1
|
Gotti C, Roux-Dalvai F, Bérubé È, Lacombe-Rastoll A, Leclercq M, Jacob CC, Boissinot M, Martins C, Wijeratne NR, Bergeron MG, Droit A. LC-SRM combined with machine learning enables fast identification and quantification of bacterial pathogens in urinary tract infections. Mol Cell Proteomics 2024:100832. [PMID: 39178943 DOI: 10.1016/j.mcpro.2024.100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024] Open
Abstract
Urinary tract infections (UTIs) are a worldwide health problem. Fast and accurate detection of bacterial infection is essential to provide appropriate antibiotherapy to patients and to avoid the emergence of drug-resistant pathogens. While the gold standard requires 24h to 48h of bacteria culture prior MALDI-TOF species identification, we propose a culture-free workflow, enabling a bacterial identification and quantification in less than 4 hours using 1mL of urine. After a rapid and automatable sample preparation, a signature of 82 bacterial peptides, defined by machine learning, was monitored in LC-MS, to distinguish the 15 species causing 84% of the UTIs. The combination of the sensitivity of the SRM mode on a triple quadrupole TSQ Altis instrument and the robustness of capillary flow enabled us to analyze up to 75 samples per day, with 99.2% accuracy on bacterial inoculations of healthy urines. We have also shown our method can be used to quantify the spread of the infection, from 8x104 to 3x107 CFU/mL. Finally, the workflow was validated on 45 inoculated urines and on 84 UTI-positive urine from patients, with respectively 93.3% and 87.1% of agreement with the culture-MALDI procedure at a level above 1x105 CFU/mL corresponding to an infection requiring antibiotherapy.
Collapse
Affiliation(s)
- Clarisse Gotti
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada; Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Florence Roux-Dalvai
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada; Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Ève Bérubé
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada
| | - Antoine Lacombe-Rastoll
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada; Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | | | - Maurice Boissinot
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada
| | | | | | - Michel G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC, Canada
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada; Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada.
| |
Collapse
|
2
|
Pang M, Jones JJ, Wang TY, Quan B, Kubat NJ, Qiu Y, Roukes ML, Chou TF. Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples. J Proteome Res 2024. [PMID: 38832920 DOI: 10.1021/acs.jproteome.4c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The advancement of sophisticated instrumentation in mass spectrometry has catalyzed an in-depth exploration of complex proteomes. This exploration necessitates a nuanced balance in experimental design, particularly between quantitative precision and the enumeration of analytes detected. In bottom-up proteomics, a key challenge is that oversampling of abundant proteins can adversely affect the identification of a diverse array of unique proteins. This issue is especially pronounced in samples with limited analytes, such as small tissue biopsies or single-cell samples. Methods such as depletion and fractionation are suboptimal to reduce oversampling in single cell samples, and other improvements on LC and mass spectrometry technologies and methods have been developed to address the trade-off between precision and enumeration. We demonstrate that by using a monosubstrate protease for proteomic analysis of single-cell equivalent digest samples, an improvement in quantitative accuracy can be achieved, while maintaining high proteome coverage established by trypsin. This improvement is particularly vital for the field of single-cell proteomics, where single-cell samples with limited number of protein copies, especially in the context of low-abundance proteins, can benefit from considering analyte complexity. Considerations about analyte complexity, alongside chromatographic complexity, integration with data acquisition methods, and other factors such as those involving enzyme kinetics, will be crucial in the design of future single-cell workflows.
Collapse
Affiliation(s)
- Marion Pang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Jeff J Jones
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Baiyi Quan
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nicole J Kubat
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Yanping Qiu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Michael L Roukes
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Division of Engineering and Applied Science, California Institute of Technology, 1200 East California Blvd, Pasadena, California 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| |
Collapse
|
3
|
Mansuri MS, Bathla S, Lam TT, Nairn AC, Williams KR. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. J Proteomics 2024; 297:105109. [PMID: 38325732 PMCID: PMC10939724 DOI: 10.1016/j.jprot.2024.105109] [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: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
To identify proteins by the bottom-up mass spectrometry workflow, enzymatic digestion is essential to break down proteins into smaller peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity and generation of peptides with desirable positively charged N- and C-terminal amino acid residues that are amenable to reverse phase HPLC separation and MS/MS analyses. However, trypsin can yield variable digestion profiles and its protein cleavage activity is interdependent on trypsin source and quality, digestion time and temperature, pH, denaturant, trypsin and substrate concentrations, composition/complexity of the sample matrix, and other factors. There is therefore a need for a more standardized, general-purpose trypsin digestion protocol. Based on a review of the literature we delineate optimal conditions for carrying out trypsin digestions of complex proteomes from bulk samples to limiting amounts of protein extracts. Furthermore, we highlight recent developments and technological advances used in digestion protocols to quantify complex proteomes from single cells. SIGNIFICANCE: Currently, bottom-up MS-based proteomics is the method of choice for global proteome analysis. Since trypsin is the most utilized protease in bottom-up MS proteomics, delineating optimal conditions for carrying out trypsin digestions of complex proteomes in samples ranging from tissues to single cells should positively impact a broad range of biomedical research.
