of peptides. Here, we demonstrated the advantages of the column temperature in peptide separation using state-of-the-art columns. More importantly, we also determined how temperature can impair proteomic bottom-up analyses. We found that an elevated temperature in combination with the acidic pH of the mobile phase induced in-column peptide hydrolysis with high specificity to Asp and accelerated five modification reactions of amino acids. The positive effects of temperature dominated in the 30 min long gradients since the column operated at 90 °C provided the largest number of identified peptides and proteins. However, the adverse effects of temperature on peptide integrity in longer liquid chromatography-mass spectrometry (LC-MS) analyses required its reduction to obtain optimum results. The largest number of peptides was identified using the column maintained at 75 °C in 60 min long gradients, at 60 °C in 120 min long gradients, and at 45 °C in 240 min long gradients. Our results indicate that no universal column temperature exists for bottom-up LC-MS analyses. Quite the contrary, the temperature setting must be selected rationally to exploit the full capabilities of the state-of-the-art mass spectrometers in proteomic LC-MS analyses, with the gradient time being a critical factor.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Tomáš Šemlej
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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Hallingström M, Zedníková P, Tambor V, Barman M, Vajrychová M, Lenčo J, Viklund F, Tancred L, Rabe H, Jonsson D, Kachikis A, Nilsson S, Kacerovský M, Adams Waldorf KM, Jacobsson B. Mid-trimester amniotic fluid proteome's association with spontaneous preterm delivery and gestational duration. PLoS One 2020; 15:e0232553. [PMID: 32379834 PMCID: PMC7205297 DOI: 10.1371/journal.pone.0232553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/16/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Amniotic fluid is clinically accessible via amniocentesis and its protein composition may correspond to birth timing. Early changes in the amniotic fluid proteome could therefore be associated with the subsequent development of spontaneous preterm delivery. OBJECTIVE The main objective of this study was to perform unbiased proteomics analysis of the association between mid-trimester amniotic fluid proteome and spontaneous preterm delivery and gestational duration, respectively. A secondary objective was to validate and replicate the findings by enzyme-linked immunosorbent assay using a second independent cohort. METHODS Women undergoing a mid-trimester genetic amniocentesis at Sahlgrenska University Hospital/Östra between September 2008 and September 2011 were enrolled in this study, designed in three analytical stages; 1) an unbiased proteomic discovery phase using LC-MS analysis of 22 women with subsequent spontaneous preterm delivery (cases) and 37 women who delivered at term (controls), 2) a validation phase of proteins of interest identified in stage 1, and 3) a replication phase of the proteins that passed validation using a second independent cohort consisting of 20 cases and 40 matched controls. RESULTS Nine proteins were nominally significantly associated with both spontaneous preterm delivery and gestational duration, after adjustment for gestational age at sampling, but none of the proteins were significant after correction for multiple testing. Several of these proteins have previously been described as being associated with spontaneous PTD etiology and six of them were thus validated using enzyme linked immunosorbent assay. Two of the proteins passed validation; Neutrophil gelatinase-associated lipocalin and plasminogen activator inhibitor 1, but the results could not be replicated in a second cohort. CONCLUSIONS Neutrophil gelatinase-associated lipocalin and Plasminogen activator inhibitor 1 are potential biomarkers of spontaneous preterm delivery and gestational duration but the findings could not be replicated. The negative findings are supported by the fact that none of the nine proteins from the exploratory phase were significant after correction for multiple testing.
