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Collins T, Muste C, Owens KG. Identification of Microbial Strains via 2D Cross-Correlation of LC-MS Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1352-1362. [PMID: 38742647 PMCID: PMC11197091 DOI: 10.1021/jasms.4c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
Mass spectrometry is commonly used in the identification of species present in microbial samples, but the high similarity in the peptide composition between strains of a single species has made analysis at the subspecies level challenging. Prior research in this area has employed methods such as Principal Component Analysis (PCA), the k-Nearest Neighbors' (kNN) algorithm, and Pearson correlation. Previously, 1D cross-correlation of mass spectra has been shown to be useful in the classification of small molecule compounds as well as in the identification of peptide sequences via the SEQUEST algorithm and its variants. While direct application of cross-correlation to mass spectral data has been shown to aid in the identification of many other types of compounds, this type of analysis has not been demonstrated in the literature for the purpose of LC-MS based identification of microbial strains. A method of identifying microbial strains is presented here that applies the principle of 2D cross-correlation to LC-MS data. For a set of N = 30 yeast isolate samples representing 5 yeast strains (K-97, S-33, T-58, US-05, WB-06), high-resolution LC-MS-Orbitrap data were collected. Reference spectra were then generated for each strain from the combined data of each sample of that strain. Sample strains were then predicted by computing the 2D cross-correlation of each sample against the reference spectra, followed by application of correction factors measuring the asymmetry of the 2D correlation functions.
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Affiliation(s)
- Tucker
James Collins
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Cathy Muste
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Kevin G. Owens
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
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2
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Plouviez M, Dubreucq E. Key Proteomics Tools for Fundamental and Applied Microalgal Research. Proteomes 2024; 12:13. [PMID: 38651372 PMCID: PMC11036299 DOI: 10.3390/proteomes12020013] [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: 12/29/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Microscopic, photosynthetic prokaryotes and eukaryotes, collectively referred to as microalgae, are widely studied to improve our understanding of key metabolic pathways (e.g., photosynthesis) and for the development of biotechnological applications. Omics technologies, which are now common tools in biological research, have been shown to be critical in microalgal research. In the past decade, significant technological advancements have allowed omics technologies to become more affordable and efficient, with huge datasets being generated. In particular, where studies focused on a single or few proteins decades ago, it is now possible to study the whole proteome of a microalgae. The development of mass spectrometry-based methods has provided this leap forward with the high-throughput identification and quantification of proteins. This review specifically provides an overview of the use of proteomics in fundamental (e.g., photosynthesis) and applied (e.g., lipid production for biofuel) microalgal research, and presents future research directions in this field.
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Affiliation(s)
- Maxence Plouviez
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
- The Cawthron Institute, Nelson 7010, New Zealand
| | - Eric Dubreucq
- Agropolymer Engineering and Emerging Technologies, L’Institut Agro Montpellier, 34060 Montpellier, France;
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3
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Conforti JM, Ziegler AM, Worth CS, Nambiar AM, Bailey JT, Taube JH, Gallagher ES. Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Clean-up Techniques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584881. [PMID: 38559195 PMCID: PMC10980087 DOI: 10.1101/2024.03.13.584881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identification. Single-pot, solid-phase-enhanced sample preparation (SP3) is a clean-up technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. However, recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Thus, solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer clean-up technique that employs protein-aggregation to capture proteins without modified particles. SP4 has previously enriched low-solubility proteins, though differences in protein capture could affect which proteins are detected and identified. We hypothesize that the mechanisms of capture for SP3 and SP4 are distinct. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. From these results, we recommend clean-up techniques based on protein-sample hydrophobicity to yield high proteome coverage in biological samples.
