1
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Stobernack T, Höper T, Herfurth UM. How processing affects marker peptide quantification - A comprehensive estimation on bovine material relevant for food and feed control. Food Chem 2024; 454:139768. [PMID: 38820638 DOI: 10.1016/j.foodchem.2024.139768] [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: 12/08/2023] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 06/02/2024]
Abstract
Processing food and feed challenges official control e.g. by modifying proteins, which leads to significant underestimation in targeted, MS-based protein quantification. Whereas numerous studies identified processing-induced changes on proteins in various combinations of matrices and processing conditions, studying their impact semi-quantitatively on specific protein sequences might unveil approaches to improve protein quantification accuracy. Thus, 335 post-translational modifications (e.g. oxidation, deamidation, carboxymethylation, Amadori, acrolein adduction) were identified by bottom-up proteomic analysis of 37 bovine materials relevant in food and feed (meat, bone, blood, milk) with varying processing degrees (raw, spray-dried, pressure-sterilized). To mimic protein recovery in a targeted analysis, peak areas of marker and reference peptides were compared to those of their modified versions, which revealed peptide-specific recoveries and variances across all samples. Detailed analysis suggests that incorporating two modified versions additionally to the unmodified marker may significantly improve quantification accuracy in targeted MS-based food and feed control in processed matrices.
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Affiliation(s)
- Tobias Stobernack
- German Federal Institute for Risk Assessment, Department Food Safety, National Reference Laboratory for Animal Protein in Feed, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany; Technische Universität Berlin, Institute of Biotechnology, Bioanalytics, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Tessa Höper
- German Federal Institute for Risk Assessment, Department Food Safety, National Reference Laboratory for Animal Protein in Feed, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Uta M Herfurth
- German Federal Institute for Risk Assessment, Department Food Safety, National Reference Laboratory for Animal Protein in Feed, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
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2
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Kuril AK, Saravanan K. High-throughput method for Peptide mapping and Amino acid sequencing for Calcitonin Salmon in Calcitonin Salmon injection using Ultra High Performance Liquid Chromatography - High Resolution Mass Spectrometry (UHPLC-HRMS) with the application of Bioinformatic tools. J Pharm Biomed Anal 2024; 243:116094. [PMID: 38479303 DOI: 10.1016/j.jpba.2024.116094] [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: 12/16/2023] [Revised: 02/21/2024] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Tandem mass spectrometry (MS/MS) can provide direct and accurate sequence characterization of synthetic peptide drugs, and peptide drug products including side chain modifications in the Peptide drugs. This article explains a step-by-step guide to developing a high-throughput method using high resolution mass spectrometry for characterization of Calcitonin Salmon injection containing high proportion of UV-active excipients. METHODS The major challenge in the method development of Amino acid sequencing and Peptide mapping was presence of phenol in drug product. Phenol is a UV-active excipient and reacts with both Dithiothreitol (DTT) and Trypsin. Hence Calcitonin Salmon was extracted from the Calcitonin Salmon injection using solid phase extraction after the extraction, Amino acid sequencing and peptide mapping study was performed. Upon incubation of Calcitonin Salmon with Trypsin and DTT, digested fragments were generated which were separated by mass compatible reverse phase chromatography and the molecular mass of each fragment was determined using HRMS. RESULTS A reverse phase chromatographic method was developed using UHPLC-HRMS for the determination of direct mass, peptide mapping and to determine the amino acid sequencing in the Calcitonin Salmon injection. The method was found Specific and fragments after trypsin digest are well resolved from each other and the molecular mass of each fragment was determined using HRMS. Sequencing was performed using automated identification of b and y ions annotation and identifications based on MS/MS spectra using Biopharma finder and Proteome discoverer software. CONCLUSION Using this approach 100% protein coverage was obtained and protein was identified as Calcitonin Salmon and the observed masses of tryptic digest of peptide was found similar with theoretical masses. The method can be used for both UV and MS based Peptide mapping and whereas the UV based peptide mapping method can be used as identification test for Calcitonin Salmon drug substance and drug product in quality control.
