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Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Ávila MA, Corrales F. Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta 2024; 274:125988. [PMID: 38569368 DOI: 10.1016/j.talanta.2024.125988] [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: 01/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.
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Affiliation(s)
- Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - João M L Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom; Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - José Ramón Lamas
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Gloria Alvarez-Sola
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
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2
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Brough Z, Zhao Z, Duong van Hoa F. From bottom-up to cell surface proteomics: detergents or no detergents, that is the question. Biochem Soc Trans 2024; 52:1253-1263. [PMID: 38666604 DOI: 10.1042/bst20231020] [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: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Measuring the expression levels of membrane proteins (MPs) is crucial for understanding cell differentiation and tissue specificity, defining disease characteristics, identifying biomarkers, and developing therapeutics. While bottom-up proteomics addresses the need for accurately surveying the membrane proteome, the lower abundance and hydrophobic nature of MPs pose challenges in sample preparation. As MPs normally reside in the lipid bilayer, conventional extraction methods rely on detergents, introducing here a paradox - detergents prevent aggregation and facilitate protein processing, but themselves become contaminants that interfere with downstream analytical applications. Various detergent removal methods exist to mitigate this issue, including filter-aided sample preparation, SP3, suspension trapping, and membrane mimetics. This review delves into the fundamentals of each strategy, applications, merits, and limitations, providing insights into their effectiveness in MP research.
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Affiliation(s)
- Zora Brough
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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3
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Batista F, Moreira RS, Filho VB, Moura H, Wagner G, Miletti LC. Shotgun proteomics of detergent-solubilized proteins from Trypanosoma evansi. J Proteomics 2024; 304:105231. [PMID: 38906247 DOI: 10.1016/j.jprot.2024.105231] [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: 09/13/2023] [Revised: 05/28/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Trypanosoma evansi, the causative agent of surra, is the most prevalent pathogenic salivarian trypanosome and affects the majority of domesticated and wild animals in endemic regions. This work aimed to analyze detergent-solubilized T. evansi proteins and identify potential diagnostic biomarkers for surra. Triton X-114-extracted membrane-enriched proteins (MEP) of T. evansi bloodstream forms were analyzed using a gel-free technique (LC-ESI-MS/MS). 247 proteins were identified following the MS analysis of three biological and technical replicates. Two of these proteins were predicted to have a GPI-anchor, 100 (40%) were predicted to have transmembrane domains, and 166 (67%) were predicted to be membrane-bound based on at least one of six features: location (WolfPSORT, DeepLoc-2.0, Protcomp-9.0), transmembrane, GPI, and gene ontology. It was predicted that 76 (30%) of proteins had membrane evidence. Typical membrane proteins for each organelle were identified, among them ISG families (64, 65, and 75 kDa), flagellar calcium-binding protein, 24 kDa calflagin, syntaxins and oligosaccharyltransferase some of which had previously been studied in other trypanosomatids. T. evansi lacks singletons and exclusive orthologous groups, whereas three distinct epitopes have been identified. Data are available via ProteomeXchange with identifier PXD040594. SIGNIFICANCE: Trypanosoma evansi is a highly prevalent parasite that induces a pathological condition known as "surra" in various species of ungulates across five continents. The infection gives rise to symptoms that are not pathognomonic, thereby posing challenges in its diagnosis and leading to substantial economic losses in the livestock industry. A significant challenge arises from the absence of a diagnostic test capable of distinguishing between Trypanosoma equiperdum and T. evansi, both of which are implicated in equine diseases. Therefore, there is a pressing need to conduct research on the biochemistry of the parasite in order to identify proteins that could potentially serve as targets for differential diagnosis or therapeutic interventions.
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Affiliation(s)
- Franciane Batista
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil; Instituto Federal de Santa Catarina (IFSC), Campus Gaspar, R. Adriano Kormann, 510 - Bela Vista, Gaspar, SC 89111-009, Brazil
| | - Vilmar Benetti Filho
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima. Setor F, Bloco A, Sala 318. Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Hércules Moura
- Biological Mass Spectrometry Laboratory, Centers for Disease Control and Prevention, Atlanta, USA
| | - Glauber Wagner
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima. Setor F, Bloco A, Sala 318. Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil.