Collapse
Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA.
| |
Collapse
|
4
|
Ravi Kumar R, Ndiaye MM, Haddad I, Vinh J, Verdier Y. ChipFilter: Microfluidic-Based Comprehensive Sample Preparation Methodology for Microbial Consortia. J Proteome Res 2024; 23:869-880. [PMID: 38353246 PMCID: PMC10913871 DOI: 10.1021/acs.jproteome.3c00288] [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: 05/11/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The metaproteomic approach is an attractive way to describe a microbiome at the functional level, allowing the identification and quantification of proteins across a broad dynamic range as well as the detection of post-translational modifications. However, it remains relatively underutilized, mainly due to technical challenges that should be addressed, including the complexity of extracting proteins from heterogeneous microbial communities. Here, we show that a ChipFilter microfluidic device coupled to a liquid chromatography tandem mass spectrometry (LC-MS/MS) setup can be successfully used for the identification of microbial proteins. Using cultures of Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae, we have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow the identification of a higher number of proteins and peptides than that by standard protocols, even at low cell density. The peptides produced are overall longer after ChipFilter digestion but show no change in their degree of hydrophobicity. Analysis of a more complex mixture of 17 species from the gut microbiome showed that the ChipFilter preparation was able to identify and estimate the amounts of 16 of these species. These results show that ChipFilter can be used for the proteomic study of microbiomes, particularly in the case of a low volume or cell density. The mass spectrometry data have been deposited on the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD039581.
Collapse
Affiliation(s)
- Ranjith
Kumar Ravi Kumar
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Massamba Mbacke Ndiaye
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Iman Haddad
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Joelle Vinh
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| | - Yann Verdier
- Spectrométrie de
Masse Biologique et Protéomique, LPC, UMR ESPCI CNRS 8249, 10 rue Vauquelin, F-75005 Paris, France
| |
Collapse
|
5
|
Wang Y, Guan ZY, Shi SW, Jiang YR, Zhang J, Yang Y, Wu Q, Wu J, Chen JB, Ying WX, Xu QQ, Fan QX, Wang HF, Zhou L, Wang L, Fang J, Pan JZ, Fang Q. Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell. Nat Commun 2024; 15:1279. [PMID: 38341466 PMCID: PMC10858870 DOI: 10.1038/s41467-024-45659-4] [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: 10/09/2022] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449-3500, 2278-3257 and 1621-2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.
Collapse
Affiliation(s)
- Yu Wang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Ying Guan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Shao-Wen Shi
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jie Zhang
- Department of Cell Biology, China Medical University, Shenyang, 110122, China
| | - Yi Yang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Qiong Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Xin Ying
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Feng Wang
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Li Zhou
- Shanghai Omicsolution Co., Shanghai, 201100, China
| | - Ling Wang
- Shanghai Omicsolution Co., Shanghai, 201100, China
| | - Jin Fang
- Department of Cell Biology, China Medical University, Shenyang, 110122, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
- Single-cell Proteomics Research Center, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China.
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou, 310007, China.
| |
Collapse
|
6
|
Martinez-Gomez L, Cerdán-Vélez D, Abascal F, Tress ML. Origins and Evolution of Human Tandem Duplicated Exon Substitution Events. Genome Biol Evol 2022; 14:6809199. [PMID: 36346145 PMCID: PMC9741552 DOI: 10.1093/gbe/evac162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022] Open
Abstract
The mutually exclusive splicing of tandem duplicated exons produces protein isoforms that are identical save for a homologous region that allows for the fine tuning of protein function. Tandem duplicated exon substitution events are rare, yet highly important alternative splicing events. Most events are ancient, their isoforms are highly expressed, and they have significantly more pathogenic mutations than other splice events. Here, we analyzed the physicochemical properties and functional roles of the homologous polypeptide regions produced by the 236 tandem duplicated exon substitutions annotated in the human gene set. We find that the most important structural and functional residues in these homologous regions are maintained, and that most changes are conservative rather than drastic. Three quarters of the isoforms produced from tandem duplicated exon substitution events are tissue-specific, particularly in nervous and cardiac tissues, and tandem duplicated exon substitution events are enriched in functional terms related to structures in the brain and skeletal muscle. We find considerable evidence for the convergent evolution of tandem duplicated exon substitution events in vertebrates, arthropods, and nematodes. Twelve human gene families have orthologues with tandem duplicated exon substitution events in both Drosophila melanogaster and Caenorhabditis elegans. Six of these gene families are ion transporters, suggesting that tandem exon duplication in genes that control the flow of ions into the cell has an adaptive benefit. The ancient origins, the strong indications of tissue-specific functions, and the evidence of convergent evolution suggest that these events may have played important roles in the evolution of animal tissues and organs.