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Affiliation(s)
- Jessica M. Conforti
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Amanda M. Ziegler
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Charli S. Worth
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Adhwaitha M. Nambiar
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Jacob T. Bailey
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Joseph H. Taube
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Elyssia S. Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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4
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Vreeke GJC, Meijers MGJ, Vincken JP, Wierenga PA. Towards absolute quantification of protein genetic variants in Pisum sativum extracts. Anal Biochem 2023; 665:115048. [PMID: 36657509 DOI: 10.1016/j.ab.2023.115048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
In recent years, several studies have used proteomics approaches to characterize genetic variant profiles of agricultural raw materials. In such studies, the challenge is the quantification of the individual protein variants. In this study a novel UPLC-PDA-MS method with absolute and label-free UV-based peptide quantification was applied to quantify the genetic variants of legumin, vicilin and albumins in pea extracts. The aim was to investigate the applicability of this method and to identify challenges in determining protein concentration from the measured peptide concentrations. Analysis of the protein mass balance showed significant losses of proteins in extraction (37%) and of peptides in further sample preparation (69%). The challenge in calculating the extractable individual protein concentrations was how to deal with these insoluble peptides. The quantification approach using average amino acid concentrations in each position of the sequence showed most reproducible results and allowed comparison of the genetic protein composition of 8 different cultivars. The extractable protein composition (μM/μM) was remarkably similar for all cultivar extracts and consisted of legumins A1 (12.8 ± 1.2%), A2 (1.1 ± 0.4%), B (9.9 ± 1.6%), J (7.5 ± 1.0%) and K (10.3 ± 2.1%), vicilin (15.2 ± 1.7%), provicilin (15.7 ± 2.5%), convicilin (9.8 ± 0.8%), albumin A1 (7.4 ± 2.0%), albumin 2 (10.0 ± 1.5%) and protease inhibitor (0.4 ± 0.4%).
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Affiliation(s)
- Gijs J C Vreeke
- Laboratory of Food Chemistry, Wageningen University and Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Maud G J Meijers
- Laboratory of Food Chemistry, Wageningen University and Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands; TiFN, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University and Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Peter A Wierenga
- Laboratory of Food Chemistry, Wageningen University and Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands.
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5
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Brajkovic S, Rugen N, Agius C, Berner N, Eckert S, Sakhteman A, Schwechheimer C, Kuster B. Getting Ready for Large-Scale Proteomics in Crop Plants. Nutrients 2023; 15:nu15030783. [PMID: 36771489 PMCID: PMC9921824 DOI: 10.3390/nu15030783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.
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Affiliation(s)
- Sarah Brajkovic
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nils Rugen
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Institute of Plant Genetics, Leibniz University Hannover, 30167 Hannover, Germany
| | - Carlos Agius
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nicola Berner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Claus Schwechheimer
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Correspondence:
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6
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Leonova T, Ihling C, Saoud M, Frolova N, Rennert R, Wessjohann LA, Frolov A. Does filter-aided sample preparation provide sufficient method linearity for quantitative plant shotgun proteomics? FRONTIERS IN PLANT SCIENCE 2022; 13:874761. [PMID: 36507396 PMCID: PMC9728026 DOI: 10.3389/fpls.2022.874761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Due to its outstanding throughput and analytical resolution, gel-free LC-based shotgun proteomics represents the gold standard of proteome analysis. Thereby, the efficiency of sample preparation dramatically affects the correctness and reliability of protein quantification. Thus, the steps of protein isolation, solubilization, and proteolysis represent the principal bottleneck of shotgun proteomics. The desired performance of the sample preparation protocols can be achieved by the application of detergents. However, these compounds ultimately compromise reverse-phase chromatographic separation and disrupt electrospray ionization. Filter-aided sample preparation (FASP) represents an elegant approach to overcome these limitations. Although this method is comprehensively validated for cell proteomics, its applicability to plants and compatibility with plant-specific protein isolation protocols remain to be confirmed. Thereby, the most important gap is the absence of the data on the linearity of underlying protein quantification methods for plant matrices. To fill this gap, we address here the potential of FASP in combination with two protein isolation protocols for quantitative analysis of pea (Pisum sativum) seed and Arabidopsis thaliana leaf proteomes by the shotgun approach. For this aim, in comprehensive spiking experiments with bovine serum albumin (BSA), we evaluated the linear dynamic range (LDR) of protein quantification in the presence of plant matrices. Furthermore, we addressed the interference of two different plant matrices in quantitative experiments, accomplished with two alternative sample preparation workflows in comparison to conventional FASP-based digestion of cell lysates, considered here as a reference. The spiking experiments revealed high sensitivities (LODs of up to 4 fmol) for spiked BSA and LDRs of at least 0.6 × 102. Thereby, phenol extraction yielded slightly better recoveries, whereas the detergent-based method showed better linearity. Thus, our results indicate the very good applicability of FASP to quantitative plant proteomics with only limited impact of the protein isolation technique on the method's overall performance.