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Affiliation(s)
| | - K Saravanan
- Bhagwant University, Sikar Road, Ajmer, Rajasthan, India
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3
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Chiva C, Elhamraoui Z, Solé A, Serret M, Wilhelm M, Sabidó E. Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification. Anal Chem 2023; 95:13746-13749. [PMID: 37676919 PMCID: PMC10515110 DOI: 10.1021/acs.analchem.3c02269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Mass spectrometry coupled to liquid chromatography is one of the most powerful technologies for proteome quantification in biomedical samples. In peptide-centric workflows, protein mixtures are enzymatically digested to peptides prior their analysis. However, proteome-wide quantification studies rarely identify all potential peptides for any given protein, and targeted proteomics experiments focus on a set of peptides for the proteins of interest. Consequently, proteomics relies on the use of a limited subset of all possible peptides as proxies for protein quantitation. In this work, we evaluated the stability of the human proteotypic peptides during 21 days and trained a deep learning model to predict peptide stability directly from tryptic sequences, which together constitute a resource of broad interest to prioritize and select peptides in proteome quantification experiments.
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Affiliation(s)
- Cristina Chiva
- Centre
for Genomics Regulation, Barcelona Institute of Science and Technology
(BIST), Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08003, Spain
| | - Zahra Elhamraoui
- Centre
for Genomics Regulation, Barcelona Institute of Science and Technology
(BIST), Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08003, Spain
| | - Amanda Solé
- Centre
for Genomics Regulation, Barcelona Institute of Science and Technology
(BIST), Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08003, Spain
| | - Marc Serret
- Centre
for Genomics Regulation, Barcelona Institute of Science and Technology
(BIST), Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08003, Spain
| | | | - Eduard Sabidó
- Centre
for Genomics Regulation, Barcelona Institute of Science and Technology
(BIST), Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08003, Spain
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4
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Hediyeh-Zadeh S, Webb AI, Davis MJ. MsImpute: Estimation of Missing Peptide Intensity Data in Label-Free Quantitative Mass Spectrometry. Mol Cell Proteomics 2023; 22:100558. [PMID: 37105364 PMCID: PMC10368900 DOI: 10.1016/j.mcpro.2023.100558] [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: 06/16/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023] Open
Abstract
Mass spectrometry (MS) enables high-throughput identification and quantification of proteins in complex biological samples and can provide insights into the global function of biological systems. Label-free quantification is cost-effective and suitable for the analysis of human samples. Despite rapid developments in label-free data acquisition workflows, the number of proteins quantified across samples can be limited by technical and biological variability. This variation can result in missing values which can in turn challenge downstream data analysis tasks. General purpose or gene expression-specific imputation algorithms are widely used to improve data completeness. Here, we propose an imputation algorithm designated for label-free MS data that is aware of the type of missingness affecting data. On published datasets acquired by data-dependent and data-independent acquisition workflows with variable degrees of biological complexity, we demonstrate that the proposed missing value estimation procedure by barycenter computation competes closely with the state-of-the-art imputation algorithms in differential abundance tasks while outperforming them in the accuracy of variance estimates of the peptide abundance measurements, and better controls the false discovery rate in label-free MS experiments. The barycenter estimation procedure is implemented in the msImpute software package and is available from the Bioconductor repository.
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Affiliation(s)
- Soroor Hediyeh-Zadeh
- Bioinformatics Division, WEHI, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia; Colonial Foundation Healthy Ageing Centre, WEHI, Melbourne, Australia
| | - Andrew I Webb
- Department of Medical Biology, University of Melbourne, Melbourne, Australia; Colonial Foundation Healthy Ageing Centre, WEHI, Melbourne, Australia; Advanced Technology and Biology Division, WEHI, Melbourne, Australia
| | - Melissa J Davis
- Bioinformatics Division, WEHI, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia; The Diamantina Institute, The University of Queensland, Brisbane, Australia; The South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia.