Collapse
Affiliation(s)
- Laura Martinez-Gomez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Daniel Cerdán-Vélez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), C. Melchor Fernandez Almagro, 3, 28029 Madrid, Spain
| | - Federico Abascal
- Somatic Evolution Group, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | | |
Collapse
|
7
|
He M, Wang J, Herold S, Xi L, Schulze WX. A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals. Curr Protoc 2022; 2:e425. [PMID: 35674286 DOI: 10.1002/cpz1.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proteomics and phosphoproteomics are robust tools to analyze dynamics of post-transcriptional processes during growth and development. A variety of experimental methods and workflows have been published, but most of them were developed for model plants and have not been adapted to high-throughput platforms. Here, we describe an experimental workflow for proteome and phosphoproteome studies tailored to cereal crop tissues. The workflow consists of two parallel parts that are suitable for analyzing protein/phosphoprotein from total proteins and the microsomal membrane fraction. We present phosphoproteomic data regarding quantification coverage and analytical reproducibility for example preparations from maize root and shoot, wheat leaf, and a microsomal protein preparation from maize leaf. To enable users to adjust for tissue specific requirements, we provide two different methods of protein clean-up: traditional ethanol precipitation (PC) and a recently developed technology termed single-pot, solid-phase-enhanced sample preparation (SP3). Both the PC and SP3 methods are effective in the removal of unwanted substances in total protein crude extracts. In addition, two different methods of phosphopeptide enrichment are presented: a TiO2 -based method and Fe(III)-NTA cartridges on a robotized platform. Although the overall number of phosphopeptides is stable across protein clean-up and phosphopeptide enrichment methods, there are differences in the preferred phosphopeptides in each enrichment method. The preferred protocol depends on laboratory capabilities and research objective. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Total protein crude extraction Basic Protocol 2: Total protein clean-up with ethanol precipitation Alternate Protocol 1: Total protein clean-up with SP3 method Basic Protocol 3: Microsomal fraction protein extraction Basic Protocol 4: Protein concentration determination by Bradford assay Basic Protocol 5: In-solution digestion with trypsin Basic Protocol 6: Phosphopeptide enrichment with TiO2 Alternate Protocol 2: Phosphopeptide enrichment with Fe(III)-NTA cartridges Basic Protocol 7: Peptide desalting with C18 material Basic Protocol 8: LC-MS/MS analysis of (phospho)peptides and spectrum matching.
Collapse
Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Jiahui Wang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
8
|
Aggarwal S, Ikram S. Zinc oxide nanoparticles-impregnated chitosan surfaces for covalent immobilization of trypsin: Stability & kinetic studies. Int J Biol Macromol 2022; 207:205-221. [PMID: 35259431 DOI: 10.1016/j.ijbiomac.2022.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/31/2022] [Accepted: 03/03/2022] [Indexed: 11/25/2022]
Abstract
Trypsin (Try, EC. 3.4.21.4) was effectively immobilized on the surface of glutaraldehyde(GA)-activated ZnO/Chitosan nanocomposite through covalent attachment via Schiff-base linkages. Size, structure, surface morphology, & percentage elemental composition of the prepared ZnO nanoparticles and chitosan-coated ZnO nanocomposite were studied by UV-Visible spectroscopy, Fourier-transform infrared spectroscopy (FTIR), X-Ray diffraction analysis (XRD), transmission electron microscopy (TEM), Scanning electron microscopy (SEM), and Energy-Dispersive X-Ray Microanalysis (EDAX) techniques. Optimal immobilization conditions (incubation time (16 h), enzyme concentration (1.8 mg/ml), and pH (7.8)) were investigated to obtain the maximum expressed activity of the immobilized trypsin. Immobilized & solubilized trypsin exhibited the optimum catalytic activity at pH 8.5, 60 °C, and pH 7.8, 45 °C respectively. Kinetic parameters (Km, Vmax) of immobilized (27.12 μM, 8.82 μM/min) & free trypsin (25.76 μM, 4.16 μM/min) were determined, indicating that efficiency of trypsin improves after immobilization. Immobilized trypsin preserved 67% of initial activity at 50 °C during 2 h of incubation & sustained nearly 50% of catalytic activity until the 9th repeated cycle of utilization. Moreover, immobilized trypsin retained 50% of enzymatic activity after 90 days of storage at 4 °C. Hence, the current findings suggest that ZnO/Chitosan-GA-Trypsin would be a promising biocatalyst for large-scale biotechnological applications.