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Affiliation(s)
- Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, Russia
| | - Christian Ihling
- Institute of Pharmacy, Department of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Mohamad Saoud
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Nadezhda Frolova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, Russia
| | - Robert Rennert
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Department of Biochemistry, St Petersburg State University, St Petersburg, Russia
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7
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Danko K, Lukasheva E, Zhukov VA, Zgoda V, Frolov A. Detergent-Assisted Protein Digestion-On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics. Int J Mol Sci 2022; 23:13903. [PMID: 36430380 PMCID: PMC9695859 DOI: 10.3390/ijms232213903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022] Open
Abstract
Gel-free bottom-up shotgun proteomics is the principal methodological platform for the state-of-the-art proteome research. This methodology assumes quantitative isolation of the total protein fraction from a complex biological sample, its limited proteolysis with site-specific proteases, analysis of the resulted peptides with nanoscaled reversed-phase high-performance liquid chromatography-(tandem) mass spectrometry (nanoRP-HPLC-MS and MS/MS), protein identification by sequence database search and peptide-based quantitative analysis. The most critical steps of this workflow are protein reconstitution and digestion; therefore, detergents and chaotropic agents are strongly mandatory to ensure complete solubilization of complex protein isolates and to achieve accessibility of all protease cleavage sites. However, detergents are incompatible with both RP separation and electrospray ionization (ESI). Therefore, to make LC-MS analysis possible, several strategies were implemented in the shotgun proteomics workflow. These techniques rely either on enzymatic digestion in centrifugal filters with subsequent evacuation of the detergent, or employment of MS-compatible surfactants, which can be degraded upon the digestion. In this review we comprehensively address all currently available strategies for the detergent-assisted proteolysis in respect of their relative efficiency when applied to different biological matrices. We critically discuss the current progress and the further perspectives of these technologies in the context of its advances and gaps.
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Affiliation(s)
- Katerina Danko
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee 3, Pushkin, 196608 St. Petersburg, Russia
| | - Viktor Zgoda
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Andrej Frolov
- K.A. Timiryazev Institute of Plant Physiology RAS, 127276 Moscow, Russia
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8
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Jadhav DB, Sriramkumar Y, Roy S. The enigmatic clock of dinoflagellates, is it unique? Front Microbiol 2022; 13:1004074. [PMID: 36338102 PMCID: PMC9627503 DOI: 10.3389/fmicb.2022.1004074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/29/2022] [Indexed: 12/01/2022] Open
Abstract
Dinoflagellate clocks are unique as they show no resemblance to any known model eukaryotic or prokaryotic clock architecture. Dinoflagellates are unicellular, photosynthetic, primarily marine eukaryotes are known for their unique biology and rhythmic physiology. Their physiological rhythms are driven by an internal oscillator whose molecular underpinnings are yet unknown. One of the primary reasons that slowed the progression of their molecular studies is their extremely large and repetitive genomes. Dinoflagellates are primary contributors to the global carbon cycle and oxygen levels, therefore, comprehending their internal clock architecture and its interaction with their physiology becomes a subject of utmost importance. The advent of high throughput Omics technology provided the momentum to understand the molecular architecture and functioning of the dinoflagellate clocks. We use these extensive databases to perform meta-analysis to reveal the status of clock components in dinoflagellates. In this article, we will delve deep into the various “Omics” studies that catered to various breakthroughs in the field of circadian biology in these organisms that were not possible earlier. The overall inference from these omics studies points toward an uncommon eukaryotic clock model, which can provide promising leads to understand the evolution of molecular clocks.