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Affiliation(s)
- Maria Hallingström
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Petra Zedníková
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Biological and Biochemical Science, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Vojtěch Tambor
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Malin Barman
- Department of Biology and Biological Engineering, Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czech Republic
| | - Juraj Lenčo
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic
| | - Felicia Viklund
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Stockholm South General Hospital, Stockholm, Sweden
| | - Linda Tancred
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Biobank Väst, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hardis Rabe
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Jonsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alisa Kachikis
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Marian Kacerovský
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
- Department of Obstetrics and Gynecology, Charles University in Prague, Faculty of Medicine in Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kristina M. Adams Waldorf
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Maria A. Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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Lenčo J, Vajrychová M, Pimková K, Prokšová M, Benková M, Klimentová J, Tambor V, Soukup O. Conventional-Flow Liquid Chromatography-Mass Spectrometry for Exploratory Bottom-Up Proteomic Analyses. Anal Chem 2018; 90:5381-5389. [PMID: 29582996 DOI: 10.1021/acs.analchem.8b00525] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Due to its sensitivity and productivity, bottom-up proteomics based on liquid chromatography-mass spectrometry (LC-MS) has become the core approach in the field. The de facto standard LC-MS platform for proteomics operates at sub-μL/min flow rates, and nanospray is required for efficiently introducing peptides into a mass spectrometer. Although this is almost a "dogma", this view is being reconsidered in light of developments in highly efficient chromatographic columns, and especially with the introduction of exceptionally sensitive MS instruments. Although conventional-flow LC-MS platforms have recently penetrated targeted proteomics successfully, their possibilities in discovery-oriented proteomics have not yet been thoroughly explored. Our objective was to determine what are the extra costs and what optimization and adjustments to a conventional-flow LC-MS system must be undertaken to identify a comparable number of proteins as can be identified on a nanoLC-MS system. We demonstrate that the amount of a complex tryptic digest needed for comparable proteome coverage can be roughly 5-fold greater, providing the column dimensions are properly chosen, extra-column peak dispersion is minimized, column temperature and flow rate are set to levels appropriate for peptide separation, and the composition of mobile phases is fine-tuned. Indeed, we identified 2 835 proteins from 2 μg of HeLa cells tryptic digest separated during a 60 min gradient at 68 μL/min on a 1.0 mm × 250 mm column held at 55 °C and using an aqua-acetonitrile mobile phases containing 0.1% formic acid, 0.4% acetic acid, and 3% dimethyl sulfoxide. Our results document that conventional-flow LC-MS is an attractive alternative for bottom-up exploratory proteomics.
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Affiliation(s)
- Juraj Lenčo
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic.,Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic.,Department of Analytical Chemistry, Faculty of Pharmacy , Charles University in Prague , Heyrovského 1203 , 500 05 Hra-dec Králové , Czech Republic
| | - Marie Vajrychová
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic.,Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic
| | - Kristýna Pimková
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
| | - Magdaléna Prokšová
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic
| | - Markéta Benková
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
| | - Jana Klimentová
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences , University of Defence , Třebešská 1575 , 500 01 Hradec Králové , Czech Republic
| | - Vojtěch Tambor
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
| | - Ondřej Soukup
- Biomedical Research Center , University Hospital Hradec Králové , Sokolská 581 , 500 05 Hradec Králové , Czech Republic
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9
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Procházková I, Lenčo J, Fučíková A, Dresler J, Čápková L, Hrstka R, Nenutil R, Bouchal P. Targeted proteomics driven verification of biomarker candidates associated with breast cancer aggressiveness. Biochim Biophys Acta Proteins Proteom 2017; 1865:488-498. [PMID: 28216224 DOI: 10.1016/j.bbapap.2017.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/07/2017] [Accepted: 02/15/2017] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most common and molecularly relatively well characterized malignant disease in women, however, its progression to metastatic cancer remains lethal for 78% of patients 5years after diagnosis. Novel markers could identify the high risk patients and their verification using quantitative methods is essential to overcome genetic, inter-tumor and intra-tumor variability and translate novel findings into cancer diagnosis and treatment. We recently identified 13 proteins associated with estrogen receptor, tumor grade and lymph node status, the key factors of breast cancer aggressiveness, using untargeted proteomics. Here we verified these findings in the same set of 96 tumors using targeted proteomics based on selected reaction monitoring with mTRAQ labeling (mTRAQ-SRM), transcriptomics and immunohistochemistry and validated in 5 independent sets of 715 patients using transcriptomics. We confirmed: (i) positive association of anterior gradient protein 2 homolog (AGR2) and periostin (POSTN) and negative association of annexin A1 (ANXA1) with estrogen receptor status; (ii) positive association of stathmin (STMN1), cofilin-1 (COF1), plasminogen activator inhibitor 1 RNA-binding protein (PAIRBP1) and negative associations of thrombospondin-2 (TSP2) and POSTN levels with tumor grade; and (iii) positive association of POSTN, alpha-actinin-4 (ACTN4) and STMN1 with lymph node status. This study highlights a panel of gene products that can contribute to breast cancer aggressiveness and metastasis, the understanding of which is important for development of more precise breast cancer treatment.