Collapse
Affiliation(s)
- Shalu Aggarwal
- Bio/Polymers Research Laboratory, Department of Chemistry, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Saiqa Ikram
- Bio/Polymers Research Laboratory, Department of Chemistry, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| |
Collapse
|
9
|
Baxi AB, Pade LR, Nemes P. Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo. J Vis Exp 2022:10.3791/63586. [PMID: 35532271 PMCID: PMC9513837 DOI: 10.3791/63586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Characterization of molecular events as cells give rise to tissues and organs raises a potential to better understand normal development and design efficient remedies for diseases. Technologies enabling accurate identification and quantification of diverse types and large numbers of proteins would provide still missing information on molecular mechanisms orchestrating tissue and organism development in space and time. Here, we present a mass spectrometry-based protocol that enables the measurement of thousands of proteins in identified cell lineages in Xenopus laevis (frog) embryos. The approach builds on reproducible cell-fate maps and established methods to identify, fluorescently label, track, and sample cells and their progeny (clones) from this model of vertebrate development. After collecting cellular contents using microsampling or isolating cells by dissection or fluorescence-activated cell sorting, proteins are extracted and processed for bottom-up proteomic analysis. Liquid chromatography and capillary electrophoresis are used to provide scalable separation for protein detection and quantification with high-resolution mass spectrometry (HRMS). Representative examples are provided for the proteomic characterization of neural-tissue fated cells. Cell-lineage-guided HRMS proteomics is adaptable to different tissues and organisms. It is sufficiently sensitive, specific, and quantitative to peer into the spatio-temporal dynamics of the proteome during vertebrate development.
Collapse
Affiliation(s)
- Aparna B Baxi
- Department of Chemistry & Biochemistry, University of Maryland; Department of Anatomy & Cell Biology, The George Washington University
| | - Leena R Pade
- Department of Chemistry & Biochemistry, University of Maryland
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland; Department of Anatomy & Cell Biology, The George Washington University;
| |
Collapse
|
10
|
Becher S, Wang H, Leeming MG, Donald WA, Heiles S. Influence of protein ion charge state on 213 nm top-down UVPD. Analyst 2021; 146:3977-3987. [PMID: 34009215 DOI: 10.1039/d1an00571e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultraviolet photodissociation (UVPD) is a powerful and rapidly developing method in top-down proteomics. Sequence coverages can exceed those obtained with collision- and electron-induced fragmentation methods. Because of the recent interest in UVPD, factors that influence protein fragmentation and sequence coverage are actively debated in the literature. Here, we performed top-down 213 nm UVPD experiments on a 7 T Fourier-transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for the model proteins ubiquitin, myoglobin and cytochrome c that were electrosprayed from native, denaturing and supercharging solutions in order to investigate the effect of protein charge states on UVPD fragments. By performing UVPD in ultrahigh vacuum, factors associated with collisional cooling and any ion activation during transfer between mass analyzers can be largely eliminated. Sequence coverage increased from <10% for low charge states to >60% for high charge states for all three proteins. This trend is influenced by the overall charge state, i.e., charges per number of amino acid residues, and to a lesser degree by associated structural changes of protein ions of different charge states based on comparisons to published collision-cross section measurements. To rationalize this finding, and correlate sequence ion formation and identity with the number and location of protons, UVPD results were compared to protonation sites predicted based on electrostatic modelling. Assuming confined protonation sites, these results indicate the presence of two general fragmentation types; i.e., charge remote and charge directed. For moderately high protein charge states, fragment ions mostly originate in regions between likely protonation sites (charge remote), whereas sequence ions of highly charge protein ions occur either near backbone amide protonation sites at low-basicity residues (charge directed) or at charge remote sites (i.e., high-basicity residues). Overall, our results suggest that top-down 213 UVPD performance in the zero-pressure limit depends strongly on protein charge states and protonation sites can influence the location of backbone cleavages.
Collapse
Affiliation(s)
- Simon Becher
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| | - Huixin Wang
- Mark Wainwright Analytical Centre, University of New South Wales, New South Wales, Australia
| | - Michael G Leeming
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, Australia
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany.
| |
Collapse
|
11
|
Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate. Processes (Basel) 2021. [DOI: 10.3390/pr9060983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, LHCs which were maintained in an active phosphorylated state by serine/threonine-protein kinase were also upregulated to 10-fold over control. Collectively, our results show that the SP3 method is an efficient high-throughput proteotyping tool for Symbiodiniaceae algal research.