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9
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Sialana F, Roumeliotis TI, Bouguenina H, Chan Wah Hak L, Wang H, Caldwell J, Collins I, Chopra R, Choudhary JS. SimPLIT: Simplified Sample Preparation for Large-Scale Isobaric Tagging Proteomics. J Proteome Res 2022; 21:1842-1856. [PMID: 35848491 PMCID: PMC9361352 DOI: 10.1021/acs.jproteome.2c00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Large scale proteomic profiling of cell lines can reveal molecular signatures attributed to variable genotypes or induced perturbations, enabling proteogenomic associations and elucidation of pharmacological mechanisms of action. Although isobaric labeling has increased the throughput of proteomic analysis, the commonly used sample preparation workflows often require time-consuming steps and costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost-effective one-pot reaction workflow in a 96-well plate format (SimPLIT) that minimizes processing steps and demonstrates improved reproducibility compared to alternative approaches. The workflow is based on a sodium deoxycholate lysis buffer and a single detergent cleanup step after peptide labeling, followed by quick off-line fractionation and MS2 analysis. We showcase the applicability of the workflow in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we report frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of seven cereblon E3 ligase modulators (CRL4CRBN). Overall, SimPLIT is a robust method that can be easily implemented in any proteomics laboratory for medium-to-large scale TMT-based studies for deep profiling of cell lines.
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Affiliation(s)
- Fernando
J. Sialana
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Theodoros I. Roumeliotis
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
| | - Habib Bouguenina
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Laura Chan Wah Hak
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Hannah Wang
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - John Caldwell
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Ian Collins
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rajesh Chopra
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London SM2 5NG, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, U.K.
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10
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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11
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Weke K, Kote S, Faktor J, Al Shboul S, Uwugiaren N, Brennan PM, Goodlett DR, Hupp TR, Dapic I. DIA-MS proteome analysis of formalin-fixed paraffin-embedded glioblastoma tissues. Anal Chim Acta 2022; 1204:339695. [DOI: 10.1016/j.aca.2022.339695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/11/2022]
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12
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Liu Y, Wang K, Wang Y, Wang L, Yan S, Du X, Zhang P, Chen HY, Huang S. Machine Learning Assisted Simultaneous Structural Profiling of Differently Charged Proteins in a Mycobacterium smegmatis Porin A (MspA) Electroosmotic Trap. J Am Chem Soc 2022; 144:757-768. [PMID: 34994548 DOI: 10.1021/jacs.1c09259] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The nanopore is emerging as a means of single-molecule protein sensing. However, proteins demonstrate different charge properties, which complicates the design of a sensor that can achieve simultaneous sensing of differently charged proteins. In this work, we introduce an asymmetric electrolyte buffer combined with the Mycobacterium smegmatis porin A (MspA) nanopore to form an electroosmotic flow (EOF) trap. Apo- and holo-myoglobin, which differ in only a single heme, can be fully distinguished by this method. Direct discrimination of lysozyme, apo/holo-myoglobin, and the ACTR/NCBD protein complex, which are basic, neutral, and acidic proteins, respectively, was simultaneously achieved by the MspA EOF trap. To automate event classification, multiple event features were extracted to build a machine learning model, with which a 99.9% accuracy is achieved. The demonstrated method was also applied to identify single molecules of α-lactalbumin and β-lactoglobulin directly from whey protein powder. This protein-sensing strategy is useful in direct recognition of a protein from a mixture, suggesting its prospective use in rapid and sensitive detection of biomarkers or real-time protein structural analysis.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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13
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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. Proteomes 2022; 10:5. [PMID: 35225985 PMCID: PMC8883913 DOI: 10.3390/proteomes10010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
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Affiliation(s)
- Sadegh Balotf
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
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14
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Milkovska-Stamenova S, Wölk M, Hoffmann R. Evaluation of Sample Preparation Strategies for Human Milk and Plasma Proteomics. Molecules 2021; 26:molecules26226816. [PMID: 34833908 PMCID: PMC8618985 DOI: 10.3390/molecules26226816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is the most critical step in proteomics as it directly affects the subset of proteins and peptides that can be reliably identified and quantified. Although a variety of efficient and reproducible sample preparation strategies have been developed, their applicability and efficacy depends much on the biological sample. Here, three approaches were evaluated for the human milk and plasma proteomes. Protein extracts were digested either in an ultrafiltration unit (filter-aided sample preparation, FASP) or in-solution (ISD). ISD samples were desalted by solid-phase extraction prior to nRPC-ESI-MS/MS. Additionally, milk and plasma samples were directly digested by FASP without prior protein precipitation. Each strategy provided inherent advantages and disadvantages for milk and plasma. FASP appeared to be the most time efficient procedure with a low miscleavage rate when used for a biological sample aliquot, but quantitation was less reproducible. A prior protein precipitation step improved the quantitation by FASP due to significantly higher peak areas for plasma and a much better reproducibility for milk. Moreover, the miscleavage rate for milk, the identification rate for plasma, and the carbamidomethylation efficiency were improved. In contrast, ISD of both milk and plasma resulted in higher miscleavage rates and is therefore less suitable for targeted proteomics.