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Affiliation(s)
- Iva Procházková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic; Masaryk University, Faculty of Science, Department of Biochemistry, Kotlarska 2, 61137 Brno, Czech Republic
| | - Juraj Lenčo
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic
| | - Alena Fučíková
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic
| | - Jiří Dresler
- University of Defence, Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; Military Health Institute, Tychonova 1, 160 00 Prague, Czech Republic
| | - Lenka Čápková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic; Masaryk University, Faculty of Science, Department of Biochemistry, Kotlarska 2, 61137 Brno, Czech Republic
| | - Roman Hrstka
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Rudolf Nenutil
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic
| | - Pavel Bouchal
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Zluty kopec 7, 65653 Brno, Czech Republic; Masaryk University, Faculty of Science, Department of Biochemistry, Kotlarska 2, 61137 Brno, Czech Republic.
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Lenčo J, Lenčová-Popelová O, Link M, Jirkovská A, Tambor V, Potůčková E, Stulík J, Šimůnek T, Štěrba M. Proteomic investigation of embryonic rat heart-derived H9c2 cell line sheds new light on the molecular phenotype of the popular cell model. Exp Cell Res 2015; 339:174-86. [DOI: 10.1016/j.yexcr.2015.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 01/15/2023]
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11
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Dvořáková M, Jeřábková J, Procházková I, Lenčo J, Nenutil R, Bouchal P. Transgelin is upregulated in stromal cells of lymph node positive breast cancer. J Proteomics 2015; 132:103-11. [PMID: 26639304 DOI: 10.1016/j.jprot.2015.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/12/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022]
Abstract
UNLABELLED Transgelin and transgelin-2 have been discussed as potential markers of various cancers. Here we identified increased transgelin level in lymph node positive vs. negative, low grade primary breast cancer tissues using 2-DE in the cohort of 12 patients. We further clinically validated 2-DE results in an independent cohort of 48 low grade breast cancer patients through untargeted and targeted proteomics analysis (iTRAQ-2D-LC-MS/MS, mTRAQ-SRM), at transcript level and using immunohistochemistry. Another group of 48 high grade tumors of different breast cancer subtypes was analyzed together with the low grade samples to test transgelin specificity for low grade tumors and to study transgelin relation to known molecular markers and histological features. The results confirmed transgelin connection with the lymph node metastasis. As a marker of a reactive tumor stroma, transgelin can be connected with the higher risk of metastasis development. Moreover, we observed significant down-regulation of transgelin in high vs. low grade tumors caused by decreased content of stromal cells (mainly expressing transgelin) in high grade tumor tissue. We also analyzed expression of transgelin-2 in the second cohort using proteomics and immunohistochemistry. Transgelin-2 was mainly expressed by epithelial cancer cells and its levels were increased in metastatic and poorly differentiated tumors. BIOLOGICAL SIGNIFICANCE Both transgelin and transgelin-2 have been previously described as potential markers of many types of cancer. We are specifying this connection to metastatic affection of lymph nodes and cell differentiation in breast cancer. In the wider context, the results of our study highlight tumor stroma as a source of cancer biomarkers and point out how measured levels of tissue markers can actually reflect cellular feature of cancer mass.