Collapse
|
12
|
Tapdigov SZ. The bonding nature of the chemical interaction between trypsin and chitosan based carriers in immobilization process depend on entrapped method: A review. Int J Biol Macromol 2021; 183:1676-1696. [PMID: 34015409 DOI: 10.1016/j.ijbiomac.2021.05.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/13/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
The review article is dedicated to a comprehensive study of the chemical bond formed during the immobilization of the proteolytic enzyme pancreatic trypsin in chitosan-based polymer matrixes and its derivatives. The main focus of the study is to describe the chemical bond that causes immobilization between chitosan based carriers and trypsin. Because the nature of the chemical bond between the carrier and trypsin is a key factor in determining the area of application of the conjugate. It has been found out that after the chemical nature of functional groups, their degree of ionization, the structure of the chemical cross-linking, the medium pH and ionic strength of chitosan are modified, the mechanism of trypsin immobilization is affected. As a result, the attraction enzyme to the matrix occurs due to polar covalent and hydrogen bonds, as well as electrostatic, hydrophobic, Van der Waals forces. The collected research works on the immobilization of trypsin on chitosan-based carriers have been systematized in the paper and shown schematically in subsystems according to the type of chemical interaction. It has been shown that the immobilization of trypsin on chitosan based matrixes occur more often due to the covalent and hydrogen bonds between the protein and the carrier.
Collapse
Affiliation(s)
- Shamo Zokhrab Tapdigov
- Department of Nanostructured Metal-polymer Catalysist, Institute Catalysis and Inorganic Chemistry, Azerbaijan National Academy of Sciences, H. Javid ave. 113, AZ1143, Azerbaijan; Department of Prevention of Sand and Water Appearance, Oil-gas Research and Design Institute, The State Oil Company of the Azerbaijan Republic, H. Zardabi ave. 88, AZ1012 Baku, Azerbaijan.
| |
Collapse
|
13
|
Yang M, Villarreal JC, Ariyasinghe N, Kruithoff R, Ros R, Ros A. Quantitative Approach for Protein Analysis in Small Cell Ensembles by an Integrated Microfluidic Chip with MALDI Mass Spectrometry. Anal Chem 2021; 93:6053-6061. [PMID: 33819014 PMCID: PMC8128341 DOI: 10.1021/acs.analchem.0c04112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Increasing evidence has demonstrated that cells are individually heterogeneous. Advancing the technologies for single-cell analysis will improve our ability to characterize cells, study cell biology, design and screen drugs, and aid cancer diagnosis and treatment. Most current single-cell protein analysis approaches are based on fluorescent antibody-binding technology. However, this technology is limited by high background and cross-talk of multiple tags introduced by fluorescent labels. Stable isotope labels used in mass cytometry can overcome the spectral overlap of fluorophores. Nevertheless, the specificity of each antibody and heavy-metal-tagged antibody combination must be carefully validated to ensure detection of the intended target. Thus, novel single-cell protein analysis methods without using labels are urgently needed. Moreover, the labeling approach targets already known motifs, hampering the discovery of new biomarkers relevant to single-cell population variation. Here, we report a combined microfluidic and matrix-assisted laser desorption and ionization (MALDI) mass spectrometric approach for the analysis of protein biomarkers suitable for small cell ensembles. All necessary steps for cell analysis including cell lysis, protein capture, and digestion as well as MALDI matrix deposition are integrated on a microfluidic chip prior to the downstream MALDI-time-of-flight (TOF) detection. For proof of principle, this combined method is used to assess the amount of Bcl-2, an apoptosis regulator, in metastatic breast cancer cells (MCF-7) by using an isotope-labeled peptide as an internal standard. The proposed approach will eventually provide a new means for proteome studies in small cell ensembles with the potential for single-cell analysis and improve our ability in disease diagnosis, drug discovery, and personalized therapy.
Collapse
Affiliation(s)
- Mian Yang
- Department of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan City, Hubei Province, 430081, P.R.China
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
| | - Nethmi Ariyasinghe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe AZ, 85287-1504, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe AZ, 85287-1604, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe AZ, 85287-7401, USA
| |
Collapse
|
14
|
Electrostatic and Hydrogen Bond Immobilization of Trypsine onto pH-Sensitive N-Vinylpyrrolidone and 4-Vinylpyridine Radical co-Grafted Chitosan Based on Hydrogel. Macromol Res 2021. [DOI: 10.1007/s13233-021-9015-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
Sürmen MG, Sürmen S, Ali A, Musharraf SG, Emekli N. Phosphoproteomic strategies in cancer research: a minireview. Analyst 2020; 145:7125-7149. [PMID: 32996481 DOI: 10.1039/d0an00915f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the cellular processes is central to comprehend disease conditions and is also true for cancer research. Proteomic studies provide significant insight into cancer mechanisms and aid in the diagnosis and prognosis of the disease. Phosphoproteome is one of the most studied complements of the whole proteome given its importance in the understanding of cellular processes such as signaling and regulations. Over the last decade, several new methods have been developed for phosphoproteome analysis. A significant amount of these efforts pertains to cancer research. The current use of powerful analytical instruments in phosphoproteomic approaches has paved the way for deeper and sensitive investigations. However, these methods and techniques need further improvements to deal with challenges posed by the complexity of samples and scarcity of phosphoproteins in the whole proteome, throughput and reproducibility. This review aims to provide a comprehensive summary of the variety of steps used in phosphoproteomic methods applied in cancer research including the enrichment and fractionation strategies. This will allow researchers to evaluate and choose a better combination of steps for their phosphoproteome studies.