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5
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Yildiz P, Ozcan S. A single protein to multiple peptides: Investigation of protein-peptide correlations using targeted alpha-2-macroglobulin analysis. Talanta 2023; 265:124878. [PMID: 37392709 DOI: 10.1016/j.talanta.2023.124878] [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: 01/23/2023] [Revised: 04/30/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023]
Abstract
Recent advances in proteomics technologies have enabled the analysis of thousands of proteins in a high-throughput manner. Mass spectrometry (MS) based proteomics uses a peptide-centric approach where biological samples undergo specific proteolytic digestion and then only unique peptides are used for protein identification and quantification. Considering the fact that a single protein may have multiple unique peptides and a number of different forms, it becomes essential to understand dynamic protein-peptide relationships to ensure robust and reliable peptide-centric protein analysis. In this study, we investigated the correlation between protein concentration and corresponding unique peptide responses under a conventional proteolytic digestion condition. Protein-peptide correlation, digestion efficiency, matrix-effect, and concentration-effect were evaluated. Twelve unique peptides of alpha-2-macroglobulin (A2MG) were monitored using a targeted MS approach to acquire insights into protein-peptide dynamics. Although the peptide responses were reproducible between replicates, protein-peptide correlation was moderate in protein standards and low in complex matrices. The results suggest that reproducible peptide signal could be misleading in clinical studies and a peptide selection could dramatically change the outcome at protein level. This is the first study investigating quantitative protein-peptide correlations in biological samples using all unique peptides representing the same protein and opens a discussion on peptide-based proteomics.
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Affiliation(s)
- Pelin Yildiz
- Department of Chemistry, Middle East Technical University (METU), 06800, Ankara, Turkiye; Nanografi Nanotechnology Co, Middle East Technical University (METU) Technopolis, 06531, Ankara, Turkiye
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University (METU), 06800, Ankara, Turkiye; Cancer Systems Biology Laboratory (CanSyL), Middle East Technical University (METU), 06800, Ankara, Turkiye.
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6
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Kohler D, Staniak M, Tsai TH, Huang T, Shulman N, Bernhardt OM, MacLean BX, Nesvizhskii AI, Reiter L, Sabido E, Choi M, Vitek O. MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale. J Proteome Res 2023; 22:1466-1482. [PMID: 37018319 PMCID: PMC10629259 DOI: 10.1021/acs.jproteome.2c00834] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 04/06/2023]
Abstract
The MSstats R-Bioconductor family of packages is widely used for statistical analyses of quantitative bottom-up mass spectrometry-based proteomic experiments to detect differentially abundant proteins. It is applicable to a variety of experimental designs and data acquisition strategies and is compatible with many data processing tools used to identify and quantify spectral features. In the face of ever-increasing complexities of experiments and data processing strategies, the core package of the family, with the same name MSstats, has undergone a series of substantial updates. Its new version MSstats v4.0 improves the usability, versatility, and accuracy of statistical methodology, and the usage of computational resources. New converters integrate the output of upstream processing tools directly with MSstats, requiring less manual work by the user. The package's statistical models have been updated to a more robust workflow. Finally, MSstats' code has been substantially refactored to improve memory use and computation speed. Here we detail these updates, highlighting methodological differences between the new and old versions. An empirical comparison of MSstats v4.0 to its previous implementations, as well as to the packages MSqRob and DEqMS, on controlled mixtures and biological experiments demonstrated a stronger performance and better usability of MSstats v4.0 as compared to existing methods.
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Affiliation(s)
- Devon Kohler
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | | | - Tsung-Heng Tsai
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ting Huang
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | | | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Alexey I. Nesvizhskii
- Department
of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Eduard Sabido
- Center for
Genomic Regulation, Barcelona Institute
of Science and Technology, Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08002, Spain
| | - Meena Choi
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Olga Vitek
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
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7
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Quality Control—A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome. Biomolecules 2023; 13:biom13030491. [PMID: 36979426 PMCID: PMC10046854 DOI: 10.3390/biom13030491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/08/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Proteomic studies using mass spectrometry (MS)-based quantification are a main approach to the discovery of new biomarkers. However, a number of analytical conditions in front and during MS data acquisition can affect the accuracy of the obtained outcome. Therefore, comprehensive quality assessment of the acquired data plays a central role in quantitative proteomics, though, due to the immense complexity of MS data, it is often neglected. Here, we address practically the quality assessment of quantitative MS data, describing key steps for the evaluation, including the levels of raw data, identification and quantification. With this, four independent datasets from cerebrospinal fluid, an important biofluid for neurodegenerative disease biomarker studies, were assessed, demonstrating that sample processing-based differences are already reflected at all three levels but with varying impacts on the quality of the quantitative data. Specifically, we provide guidance to critically interpret the quality of MS data for quantitative proteomics. Moreover, we provide the free and open source quality control tool MaCProQC, enabling systematic, rapid and uncomplicated data comparison of raw data, identification and feature detection levels through defined quality metrics and a step-by-step quality control workflow.