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Affiliation(s)
- Sanja Milkovska-Stamenova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
- Correspondence:
| | - Michele Wölk
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (M.W.); (R.H.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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15
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Møller IM, Rasmusson AG, Van Aken O. Plant mitochondria - past, present and future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:912-959. [PMID: 34528296 DOI: 10.1111/tpj.15495] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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16
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Biedka S, Schmidt BF, Frey NM, Boothman SM, Minden JS, Lucas A. Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis. J Proteome Res 2021; 20:4787-4800. [PMID: 34524823 DOI: 10.1021/acs.jproteome.1c00443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Successful proteome analysis requires reliable sample preparation beginning with protein solubilization and ending with a sample free of contaminants, ready for downstream analysis. Most proteome sample preparation technologies utilize precipitation or filter-based separation, both of which have significant disadvantages. None of the current technologies are able to prepare both intact proteins or digested peptides. Here, we introduce a reversible protein tag, ProMTag, that enables whole proteome capture, cleanup, and release of intact proteins for top-down analysis. Alternatively, the addition of a novel Trypsin derivative to the workflow generates peptides for bottom-up analysis. We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests. For top-down analysis, ProMTag cleanup improves resolution on 2D gels; for bottom-up exploration, this methodology produced reproducible mass spectrometry results, demonstrating that the ProMTag method is a truly universal approach that produces high-quality proteome samples compatible with multiple downstream analytical techniques. Data are available via ProteomeXchange with identifier PXD027799.
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Affiliation(s)
- Stephanie Biedka
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States
| | - Brigitte F Schmidt
- JGS Research Co., Pittsburgh, Pennsylvania 15212, United States.,Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nolan M Frey
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sarah M Boothman
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jonathan S Minden
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States.,Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Amber Lucas
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States
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17
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Bahmani M, O’Lone CE, Juhász A, Nye-Wood M, Dunn H, Edwards IB, Colgrave ML. Application of Mass Spectrometry-Based Proteomics to Barley Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8591-8609. [PMID: 34319719 PMCID: PMC8389776 DOI: 10.1021/acs.jafc.1c01871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.
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Affiliation(s)
- Mahya Bahmani
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Clare E. O’Lone
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Angéla Juhász
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Mitchell Nye-Wood
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Hugh Dunn
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
| | - Ian B. Edwards
- Edstar
Genetics Pty Ltd, SABC - Loneragan Building, Murdoch University, 90 South Street, Murdoch, Western Australia 6150, Australia
| | - Michelle L. Colgrave
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Edith Cowan University, School of Science, 270 Joondalup
Drive, Joondalup, Western
Australia 6027, Australia
- CSIRO
Agriculture and Food, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
- Phone: +61-7-3214-2697. . Fax: +61-7-3214-2900
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18
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McCormack M, Dillon E, O’Connor I, MacCarthy E. Investigation of the Initial Host Response of Naïve Atlantic Salmon ( Salmo salar) Inoculated with Paramoeba perurans. Microorganisms 2021; 9:microorganisms9040746. [PMID: 33918228 PMCID: PMC8066739 DOI: 10.3390/microorganisms9040746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 01/15/2023] Open
Abstract
Amoebic Gill Disease (AGD), caused by the ectoparasite Paramoeba perurans is characterised by hyperplasia of the gill epithelium and lamellar fusion. In this study, the initial host response of naïve Atlantic salmon (Salmo salar) inoculated with P. perurans was investigated. Using gel-free proteomic techniques and mass spectrometry gill and serum samples were analysed at 7 timepoints (2, 3, 4, 7, 9, 11 and 14 days) post-inoculation with P. perurans. Differential expression of immune related proteins was assessed by comparison of protein expression from each time point against naïve controls. Few host immune molecules associated with innate immunity showed increased expression in response to gill colonisation by amoebae. Furthermore, many proteins with roles in immune signalling, phagocytosis and T-cell proliferation were found to be inhibited upon disease progression. Initially, various immune factors demonstrated the anticipated increase in expression in response to infection in the serum while some immune inhibition became apparent at the later stages of disease progression. Taken together, the pro-immune trend observed in serum, the lack of a robust early immune response in the gill and the diversity of those proteins in the gill whose altered expression negatively impact the immune response, support the concept of a pathogen-derived suppression of the host response.