Collapse
Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Arslan Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Syed Ghulam Musharraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| |
Collapse
|
16
|
Doellinger J, Schneider A, Hoeller M, Lasch P. Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction. Mol Cell Proteomics 2020; 19:209-222. [PMID: 31754045 PMCID: PMC6944244 DOI: 10.1074/mcp.tir119.001616] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.
Collapse
Affiliation(s)
- Joerg Doellinger
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany.
| | - Andy Schneider
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Marcell Hoeller
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Peter Lasch
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| |
Collapse
|
17
|
Judd AM, Gutierrez DB, Moore JL, Patterson NH, Yang J, Romer CE, Norris JL, Caprioli RM. A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:716-727. [PMID: 31254303 PMCID: PMC6711785 DOI: 10.1002/jms.4384] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 06/20/2019] [Indexed: 05/06/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a molecular imaging technology uniquely capable of untargeted measurement of proteins, lipids, and metabolites while retaining spatial information about their location in situ. This powerful combination of capabilities has the potential to bring a wealth of knowledge to the field of molecular histology. Translation of this innovative research tool into clinical laboratories requires the development of reliable sample preparation protocols for the analysis of proteins from formalin-fixed paraffin-embedded (FFPE) tissues, the standard preservation process in clinical pathology. Although ideal for stained tissue analysis by microscopy, the FFPE process cross-links, disrupts, or can remove proteins from the tissue, making analysis of the protein content challenging. To date, reported approaches differ widely in process and efficacy. This tutorial presents a strategy derived from systematic testing and optimization of key parameters, for reproducible in situ tryptic digestion of proteins in FFPE tissue and subsequent MALDI IMS analysis. The approach describes a generalized method for FFPE tissues originating from virtually any source.
Collapse
Affiliation(s)
- Audra M. Judd
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Correspondence: Dr. Richard M. Caprioli, 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA, Phone: (615) 322-4336, Fax: (615) 343-8372,
| | - Danielle B. Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Correspondence: Dr. Richard M. Caprioli, 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA, Phone: (615) 322-4336, Fax: (615) 343-8372,
| | - Jessica L. Moore
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
| | - Junhai Yang
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
| | - Carrie E. Romer
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
| | - Jeremy L. Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Departments of Chemistry, Vanderbilt University, Nashville TN, 37235
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Departments of Chemistry, Vanderbilt University, Nashville TN, 37235
- Departments of Pharmacology, Vanderbilt University, Nashville TN, 37235
- Departments of Medicine, Vanderbilt University, Nashville TN, 37235
| |
Collapse
|
18
|
Ryan DJ, Patterson NH, Putnam NE, Wilde AD, Weiss A, Perry WJ, Cassat JE, Skaar EP, Caprioli RM, Spraggins JM. MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. Anal Chem 2019; 91:7578-7585. [PMID: 31149808 PMCID: PMC6652190 DOI: 10.1021/acs.analchem.8b05889] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ability to target discrete features within tissue using liquid surface extractions enables the identification of proteins while maintaining the spatial integrity of the sample. Here, we present a liquid extraction surface analysis (LESA) workflow, termed microLESA, that allows proteomic profiling from discrete tissue features of ∼110 μm in diameter by integrating nondestructive autofluorescence microscopy and spatially targeted liquid droplet micro-digestion. Autofluorescence microscopy provides the visualization of tissue foci without the need for chemical stains or the use of serial tissue sections. Tryptic peptides are generated from tissue foci by applying small volume droplets (∼250 pL) of enzyme onto the surface prior to LESA. The microLESA workflow reduced the diameter of the sampled area almost 5-fold compared to previous LESA approaches. Experimental parameters, such as tissue thickness, trypsin concentration, and enzyme incubation duration, were tested to maximize proteomics analysis. The microLESA workflow was applied to the study of fluorescently labeled Staphylococcus aureus infected murine kidney to identify unique proteins related to host defense and bacterial pathogenesis. Proteins related to nutritional immunity and host immune response were identified by performing microLESA at the infectious foci and surrounding abscess. These identifications were then used to annotate specific proteins observed in infected kidney tissue by MALDI FT-ICR IMS through accurate mass matching.