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8
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Murar M, Pujals S, Albertazzi L. Multivalent effect of peptide functionalized polymeric nanoparticles towards selective prostate cancer targeting. NANOSCALE ADVANCES 2023; 5:1378-1385. [PMID: 36866255 PMCID: PMC9972852 DOI: 10.1039/d2na00601d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The concept of selective tumor targeting using nanomedicines has been around for decades; however, no targeted nanoparticle has yet reached the clinic. A key bottleneck is the non-selectivity of targeted nanomedicines in vivo, which is attributed to the lack of characterization of their surface properties, especially the ligand number, thereby calling for robust techniques that allow quantifiable outcomes for an optimal design. Multivalent interactions comprise multiple copies of ligands attached to scaffolds, allowing simultaneous binding to receptors, and they play an important role in targeting. As such, 'multivalent' nanoparticles facilitate simultaneous interaction of weak surface ligands with multiple target receptors resulting in higher avidity and enhanced cell selectivity. Therefore, the study of weak binding ligands for membrane-exposed biomarkers is crucial for the successful development of targeted nanomedicines. Here we carried out a study of a cell targeting peptide known as WQP having weak binding affinity for prostate specific membrane antigen, a known prostate cancer biomarker. We evaluated the effect of its multivalent targeting using polymeric NPs over its monomeric form on the cellular uptake in different prostate cancer cell lines. We developed a method of specific enzymatic digestion to quantify the number of WQPs on NPs having different surface valencies and observed that increasing valencies resulted in a higher cellular uptake of WQP-NPs over the peptide alone. We also found that WQP-NPs showed higher uptake in PSMA over-expressing cells, attributed to a stronger avidity for selective PSMA targeting. This kind of strategy can be useful for improving the binding affinity of a weak ligand as a means for selective tumor targeting.
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Affiliation(s)
- Madhura Murar
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Silvia Pujals
- Institute for Advanced Chemistry of Catalonia (IQAC) Barcelona Spain
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) Barcelona Spain
- Department of Biomedical Engineering, Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology Eindhoven The Netherlands
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9
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Khanal N, Chen Z, Alelyunas YW, Szapacs ME, Wrona MD, Sikorski TW. Systematic optimization of targeted and multiplexed MS-based screening workflows for protein biomarkers. Bioanalysis 2022; 14:341-356. [PMID: 35255714 DOI: 10.4155/bio-2021-0245] [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: 11/17/2022] Open
Abstract
Background: The capability of targeted MS-based methods to simultaneously measure multiple analytes with high selectivity and sensitivity greatly facilitates the discovery and quantitation of novel biomarkers. However, the complexity of biological samples is a major bottleneck that requires extensive sample preparation. Results: This paper reports a generic workflow to optimize surrogate peptide-based protein biomarker screening for seven human proteins in a multiplexed manner without the need for any specific affinity reagents. Each step of the sample processing and LC-MS methods is systematically assessed and optimized for better analytical performance. Conclusion: The established method is used for the screening of multiple myeloma patient samples to determine which proteins could be robustly measured and serve as potential biomarkers of the disease.
