1
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Jia C, Li F, Li A, Li Q, Huang L. Study of the Enantioselectivity and Recognition Mechanism of Allyl-β-CD Modified Organic Polymer Monolithic Capillary Column. Chirality 2024; 36:e23697. [PMID: 38982739 DOI: 10.1002/chir.23697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/16/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024]
Abstract
Allyl-β-CD was synthesized and used as the chiral functional monomer to prepare chiral organic polymer monolithic columns in capillary HPLC. First, the enantioselectivity of the prepared allyl-β-CD modified organic polymer monolithic capillary columns was investigated. Then, the influences of enantioseparation conditions of chiral drugs were further explored. Finally, the recognition mechanism was studied by molecular docking with AutoDock. Complete enantioseparations of four chiral drugs as well as partial enantioseparations of eight chiral drugs have been achieved. Results showed that the RSD values for run-to-run, day-to-day, and column-to-column variations ranged from 1.2% to 4.6%, 1.4% to 4.7%, and 2.0% to 6.1%, respectively. The enantioselectivity factor rather than resolution is correlated with the binding free energy difference between enantiomers with allyl-β-CD. Furthermore, the abundant ether bonds, hydroxyl groups, and hydrophobic cavities in cyclodextrin are responsible for the enantioseparation ability of the chiral monolithic capillary columns.
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Affiliation(s)
- Chaoheng Jia
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
- College of Materials and Chemical Engineering, Fujian Provincial University Engineering Research Center of Green Materials and Chemical Engineering, Minjiang University, Fuzhou, China
| | - Futao Li
- College of Materials and Chemical Engineering, Fujian Provincial University Engineering Research Center of Green Materials and Chemical Engineering, Minjiang University, Fuzhou, China
| | - Anqi Li
- College of Materials and Chemical Engineering, Fujian Provincial University Engineering Research Center of Green Materials and Chemical Engineering, Minjiang University, Fuzhou, China
| | - Qiwen Li
- College of Materials and Chemical Engineering, Fujian Provincial University Engineering Research Center of Green Materials and Chemical Engineering, Minjiang University, Fuzhou, China
| | - Lu Huang
- College of Materials and Chemical Engineering, Fujian Provincial University Engineering Research Center of Green Materials and Chemical Engineering, Minjiang University, Fuzhou, China
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2
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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3
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Fröhlich K, Furrer R, Schori C, Handschin C, Schmidt A. Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme. J Proteome Res 2024; 23:1028-1038. [PMID: 38275131 PMCID: PMC10913089 DOI: 10.1021/acs.jproteome.3c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
In recent years, a plethora of different data-independent acquisition methods have been developed for proteomics to cover a wide range of requirements. Current deep proteome profiling methods rely on fractionations, elaborate chromatography, and mass spectrometry setups or display suboptimal quantitative precision. We set out to develop an easy-to-use one shot DIA method that achieves high quantitative precision and high proteome coverage. We achieve this by focusing on a small mass range of 430-670 m/z using small isolation windows without overlap. With this new method, we were able to quantify >9200 protein groups in HEK lysates with an average coefficient of variance of 3.2%. To demonstrate the power of our newly developed narrow mass range method, we applied it to investigate the effect of PGC-1α knockout on the skeletal muscle proteome in mice. Compared to a standard data-dependent acquisition method, we could double proteome coverage and, most importantly, achieve a significantly higher quantitative precision, as compared to a previously proposed DIA method. We believe that our method will be especially helpful in quantifying low abundant proteins in samples with a high dynamic range. All raw and result files are available at massive.ucsd.edu (MSV000092186).