Collapse
Affiliation(s)
- Daniel J. Ryan
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South #9160, Nashville, Tennessee 37235, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| | - Nicole E. Putnam
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Aimee D. Wilde
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - William J. Perry
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South #9160, Nashville, Tennessee 37235, United States
| | - James E. Cassat
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- United States (U.S.) Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Department of Pharmacology, Vanderbilt University, 442 Robinson Research Building, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Ave South #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M. Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South #9160, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
| |
Collapse
|
19
|
Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K. Quality control in mass spectrometry-based proteomics. MASS SPECTROMETRY REVIEWS 2018; 37:697-711. [PMID: 28802010 DOI: 10.1002/mas.21544] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 05/21/2023]
Abstract
Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results. A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages. We review potential sources of variability that can impact the results of a mass spectrometry experiment occurring in all of these steps, and we discuss how to monitor and remedy the negative influences on the experimental results. Furthermore, we describe how specialized quality control samples of varying sample complexity can be incorporated into the experimental workflow and how they can be used to rigorously assess detailed aspects of the instrument performance.
Collapse
Affiliation(s)
- Wout Bittremieux
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg Hospital, Cape Town, South Africa
| | - Francis Impens
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - An Staes
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Evy Timmerman
- VIB Proteomics Core, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Zwijnaarde, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| |
Collapse
|
20
|
Isolation and mass spectrometry analysis of urinary extraexosomal proteins. Sci Rep 2016; 6:36331. [PMID: 27805059 PMCID: PMC5090863 DOI: 10.1038/srep36331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022] Open
Abstract
The aim of the present study was to develop a LC-MS/MS-based proteomic analysis method of urinary exosomal proteins that has the potential to discover disease biomarkers. In short, urinary exosomes from healthy subjects were isolated by immunocapture on magnetic beads, detected by immunofluorescence and TEM, trypsin digested directly on the beads for an accelerated time with no addition of detergents before performing an LC-MS analysis of the trypsinate. To our knowledge, this is the first proteomic analysis of proteins displayed on the outer surface of exosomes. The outer exosome proteome may contain proteins that are of higher biomarker value compared to soluble cargo protein as the proteins projecting into the extracellular milieu might be more directly involved in physiological functions of exosomes. The proteomic analysis identified 49 proteins that were considered significant; the majority is involved in carbohydrate and lipid metabolism or in immune responses. Thirty of the proteins are linked to diseases. The developed proteomic method exploiting urinary exosomes might be of great value in search for diagnostic or prognostic biomarkers of especially metabolic and immune-related diseases.
Collapse
|
21
|
Optimization of Urea Based Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissue for Shotgun Proteomics. INTERNATIONAL JOURNAL OF PROTEOMICS 2016; 2016:4324987. [PMID: 27660725 PMCID: PMC5021876 DOI: 10.1155/2016/4324987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/09/2016] [Indexed: 01/19/2023]
Abstract
Urea based protein extraction of formalin-fixed paraffin-embedded (FFPE) tissue provides the most efficient workflow for proteomics due to its compatibility with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This study optimizes the use of urea for proteomic analysis of clinical FFPE tissue. A series of protein extraction conditions manipulating temperature and buffer composition were compared to reduce carbamylation introduced by urea and increase protein detection. Each extraction was performed on a randomized pair of serial sections of homogenous FFPE tissue and analyzed with LC-ESI-MS/MS. Results were compared in terms of yield, missed cleavages, and peptide carbamylation. Lowering extraction temperature to 60°C decreased carbamylation at the cost of decreased protein detection and yield. Protein extraction for at least 20 minutes at 95°C followed by 60°C for 2 hours maximized total protein yield while maintaining protein detection and reducing carbamylation by 7.9%. When accounting for carbamylation during analysis, this modified extraction temperature provides equivalent peptide and protein detection relative to the commercially available Qproteome® FFPE Tissue Kit. No changes to buffer composition containing 7 M urea, 2 M thiourea, and 1 M ammonium bicarbonate resulted in improvements to control conditions. Optimized urea in-solution digestion provides an efficient workflow with maximized yields for proteomic analysis of clinically relevant FFPE tissue.