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Affiliation(s)
- Michelle McCormack
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (I.O.); (E.M.)
- Correspondence:
| | - Eugene Dillon
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Ian O’Connor
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (I.O.); (E.M.)
| | - Eugene MacCarthy
- Marine and Freshwater Research Centre, Galway Mayo Institute of Technology, Dublin Road, H91 TRNW Galway, Ireland; (I.O.); (E.M.)
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19
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Mikulášek K, Konečná H, Potěšil D, Holánková R, Havliš J, Zdráhal Z. SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. FRONTIERS IN PLANT SCIENCE 2021; 12:635550. [PMID: 33777071 PMCID: PMC7988192 DOI: 10.3389/fpls.2021.635550] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.
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Affiliation(s)
- Kamil Mikulášek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hana Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Renata Holánková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Havliš
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
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20
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Method to Disassemble Spheroids into Core and Rim for Downstream Applications Such as Flow Cytometry, Comet Assay, Transcriptomics, Proteomics, and Lipidomics. Methods Mol Biol 2021. [PMID: 33604853 DOI: 10.1007/978-1-0716-1246-0_12] [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: 10/21/2023]
Abstract
Cells cultured in a monolayer have been a central tool in molecular and cell biology, toxicology, biochemistry, and so on. Therefore, most methods for adherent cells in cell biology are tailored to this format of cell culturing. Limitations and disadvantages of monolayer cultures, however, have resulted in the ongoing development of advanced cell culturing techniques. One such technique is culturing cells as multicellular spheroids, that had been shown to mimic the physiological conditions found in vivo more accurately. This chapter presents a novel method for separation of the spheroid rim and core in mature spheroids (>21 days) for further analysis using advanced molecular biology techniques such as flow cytometry, viability estimations, comet assay, transcriptomics, proteomics and lipidomic. This fast and gentle disassembly of intact spheroids into rim and core fractions, and further into viable single-cell suspension provides an opportunity to bridge the gap from 3D cell culture to current state-of-the-art analysis methods.
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21
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [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: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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22
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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23
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Othman N, Sasidharan S. Validation of target proteins of down-regulated miR-221-5p in HeLa cells treated with Polyalthia longifolia leaf extract using label-free quantitative proteomics approaches. 3 Biotech 2020; 10:399. [PMID: 32850286 DOI: 10.1007/s13205-020-02396-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
The current study was conducted to validate the target proteins of down-regulated miR-221-5p in HeLa cells treated with P. longifolia leaf extract. The validation was done by label-free quantitative proteomics approaches, Gene Ontology (GO) and protein-protein interaction analyses after the cells transfected with miRNA mimics or miRNA inhibitor. The LC-ESI-MS/MS identified a total of 1061, 668, 564 and 940 proteins from untransfected and untreated HeLa cells, untransfected P. longifolia leaf extract-treated HeLa cells, miR-221-5p mimic-transfected P. longifolia leaf extract-treated HeLa cells and anti-miR-221-5p-transfected P. longifolia leaf extract-treated HeLa cells, respectively. The proteomic, GO and protein-protein interaction analyses showed that P. longifolia treatment regulated various protein expressions in HeLa cells, namely tropomyosin, PRKC apoptosis WT1 regulator protein (PAWR), alpha-enolase and beta-enolase, which induced apoptotic cell death after the down-regulation of miR-221-5p. Conclusively, this study showed P. longifolia leaf extract's vital contribution in regulating various protein expressions in HeLa cervical cancer cells to induce apoptotic cell death after downregulation miR-221-5p.