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Affiliation(s)
- Klemens Fröhlich
- Proteomics
Core Facility, Biozentrum Basel, University
of Basel, 4056 Basel, Switzerland
| | - Regula Furrer
- Biozentrum
Basel, University of Basel, 4056 Basel, Switzerland
| | - Christian Schori
- Proteomics
Core Facility, Biozentrum Basel, University
of Basel, 4056 Basel, Switzerland
| | | | - Alexander Schmidt
- Proteomics
Core Facility, Biozentrum Basel, University
of Basel, 4056 Basel, Switzerland
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4
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Schweizer L, Krishnan R, Shimizu A, Metousis A, Kenny H, Mendoza R, Nordmann TM, Rauch S, Kelliher L, Heide J, Rosenberger FA, Bilecz A, Borrego SN, Strauss MT, Thielert M, Rodriguez E, Müller-Reif JB, Chen M, Yamada SD, Mund A, Lastra RR, Mann M, Lengyel E. Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.13.23298409. [PMID: 38014221 PMCID: PMC10680885 DOI: 10.1101/2023.11.13.23298409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Serous borderline tumors (SBT) are epithelial neoplastic lesions of the ovaries that commonly have a good prognosis. In 10-15% of cases, however, SBT will recur as low-grade serous cancer (LGSC), which is deeply invasive and responds poorly to current standard chemotherapy1,2,3. While genetic alterations suggest a common origin, the transition from SBT to LGSC remains poorly understood4. Here, we integrate spatial proteomics5 with spatial transcriptomics to elucidate the evolution from SBT to LGSC and its corresponding metastasis at the molecular level in both the stroma and the tumor. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features (SBT-MP), which involves a gradual increase in MAPK signaling. A distinct subset of proteins and transcripts was associated with the transition to invasive tumor growth, including the neuronal splicing factor NOVA2, which was limited to expression in LGSC and its corresponding metastasis. An integrative pathway analysis exposed aberrant molecular signaling of tumor cells supported by alterations in angiogenesis and inflammation in the tumor microenvironment. Integration of spatial transcriptomics and proteomics followed by knockdown of the most altered genes or pharmaceutical inhibition of the most relevant targets confirmed their functional significance in regulating key features of invasiveness. Combining cell-type resolved spatial proteomics and transcriptomics allowed us to elucidate the sequence of tumorigenesis from SBT to LGSC. The approach presented here is a blueprint to systematically elucidate mechanisms of tumorigenesis and find novel treatment strategies.
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Affiliation(s)
- Lisa Schweizer
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Rahul Krishnan
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Aasa Shimizu
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Andreas Metousis
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Hilary Kenny
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Rachelle Mendoza
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Thierry M. Nordmann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sarah Rauch
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Lucy Kelliher
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Janna Heide
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Florian A. Rosenberger
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Agnes Bilecz
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Sanaa Nakad Borrego
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Maximillian T. Strauss
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marvin Thielert
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Edwin Rodriguez
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B. Müller-Reif
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mengjie Chen
- Medicine/Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - S. Diane Yamada
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo R. Lastra
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
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5
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Schweizer L, Schaller T, Zwiebel M, Karayel Ö, Müller‐Reif JB, Zeng W, Dintner S, Nordmann TM, Hirschbühl K, Märkl B, Claus R, Mann M. Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation. EMBO Mol Med 2023; 15:e17459. [PMID: 37519267 PMCID: PMC10493576 DOI: 10.15252/emmm.202317459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
SARS-CoV-2 may directly and indirectly damage lung tissue and other host organs, but there are few system-wide, untargeted studies of these effects on the human body. Here, we developed a parallelized mass spectrometry (MS) proteomics workflow enabling the rapid, quantitative analysis of hundreds of virus-infected FFPE tissues. The first layer of response to SARS-CoV-2 in all tissues was dominated by circulating inflammatory molecules. Beyond systemic inflammation, we differentiated between systemic and true tissue-specific effects to reflect distinct COVID-19-associated damage patterns. Proteomic changes in the lungs resembled those of diffuse alveolar damage (DAD) in non-COVID-19 patients. Extensive organ-specific changes were also evident in the kidneys, liver, and lymphatic and vascular systems. Secondary inflammatory effects in the brain were related to rearrangements in neurotransmitter receptors and myelin degradation. These MS-proteomics-derived results contribute substantially to our understanding of COVID-19 pathomechanisms and suggest strategies for organ-specific therapeutic interventions.
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Affiliation(s)
- Lisa Schweizer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tina Schaller
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Maximilian Zwiebel
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Özge Karayel
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Present address:
Department of Physiological ChemistryGenentechSouth San FranciscoUSA
| | | | - Wen‐Feng Zeng
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | | | - Thierry M Nordmann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Klaus Hirschbühl
- Hematology and Oncology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Bruno Märkl
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Rainer Claus
- Pathology, Medical FacultyUniversity of AugsburgAugsburgGermany
- Hematology and Oncology, Medical FacultyUniversity of AugsburgAugsburgGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
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6
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Shalon D, Culver RN, Grembi JA, Folz J, Treit PV, Shi H, Rosenberger FA, Dethlefsen L, Meng X, Yaffe E, Aranda-Díaz A, Geyer PE, Mueller-Reif JB, Spencer S, Patterson AD, Triadafilopoulos G, Holmes SP, Mann M, Fiehn O, Relman DA, Huang KC. Profiling the human intestinal environment under physiological conditions. Nature 2023; 617:581-591. [PMID: 37165188 PMCID: PMC10191855 DOI: 10.1038/s41586-023-05989-7] [Citation(s) in RCA: 117] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2023] [Indexed: 05/12/2023]
Abstract
The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.