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4
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Nickerson JL, Gagnon H, Wentzell PD, Doucette AA. Assessing the precision of a detergent-assisted cartridge precipitation workflow for non-targeted quantitative proteomics. Proteomics 2024; 24:e2300339. [PMID: 38299459 DOI: 10.1002/pmic.202300339] [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: 09/07/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024]
Abstract
Detergent-based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent-based workflow for quantitative proteomics, we herein evaluate the precision of a bottom-up sample preparation strategy incorporating cartridge-based protein precipitation with organic solvent to deplete SDS. The variance of data-independent acquisition (SWATH-MS) data was isolated from sample preparation error by modelling the variance as a function of peptide signal intensity. Our SDS-assisted cartridge workflow yield a coefficient of variance (CV) of 13%-14%. By comparison, conventional (detergent-free) in-solution digestion increased the CV to 50%; in-gel digestion provided lower CVs between 14% and 20%. By filtering peptides predicting to display lower precision, we further enhance the validity of data in global comparative proteomics. These results demonstrate the detergent-based precipitation workflow is a reliable approach for in depth, label-free quantitative proteome analysis.
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Affiliation(s)
| | - Hugo Gagnon
- PhenoSwitch Bioscience Inc., Sherbrooke, Quebec, Canada
| | - Peter D Wentzell
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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5
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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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6
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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7
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Yu H, Tai Q, Yang C, Gao M, Zhang X. Technological development of multidimensional liquid chromatography-mass spectrometry in proteome research. J Chromatogr A 2023; 1700:464048. [PMID: 37167805 DOI: 10.1016/j.chroma.2023.464048] [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: 02/20/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is the method of choice for high-throughput proteomic research. Limited by the peak capacity, the separation performance of conventional single-dimensional LC hampers the development of proteomics. Combining different separation modes orthogonally, multidimensional liquid chromatography (MDLC) with high peak capacity was developed to address this challenge. MDLC has evolved rapidly since its establishment, and the progress of proteomics has been greatly facilitated by the advent of novel MDLC-MS-based methods. In this paper, we will review the advances of MDLC-MS-based methodologies and technologies in proteomics studies, from different perspectives including novel application scenarios and proteomic targets, automation, miniaturization, and the improvement of the classic methods in recent years. In addition, attempts regarding new MDLC-MS models are also mentioned together with the outlook of MDLC-MS-based proteomics methods.
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Affiliation(s)
- Hailong Yu
- Department of Chemistry, Fudan University, 200438, China
| | - Qunfei Tai
- Department of Chemistry, Fudan University, 200438, China
| | - Chenjie Yang
- Department of Chemistry, Fudan University, 200438, China
| | - Mingxia Gao
- Department of Chemistry, Fudan University, 200438, China
| | - Xiangmin Zhang
- Department of Chemistry, Fudan University, 200438, China.
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8
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Pohl T, Gervais A, Dirksen E, D'Alessio V, Bechtold-Peters K, Burkitt W, Cao L, Greven S, Lennard A, Li X, Lössner C, Niu B, Reusch D, O'Riordan T, Shearer J, Spencer D, Xu W, Yi L. Technical considerations for the implementation of the Multi-Attribute-Method by mass spectrometry in a Quality Control laboratory. Eur J Pharm Biopharm 2023:S0939-6411(23)00112-1. [PMID: 37146738 DOI: 10.1016/j.ejpb.2023.04.024] [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: 03/24/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
Multi-attribute methods employing mass spectrometry are applied throughout the biopharmaceutical industry for product and process characterization purposes but are not yet widely accepted as a method for batch release and stability testing under good manufacturing practice (GMP) due to limited experience and level of comfort with the technical, compliance and regulatory aspects of its implementation at quality control (QC) laboratories. Here, current literature related to the development and application of the multi-attribute method by peptide mapping liquid chromatography mass spectrometry (MAM) is compiled with the aim of providing guidance for the implementation of MAM in a QC laboratory. This article, focusing on technical considerations, is the first part of a two-tiered publication, whereby the second part will focus on GMP compliance and regulatory aspects. This publication has been prepared by a group of industry experts representing 14 globally acting major biotechnology companies under the umbrella of the European Federation of Pharmaceutical Industries and Associations (EFPIA) Manufacturing & Quality Expert Group (MQEG).