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Affiliation(s)
- Nurulhasanah Othman
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Gelugor, Pulau Pinang Malaysia
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia (USM), 11800 Gelugor, Pulau Pinang Malaysia
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Schwämmle V, Hagensen CE, Rogowska-Wrzesinska A, Jensen ON. PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features. Mol Cell Proteomics 2020; 19:1396-1408. [PMID: 32424025 PMCID: PMC8015005 DOI: 10.1074/mcp.ra119.001777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1919] [Revised: 04/18/2020] [Indexed: 12/11/2022] Open
Abstract
Statistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass spectrometry. Statistical tests need to be sufficiently robust to deal with experiment intrinsic data structures and variations and often also reduced feature coverage across different biological samples due to ubiquitous missing values. A robust statistical test provides accurate confidence scores of large-scale proteomics results, regardless of instrument platform, experimental protocol and software tools. However, the multitude of different combinations of experimental strategies, mass spectrometry techniques and informatics methods complicate the decision of choosing appropriate statistical approaches. We address this challenge by introducing PolySTest, a user-friendly web service for statistical testing, data browsing and data visualization. We introduce a new method, Miss test, that simultaneously tests for missingness and feature abundance, thereby complementing common statistical tests by rescuing otherwise discarded data features. We demonstrate that PolySTest with integrated Miss test achieves higher confidence and higher sensitivity for artificial and experimental proteomics data sets with known ground truth. Application of PolySTest to mass spectrometry based large-scale proteomics data obtained from differentiating muscle cells resulted in the rescue of 10-20% additional proteins in the identified molecular networks relevant to muscle differentiation. We conclude that PolySTest is a valuable addition to existing tools and instrument enhancements that improve coverage and depth of large-scale proteomics experiments. A fully functional demo version of PolySTest and Miss test is available via http://computproteomics.bmb.sdu.dk/Apps/PolySTest.
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Affiliation(s)
- Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.
| | - Christina E Hagensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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The effect of phytoglobin overexpression on the plant proteome during nonhost response of barley (Hordeum vulgare) to wheat powdery mildew (Blumeria graminis f. sp. tritici). Sci Rep 2020; 10:9192. [PMID: 32513937 PMCID: PMC7280273 DOI: 10.1038/s41598-020-65907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/05/2020] [Indexed: 11/08/2022] Open
Abstract
Nonhost resistance, a resistance of plant species against all nonadapted pathogens, is considered the most durable and efficient immune system in plants. To increase our understanding of the response of barley plants to infection by powdery mildew, Blumeria graminis f. sp. tritici, we used quantitative proteomic analysis (LC-MS/MS). We compared the response of two genotypes of barley cultivar Golden Promise, wild type (WT) and plants with overexpression of phytoglobin (previously hemoglobin) class 1 (HO), which has previously been shown to significantly weaken nonhost resistance. A total of 8804 proteins were identified and quantified, out of which the abundance of 1044 proteins changed significantly in at least one of the four comparisons ('i' stands for 'inoculated')- HO/WT and HOi/WTi (giving genotype differences), and WTi/WT and HOi/HO (giving treatment differences). Among these differentially abundant proteins (DAP) were proteins related to structural organization, disease/defense, metabolism, transporters, signal transduction and protein synthesis. We demonstrate that quantitative changes in the proteome can explain physiological changes observed during the infection process such as progression of the mildew infection in HO plants that was correlated with changes in proteins taking part in papillae formation and preinvasion resistance. Overexpression of phytoglobins led to modification in signal transduction prominently by dramatically reducing the number of kinases induced, but also in the turnover of other signaling molecules such as phytohormones, polyamines and Ca2+. Thus, quantitative proteomics broaden our understanding of the role NO and phytoglobins play in barley during nonhost resistance against powdery mildew.