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Affiliation(s)
| | - Rebecca Neal Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Jessica A Grembi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Folz
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Peter V Treit
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Handuo Shi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Les Dethlefsen
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Eitan Yaffe
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes B Mueller-Reif
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Sean Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA
| | - George Triadafilopoulos
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA
- Silicon Valley Neurogastroenterology and Motility Center, Mountain View, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA.
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA.
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Thienel M, Müller-Reif JB, Zhang Z, Ehreiser V, Huth J, Shchurovska K, Kilani B, Schweizer L, Geyer PE, Zwiebel M, Novotny J, Lüsebrink E, Little G, Orban M, Nicolai L, El Nemr S, Titova A, Spannagl M, Kindberg J, Evans AL, Mach O, Vogel M, Tiedt S, Ormanns S, Kessler B, Dueck A, Friebe A, Jørgensen PG, Majzoub-Altweck M, Blutke A, Polzin A, Stark K, Kääb S, Maier D, Gibbins JM, Limper U, Frobert O, Mann M, Massberg S, Petzold T. Immobility-associated thromboprotection is conserved across mammalian species from bear to human. Science 2023; 380:178-187. [PMID: 37053338 DOI: 10.1126/science.abo5044] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/10/2023] [Indexed: 04/15/2023]
Abstract
Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a major cause of morbidity and mortality. Short-term immobility-related conditions are a major risk factor for the development of VTE. Paradoxically, long-term immobilized free-ranging hibernating brown bears and paralyzed spinal cord injury (SCI) patients are protected from VTE. We aimed to identify mechanisms of immobility-associated VTE protection in a cross-species approach. Mass spectrometry-based proteomics revealed an antithrombotic signature in platelets of hibernating brown bears with heat shock protein 47 (HSP47) as the most substantially reduced protein. HSP47 down-regulation or ablation attenuated immune cell activation and neutrophil extracellular trap formation, contributing to thromboprotection in bears, SCI patients, and mice. This cross-species conserved platelet signature may give rise to antithrombotic therapeutics and prognostic markers beyond immobility-associated VTE.
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Affiliation(s)
- Manuela Thienel
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Johannes B Müller-Reif
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Omicera Diagnostics, 82152 Martinsried, Germany
| | - Zhe Zhang
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Vincent Ehreiser
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Judith Huth
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Khrystyna Shchurovska
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Badr Kilani
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Lisa Schweizer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Omicera Diagnostics, 82152 Martinsried, Germany
| | - Maximilian Zwiebel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julia Novotny
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Enzo Lüsebrink
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Gemma Little
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, RG6 6UR, UK
| | - Martin Orban
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Leo Nicolai
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Shaza El Nemr
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Anna Titova
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Michael Spannagl
- Anesthesiology and Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Jonas Kindberg
- Norwegian Institute for Nature Research, 7034 Trondheim, Norway
- Scandinavian Brown Bear Research Project, Tackåsen 2, SE-79498 Orsa, Sweden
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden
| | - Alina L Evans
- Department of Forestry and Wildlife Management, Faculty of Applied Ecology and Agricultural Sciences, Inland Norway University of Applied Sciences, 2480 Koppang, Norway
| | - Orpheus Mach
- Zentrum für Rückenmarkverletzte mit Neuro-Urologie, BG Unfallklinik Murnau, 82418 Murnau am Staffelsee, Germany
| | - Matthias Vogel
- Zentrum für Rückenmarkverletzte mit Neuro-Urologie, BG Unfallklinik Murnau, 82418 Murnau am Staffelsee, Germany
| | - Steffen Tiedt
- Neurologische Klinik und Poliklinik, Klinikum der Universität München, Ludwig-Maximilians- University Munich, 81377 Munich, Germany
| | - Steffen Ormanns
- Pathologisches Institut, Klinikum der Universität München, Ludwig-Maximilians- University Munich, 81377 Munich, Germany
| | - Barbara Kessler
- Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Anne Dueck
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
- Institute of Pharmacology and Toxicology, Technical University of Munich, 80802 Munich, Germany
| | - Andrea Friebe
- Norwegian Institute for Nature Research, 7034 Trondheim, Norway
- Scandinavian Brown Bear Research Project, Tackåsen 2, SE-79498 Orsa, Sweden
| | - Peter Godsk Jørgensen
- Herlev and Gentofte University Hospital, Borgmester Ib Juuls Vej 1, DK-2730, Herlev, Copenhagen, Denmark
| | - Monir Majzoub-Altweck
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Andreas Blutke
- Institute of Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Amin Polzin
- Division of Cardiology, Pulmonology, and Vascular Medicine, Heinrich Heine University Medical Center Dusseldorf, 40225 Dusseldorf, Germany
| | - Konstantin Stark
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Stefan Kääb
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Doris Maier
- Zentrum für Rückenmarkverletzte mit Neuro-Urologie, BG Unfallklinik Murnau, 82418 Murnau am Staffelsee, Germany