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Affiliation(s)
- Monika Dvořáková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jarmila Jeřábková
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Iva Procházková
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic
| | - Juraj Lenčo
- Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czech Republic
| | - Rudolf Nenutil
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic
| | - Pavel Bouchal
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Brno, Czech Republic; Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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12
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Abstract
Ceramides with ultralong chains (≥30 carbons), also known as acylceramides, play a critical role in the survival of mammals on dry land. An efficient and scalable synthesis of four major classes of ultralong human skin ceramides is reported. The key approach involves the use of a succinimidyl ester that acts as a protective group, helps overcome the extremely low solubility, and simultaneously activates the fatty acid for its clean and high-yielding attachment to a sphingoid base.
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Affiliation(s)
- Lukáš Opálka
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic
| | - Andrej Kováčik
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic
| | - Michaela Sochorová
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic
| | - Jiří Kuneš
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic
| | - Juraj Lenčo
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic.,Faculty of Military Health Sciences, University of Defense , Hradec Králové 500 00, Czech Republic
| | - Kateřina Vávrová
- Faculty of Pharmacy in Hradec Králové, Charles University in Prague , Hradec Králové 500 05, Czech Republic
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Andrýs R, Zemanová L, Lenčo J, Bílková Z, Wsól V. Carbonyl-reducing enzymes as targets of a drug-immobilised affinity carrier. Chem Biol Interact 2015; 234:169-77. [PMID: 25595226 DOI: 10.1016/j.cbi.2015.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/20/2014] [Accepted: 01/02/2015] [Indexed: 01/21/2023]
Abstract
Proteins, peptides and nucleic acids are commonly isolated and purified in almost all bioscience laboratories. Methods based on molecular recognition are currently the most powerful tool in separation processes due to their selectivity and recovery. The aim of this study was to prove the versatility and the ability of an affinity carrier containing the immobilised ligand oracin (previously developed by our workgroup) to selectively bind carbonyl-reducing enzymes. These enzymes play an important role in metabolic pathways of various endogenic compounds and xenobiotics. Many important drugs, such as doxorubicin, daunorubicin, haloperidol and the model anticancer drug oracin, are metabolised by carbonyl-reducing enzymes. The functionality of the presented carrier was demonstrated with pure recombinant enzymes (AKR1A1, AKR1B1, AKR1B10, AKR1C1, AKR1C2, AKR1C3, AKR1C4, CBR1 and CBR3) as well as with two model biological samples (cell extract from genetically modified Escherichia coli and pre-purified human liver cytosol). Enzymes that show an affinity toward oracin were efficiently captured, gently eluted using 150 mM ammonium hydroxide and subsequently identified by MS. The method is highly selective and robust and may be applied to the purification and identification of various carbonyl-reducing enzymes from any biological sample.
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Affiliation(s)
- Rudolf Andrýs
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University in Prague, Heyrovského 1203, Hradec Králové 500 05, Czech Republic.
| | - Lucie Zemanová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University in Prague, Heyrovského 1203, Hradec Králové 500 05, Czech Republic.
| | - Juraj Lenčo
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University in Prague, Heyrovského 1203, Hradec Králové 500 05, Czech Republic; Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence, Třebešská 1575, Hradec Králové 500 01, Czech Republic.
| | - Zuzana Bílková
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, Pardubice 532 10, Czech Republic.
| | - Vladimír Wsól
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University in Prague, Heyrovského 1203, Hradec Králové 500 05, Czech Republic.