Collapse
|
22
|
Dual-immuno-MS technique for improved differentiation power in heterodimeric protein biomarker analysis: determination and differentiation of human chorionic gonadotropin variants in serum. Anal Bioanal Chem 2016; 408:7379-91. [DOI: 10.1007/s00216-016-9818-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/07/2016] [Accepted: 07/20/2016] [Indexed: 02/06/2023]
|
23
|
Egeland SV, Reubsaet L, Halvorsen TG. The pros and cons of increased trypsin-to-protein ratio in targeted protein analysis. J Pharm Biomed Anal 2016; 123:155-61. [DOI: 10.1016/j.jpba.2016.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/29/2016] [Accepted: 02/09/2016] [Indexed: 02/06/2023]
|
24
|
Lai E, Wang Y, Wei Y, Li G, Ma G. Covalent immobilization of trypsin onto thermo-sensitive poly(N-isopropylacrylamide-co-acrylic acid) microspheres with high activity and stability. J Appl Polym Sci 2016. [DOI: 10.1002/app.43343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Enping Lai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering; Donghua University; Shanghai 201620 People's Republic of China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Yuxia Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Yi Wei
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| | - Guang Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering; Donghua University; Shanghai 201620 People's Republic of China
| | - Guanghui Ma
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing 100190 People's Republic of China
| |
Collapse
|
25
|
Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
Collapse
Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| |
Collapse
|
26
|
Arnold SL, Stevison F, Isoherranen N. Impact of Sample Matrix on Accuracy of Peptide Quantification: Assessment of Calibrator and Internal Standard Selection and Method Validation. Anal Chem 2016; 88:746-53. [PMID: 26606514 PMCID: PMC4817721 DOI: 10.1021/acs.analchem.5b03004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein quantification based on peptides using LC-MS/MS has emerged as a promising method to measure biomarkers, protein drugs, and endogenous proteins. However, the best practices for selection, optimization, and validation of the quantification peptides are not well established, and the influence of different matrices on protein digestion, peptide stability, and MS detection has not been systematically addressed. The aim of this study was to determine how biological matrices affect digestion, detection, and stability of peptides. The microsomal retinol dehydrogenase (RDH11) and cytosolic soluble aldehyde dehydrogenases (ALDH1As) involved in the synthesis of retinoic acid (RA) were chosen as model proteins. Considerable differences in the digestion efficiency, sensitivity, and matrix effects between peptides were observed regardless of the target protein's subcellular localization. The precision and accuracy of the quantification of RDH11 and ALDH1A were affected by the choice of calibration and internal standards. The final method using recombinant protein calibrators and stable isotope labeled (SIL) peptide internal standards was validated for human liver. The results demonstrate that different sample matrices have peptide, time, and matrix specific effects on protein digestion and absolute quantification.
Collapse
Affiliation(s)
- Samuel L. Arnold
- Department of Pharmaceutics, University of Washington, Health Science Building, Room H-272M Box 357610 Seattle Washington 98195-7610 USA
| | - Faith Stevison
- Department of Pharmaceutics, University of Washington, Health Science Building, Room H-272M Box 357610 Seattle Washington 98195-7610 USA
| | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington, Health Science Building, Room H-272M Box 357610 Seattle Washington 98195-7610 USA
| |
Collapse
|
27
|
Ménoret A, Crocker SJ, Rodriguez A, Rathinam VA, Clark RB, Vella AT. Transition from identity to bioactivity-guided proteomics for biomarker discovery with focus on the PF2D platform. Proteomics Clin Appl 2015. [PMID: 26201056 DOI: 10.1002/prca.201500029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.
Collapse
Affiliation(s)
- Antoine Ménoret
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Stephen J Crocker
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, USA
| | - Annabelle Rodriguez
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Vijay A Rathinam
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Robert B Clark
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Anthony T Vella
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| |
Collapse
|
28
|
Fang P, Liu M, Xue Y, Yao J, Zhang Y, Shen H, Yang P. Controlling nonspecific trypsin cleavages in LC-MS/MS-based shotgun proteomics using optimized experimental conditions. Analyst 2015; 140:7613-21. [PMID: 26418741 DOI: 10.1039/c5an01505g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The highlight of this study is the efficient control of nonspecific trypsin cleavages in shotgun proteomics and N-glycoproteomics using optimized experimental conditions, which greatly increased the specificity of trypsin.
Collapse
Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Mingqi Liu
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Yu Xue
- Department of Chemistry
- Fudan University
- Shanghai
- P. R. China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Huali Shen
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
- Department of Systems Biology for Medicine and School of Basic Medical Sciences
| | - Pengyuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
- Department of Chemistry
| |
Collapse
|
29
|
Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. J Proteome Res 2014; 14:787-803. [PMID: 25495225 DOI: 10.1021/pr500834z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained under different experimental conditions. Here, we describe the design, synthesis, and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected either to favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion, and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements to large-scale biomarker screening in biomedical applications.
Collapse
|
30
|
Affiliation(s)
- Bernhard Spengler
- Justus Liebig University Giessen, Institute of Inorganic and Analytical
Chemistry, Schubertstrasse
60, Building 16, 35392 Giessen, Germany
| |
Collapse
|