| | - Jonathan M Gibbins
- Institute for Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, RG6 6UR, UK
| | - Ulrich Limper
- Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
- Department of Anesthesiology and Intensive Care Medicine, Merheim Medical Center, Hospitals of Cologne, University of Witten/Herdecke, 51109 Cologne, Germany
| | - Ole Frobert
- Faculty of Health, Department of Cardiology, Örebro University, 701 85 Örebro, Sweden
- Department of Clinical Medicine, Faculty of Health, Aarhus University, 8000 Aarhus, Denmark
- Department of Clinical Pharmacology, Aarhus University Hospital, 8000 Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Steffen Massberg
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
| | - Tobias Petzold
- Department of Cardiology, University Hospital, LMU Munich, 81377 Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 80802 Munich, Germany
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8
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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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9
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Perchepied S, Ritchie H, Desmet G, Eeltink S. Insights in column packing processes of narrow bore and capillary-scale columns: Methodologies, driving forces, and separation performance – A tutorial review. Anal Chim Acta 2022; 1235:340563. [DOI: 10.1016/j.aca.2022.340563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
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10
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Zheng R, Stejskal K, Pynn C, Mechtler K, Boychenko A. Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS. J Proteome Res 2022; 21:2545-2551. [PMID: 36068014 PMCID: PMC9552226 DOI: 10.1021/acs.jproteome.2c00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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This study demonstrates how the latest ultrahigh-performance
liquid
chromatography (UHPLC) technology can be combined with high-resolution
accurate-mass (HRAM) mass spectrometry (MS) and long columns packed
with fully porous particles to improve bottom-up proteomics analysis
with nanoflow liquid chromatography–mass spectrometry (nanoLC-MS)
methods. The increased back pressures from the UHPLC system enabled
the use of 75 μm I.D. × 75 cm columns packed with 2 μm
particles at a typical 300 nL/min flow rate as well as elevated and
reduced flow rates. The constant pressure pump operation at 1500 bar
reduced sample loading and column washing/equilibration stages and
overall overhead time, which maximizes MS utilization time. The versatility
of flow rate optimization to balance the sensitivity, throughput with
sample loading amount, and capability of using longer gradients contributes
to a greater number of peptide and protein identifications for single-shot
bottom-up proteomics experiments. The routine proteome profiling and
precise quantification of >7000 proteins with single-shot nanoLC-MS
analysis open possibilities for large-scale discovery studies with
a deep dive into the protein level alterations. Data are available
via ProteomeXchange with identifier PXD035665.
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Affiliation(s)
- Runsheng Zheng
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Karel Stejskal
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria.,IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria.,Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Christopher Pynn
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Karl Mechtler
- IMP─Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria.,IMBA─Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria.,Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
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11
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Liu Y, Wen H, Chen S, Wang X, Zhu X, Luo L, Wang X, Zhang B. Mass Fabrication of Capillary Columns Based on Centrifugal Packing. Anal Chem 2022; 94:8126-8131. [PMID: 35650662 DOI: 10.1021/acs.analchem.2c00442] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Packed capillary columns have become the standard front-end separation device for mass spectrometry-based proteomics. The development of simple, fast, and robust capillary column technology, especially that with mass-fabrication capacity, can greatly improve analytical throughput and reproducibility in omics research. In this technical note, we report a centrifugal packing technology, which has the capability to mass fabricate high quality capillary columns with a 2886 columns/day fabrication throughput. The centrifugally packed columns presented significantly improved efficiency (reduced plate height hmin = 1.6, 37%-40% improvement compared with slurry packed columns), advanced kinetic performance limit, and excellent column-to-column reproducibility (2.0% RSD for retention time, 50 columns). Such columns enabled ∼5300 HeLa proteins identified in single-shot proteomic analysis, displaying both intercolumn and inter-run retention time stability (retention time RSD = 0.94% between nine replicates on three columns for probing peptide sequence). The mass-fabrication technology reported in this technical note may support disposable use of high quality chromatographic columns in large-scale bioanalysis.
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Affiliation(s)
- Ya Liu
- Department of Chemistry, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hanrong Wen
- Department of Chemistry, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shiyi Chen
- Department of Chemistry, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaojuan Wang
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Xudong Zhu
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | | | | | - Bo Zhang
- Department of Chemistry, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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