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Affiliation(s)
- Thomas Pohl
- Biologics Analytical Development, Novartis Pharma AG, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Annick Gervais
- Analytical Development Sciences for Biologicals, UCB, Chemin du Foriest, 1420 Braine L'Alleud, Belgium
| | - Eef Dirksen
- Analytical Development and Quality Control, Byondis, Microweg 22, 6545 CM, Nijmegen, The Netherlands
| | - Valerio D'Alessio
- Analytical Development Biotech, Merck Serono S.p.A., Via Luigi Einaudi, 11, 00012 Guidonia Montecelio - Rome, Italy
| | - Karoline Bechtold-Peters
- Biologics Drug Product Development, Novartis Pharma AG, Klybeckstrasse 141, CH-4057 Basel, Switzerland
| | - Will Burkitt
- Biological Characterisation Product Development Sciences, UCB, 216 Bath Road, Slough, SL1 3WE, UK
| | - Li Cao
- Strategic External Development, GSK, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, USA
| | - Simone Greven
- Pharmaceuticals, Biological Development, Bayer AG, Friedrich-Ebert-Strasse 217-333, 42117 Wuppertal, Germany
| | - Andrew Lennard
- Amgen, 4 Uxbridge Business Park, Sanderson Road, Uxbridge, UB8 1DH, UK
| | - Xue Li
- Biologics Development, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08901, USA
| | - Christopher Lössner
- Analytical Dev. Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Ben Niu
- Biotherapeutics, Bristol Myers Squibb, 4224 Campus Point Court, San Diego, California 92121, USA
| | - Dietmar Reusch
- Pharma Technical Development, Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Tomás O'Riordan
- Eli Lilly Kinsale Limited, Dunderrow, Kinsale, Co. Cork, P17NY71, Ireland
| | - Justin Shearer
- Analytical Development, GSK, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA
| | - David Spencer
- BioPharmaceutical Development, Ipsen Biopharm Limited, 9 Ash Road, Wrexham Industrial Estate, Wrexham, LL13 9UF, UK
| | - Wei Xu
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, One Medimmune Way, Gaithersburg, Maryland 20878, USA
| | - Linda Yi
- Analytical Development, Biogen, 5000 Davis Drive, Research Triangle Park, North Carolina 27709, USA
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9
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Shumilina J, Kiryushkin AS, Frolova N, Mashkina V, Ilina EL, Puchkova VA, Danko K, Silinskaya S, Serebryakov EB, Soboleva A, Bilova T, Orlova A, Guseva ED, Repkin E, Pawlowski K, Frolov A, Demchenko KN. Integrative Proteomics and Metabolomics Analysis Reveals the Role of Small Signaling Peptide Rapid Alkalinization Factor 34 (RALF34) in Cucumber Roots. Int J Mol Sci 2023; 24:ijms24087654. [PMID: 37108821 PMCID: PMC10140933 DOI: 10.3390/ijms24087654] [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: 03/09/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide was proposed to be part of the gene regulatory network of lateral root initiation. Cucumber is an excellent model for studying a special form of lateral root initiation taking place in the meristem of the parental root. We attempted to elucidate the role of the regulatory pathway in which RALF34 is a participant using cucumber transgenic hairy roots overexpressing CsRALF34 for comprehensive, integrated metabolomics and proteomics studies, focusing on the analysis of stress response markers. CsRALF34 overexpression resulted in the inhibition of root growth and regulation of cell proliferation, specifically in blocking the G2/M transition in cucumber roots. Based on these results, we propose that CsRALF34 is not part of the gene regulatory networks involved in the early steps of lateral root initiation. Instead, we suggest that CsRALF34 modulates ROS homeostasis and triggers the controlled production of hydroxyl radicals in root cells, possibly associated with intracellular signal transduction. Altogether, our results support the role of RALF peptides as ROS regulators.
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Affiliation(s)
- Julia Shumilina
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Nadezhda Frolova
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Valeria Mashkina
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Vera A Puchkova
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katerina Danko
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | | | | | - Alena Soboleva
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Tatiana Bilova
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Anastasia Orlova
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Egor Repkin
- Saint Petersburg State University, 199034 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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10
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Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:ijms24065350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
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