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Li Y, Fang F, Sun M, Zhao Q, Hu Y, Sui Z, Liang Z, Zhang L, Zhang Y. Ionic liquid-assisted protein extraction method for plant phosphoproteome analysis. Talanta 2020; 213:120848. [PMID: 32200934 DOI: 10.1016/j.talanta.2020.120848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Protein phosphorylation is one of the most important post-translational modifications (PTM) and plays critical roles in maintaining many biological processes of plant species, such as being a significant signal related to resistance to tobacco mosaic virus (TMV) infection in tobacco. Compared to other organisms, in-depth profiling of plant phosphoproteome remains challenging due to the harsh extraction environment of plant proteins and low abundance of plant phosphorylation, generally requiring large amount of plant materials. Herein, we developed an integrated strategy for efficient sample preparation of amounts of plant tissues, by integrating ionic liquid (IL)-assisted protein extraction, in-solution digestion, precipitation-assisted IL removal, as well as immobilized metal ion affinity chromatography (IMAC) enrichment of phosphopeptides together. In this strategy, to improve the efficiency of protein extraction and enzymatic digestion, IL of 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) was used as the solubilizer due to its excellent solubilizing ability and enzyme compatibility demonstrated in our previous work. Briefly, the extraction capability of C12Im-Cl for protein amount from tobacco leaves was improved 1.9-fold compared to the commonly used urea-assisted method. Notably, to avoid its interference with subsequent LC-MS analysis, the IL was easily removed from the peptide solution by our proposed ion substitution-mediated C12Im + precipitation strategy with high efficiency. By handling 10 mg of starting protein materials of tobacco leaves, 14,441 unique phosphopeptides, assigned to 5153 unique phosphoproteins were confidently identified. To the best of our knowledge, this was the most comprehensive phosphorylation dataset for tobacco so far. All the results demonstrated our strategy was of great potential to promote the large-scale analysis of plant phosphoproteome.
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Affiliation(s)
- Yang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Fei Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mingwei Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510005, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Yechen Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
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Andrzejczak OA, Havelund JF, Wang WQ, Kovalchuk S, Hagensen CE, Hasler-Sheetal H, Jensen ON, Rogowska-Wrzesinska A, Møller IM, Hebelstrup KH. The Hypoxic Proteome and Metabolome of Barley ( Hordeum vulgare L.) with and without Phytoglobin Priming. Int J Mol Sci 2020; 21:E1546. [PMID: 32102473 PMCID: PMC7073221 DOI: 10.3390/ijms21041546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/13/2022] Open
Abstract
Overexpression of phytoglobins (formerly plant hemoglobins) increases the survival rate of plant tissues under hypoxia stress by the following two known mechanisms: (1) scavenging of nitric oxide (NO) in the phytoglobin/NO cycle and (2) mimicking ethylene priming to hypoxia when NO scavenging activates transcription factors that are regulated by levels of NO and O2 in the N-end rule pathway. To map the cellular and metabolic effects of hypoxia in barley (Hordeum vulgare L., cv. Golden Promise), with or without priming to hypoxia, we studied the proteome and metabolome of wild type (WT) and hemoglobin overexpressing (HO) plants in normoxia and after 24 h hypoxia (WT24, HO24). The WT plants were more susceptible to hypoxia than HO plants. The chlorophyll a + b content was lowered by 50% and biomass by 30% in WT24 compared to WT, while HO plants were unaffected. We observed an increase in ROS production during hypoxia treatment in WT seedlings that was not observed in HO seedlings. We identified and quantified 9694 proteins out of which 1107 changed significantly in abundance. Many proteins, such as ion transporters, Ca2+-signal transduction, and proteins related to protein degradation were downregulated in HO plants during hypoxia, but not in WT plants. Changes in the levels of histones indicates that chromatin restructuring plays a role in the priming of hypoxia. We also identified and quantified 1470 metabolites, of which the abundance of >500 changed significantly. In summary the data confirm known mechanisms of hypoxia priming by ethylene priming and N-end rule activation; however, the data also indicate the existence of other mechanisms for hypoxia priming in plants.
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Affiliation(s)
- Olga A. Andrzejczak
- Department of Agroecology, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark;
| | - Jesper F. Havelund
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Wei-Qing Wang
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Sergey Kovalchuk
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Christina E. Hagensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Harald Hasler-Sheetal
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
- Nordcee, Department of Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ole N. Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark; (J.F.H.); (W.-Q.W.); (S.K.); (C.E.H.); (H.H.-S.); (O.N.J.); (A.R.-W.)
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark;
| | - Kim H. Hebelstrup
- Department of Agroecology, Section of Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark;
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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