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14
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Novakova V, Hladík P, Filandrová T, Zajícová I, Krepsová V, Miletin M, Lenčo J, Zimcik P. Structural factors influencing the intramolecular charge transfer and photoinduced electron transfer in tetrapyrazinoporphyrazines. Phys Chem Chem Phys 2014; 16:5440-6. [PMID: 24509513 DOI: 10.1039/c3cp54731k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A series of unsymmetrical tetrapyrazinoporphyrazines (TPyzPzs) from the group of azaphthalocyanines with one peripherally attached amino substituent (donor) were synthesized, and their photophysical properties (fluorescence quantum yield and singlet oxygen quantum yield) were determined. The synthesized TPyzPzs were expected to undergo intramolecular charge transfer (ICT) as the main pathway for deactivating their excited states. Several structural factors were found to play a critical role in ICT efficiency. The substituent in the ortho position to the donor center significantly influences the ICT, with tert-butylsulfanyl and butoxy substituents inducing the strongest ICTs, whereas chloro, methyl, phenyl, and hydrogen substituents in this position reduce the efficiency. The strength of the donor positively influences the ICT efficiency and correlates well with the oxidation potential of the amines used as the substituents on the TPyzPz as follows: n-butylamine < N,N-diethylamine < aniline < phenothiazine. The ICT (with conjugated donors and acceptors) in the TPyzPz also proved to be much stronger than a photoinduced electron transfer in which the donor and the acceptor are connected through an aliphatic linker.
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Affiliation(s)
- Veronika Novakova
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague, Heyrovskeho 1203, 50005, Hradec Kralove, Czech Republic.
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Novakova V, Miletin M, Filandrová T, Lenčo J, Růžička A, Zimcik P. Role of steric hindrance in the Newman-Kwart rearrangement and in the synthesis and photophysical properties of arylsulfanyl tetrapyrazinoporphyrazines. J Org Chem 2014; 79:2082-93. [PMID: 24548285 DOI: 10.1021/jo402791c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Conditions for the Newman-Kwart rearrangement of phenols into thiophenols were investigated in relation to the bulkiness of substituents at the 2 and 6 positions of the starting phenol derivative with an emphasis on eliminating side reactions. Thiophenols with different 2,6-disubstitution patterns (including hydrogen, methyl, isopropyl or tert-butyl groups) were used for the synthesis of 5,6-bis(arylsulfanyl)pyrazine-2,3-dicarbonitriles that underwent cyclotetramerization leading to the corresponding zinc tetrapyrazinoporphyrazines (TPyzPz), aza-analogues of phthalocyanines. Several methods for the cyclotetramerization were attempted to eliminate problematic side reactions. Magnesium butoxide was found as the most suitable cyclotetramerization agent and afforded TPyzPzs in reasonable yields of approximately 30% under mild conditions. The varying arrangements of the peripheral substitutions resulting from the different bulkiness of the substituents were demonstrated by the X-ray structures of the pyrazine-2,3-dicarbonitriles. The prepared zinc arylsulfanyl TPyzPzs showed an absorption maximum at a Q-band over 650 nm, fluorescence quantum yields between 0.078 and 0.20, and singlet oxygen quantum yields ranging 0.58-0.69. TPyzPzs with isopropyl groups were found to be the best derivatives in this series as they combined facile cyclotetramerization, no aggregation, and good photophysical properties, which makes them potentially suitable for photodynamic therapy.
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Affiliation(s)
- Veronika Novakova
- Department of Biophysics and Physical Chemistry, ‡Department of Pharmaceutical Chemistry and Drug Control, and ⊥Department of Biochemical Sciences, Faculty of Pharmacy, Faculty of Pharmacy in Hradec Kralove, Charles University in Prague , Heyrovskeho 1203, 500 05, Hradec Kralove, Czech Republic
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Hartmanová T, Tambor V, Lenčo J, Staab-Weijnitz CA, Maser E, Wsól V. S-Nitrosoglutathione covalently modifies cysteine residues of human carbonyl reductase 1 and affects its activity. Chem Biol Interact 2013; 202:136-45. [DOI: 10.1016/j.cbi.2012.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 01/23/2023]
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17
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Štěrba M, Popelová O, Lenčo J, Fučíková A, Brčáková E, Mazurová Y, Jirkovský E, Šimůnek T, Adamcová M, Mičuda S, Stulík J, Geršl V. Proteomic insights into chronic anthracycline cardiotoxicity. J Mol Cell Cardiol 2011; 50:849-62. [DOI: 10.1016/j.yjmcc.2011.01.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 01/19/2011] [Accepted: 01/20/2011] [Indexed: 10/18/2022]
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