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Affiliation(s)
- Neelam Khanal
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
- Scientific Operations, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Zhuo Chen
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
| | - Yun W Alelyunas
- Scientific Operations, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Matthew E Szapacs
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
| | - Mark D Wrona
- Scientific Operations, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Timothy W Sikorski
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
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10
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Yang H, Cao Z, Mou R, Cao Z, Chen M. Quantification of rice α‐globulin allergen using liquid chromatography–tandem mass spectrometry combined with cysteine‐specific modifier and extended stable isotope‐labeled peptide. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Huan Yang
- Jiangxi Agricultural University Nanchang 330000 People's Republic of China
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Zhao‐yun Cao
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Ren‐xiang Mou
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Zhen‐zhen Cao
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Ming‐xue Chen
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
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11
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Yang H, Cao Z, Ma Y, Chen M. [Simultaneous determination of three allergic proteins in rice and products by high performance liquid chromatography-tandem mass spectrometry combined with stable isotope-labeled peptides]. Se Pu 2021; 39:1314-1323. [PMID: 34812003 PMCID: PMC9404202 DOI: 10.3724/sp.j.1123.2021.06039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
基于稳定同位素标记特征肽段和液相色谱-质谱联用仪建立稻米及制品中3种过敏蛋白质的同时定量方法。稻米及制品样品经盐溶液提取,赖氨酰基内切酶(Lys-C)和胰蛋白酶依次水解,C18-SD柱净化后,采用纳升高效液相色谱-线性离子阱-静电场轨道阱(NanoLC-LTQ-Orbitrap)采集和Protein Discovery软件鉴定,NCBI和Uniprot数据库的基本局部搜索比对工具(BLAST)筛选验证,最终获得表征稻米及制品中α-淀粉酶/胰蛋白酶抑制剂类蛋白质(seed allergenic protein RAG2, RAG2)、乙二醛酶Ⅰ活性蛋白(glyoxalase Ⅰ)和α-球蛋白(19 kDa globulin)3种过敏蛋白质的特异性肽段。3个特异性肽段经液相色谱梯度洗脱,在Poroshell色谱柱上实现完全分离,由三重四极杆质谱仪分析。实验通过优化多反应监测(MRM)质谱参数,比较不同溶剂体系、水解酶种类和酶量等酶解条件,结合内标法定量,实现对稻米及制品中3种蛋白质的绝对定量。实验结果表明,当酶解溶剂中含1 g/L十二烷基硫酸钠,采用Lys-C和胰蛋白酶组合消化策略,可有效提高3种蛋白质的酶切效率至65.7%~97.3%。该方法在1~200 nmol/L范围内线性关系良好,相关系数均大于0.9972, 3种蛋白质的检出限和定量限分别为3 mg/kg和10 mg/kg。3种蛋白质在空白稻米制品基质中3个水平下的加标回收率为80.6%~103.7%,日间和日内精密度均小于11.5%。该方法稳定性好,检测灵敏度高,操作简便,在分析各类稻米及制品中3种过敏蛋白质含量具有广泛的应用前景。
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Affiliation(s)
- Huan Yang
- Rice Product Quality Inspection and Supervision Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, China.,Jiangxi Agricultural University, Nanchang 330000, China
| | - Zhaoyun Cao
- Rice Product Quality Inspection and Supervision Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, China
| | - Youning Ma
- Rice Product Quality Inspection and Supervision Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, China
| | - Mingxue Chen
- Rice Product Quality Inspection and Supervision Center, Ministry of Agriculture and Rural Affairs, China National Rice Research Institute, Hangzhou 310006, China
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12
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Pavón-Pérez J, Henriquez-Aedo K, Salazar R, Herrero M, Aranda M. Chemometric optimization of trypsin digestion method applying infrared, microwave and ultrasound energies for determination of caseins and ovalbumin in wines. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2021; 58:2914-2923. [PMID: 34294953 PMCID: PMC8249656 DOI: 10.1007/s13197-020-04793-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/20/2020] [Accepted: 09/12/2020] [Indexed: 06/13/2023]
Abstract
Caseins and ovalbumin are frequently used as wine fining agents to remove undesirable compounds like polymeric phenols. Their presence in wines is a subject of concern because may cause adverse effects on susceptible consumers, especially when their presence is not labeled. A key step for its determination is trypsin digestion, which is considered the bottleneck of bottom-up approach workflow because usually requires several hours. To reduce this time, the objective of this work was to carry out a chemometric optimization of trypsin digestion method applying infrared, microwave and ultrasound energies to determine caseins and ovalbumin in wines. The conditions of each accelerated digestion method were optimized using a Response Surface Methodology based on central composite design. The parameters optimized were digestion time and trypsin: protein ratio. The response variable evaluated was digestion yield, which was determined through the peak area of each protein transition determined by liquid chromatography-mass spectrometry. The most effective technique was microwave followed by ultrasound and infrared. Since optimal values of microwave and ultrasound-assisted digestion were the same, the later was chosen considering sample preparation and cost. Applying the proposed approach, a reduction of ca. 140 and 240-fold on digestion time was achieved compared with optimized and non-optimized conventional methods, respectively. With this workflow, both proteins were digested in a single 3 min process allowing its detection by liquid chromatography-mass spectrometry at µg L-1 level, which is ca. 60 times lower than the current limit of 0.25 mg L-1.
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Affiliation(s)
- Jessy Pavón-Pérez
- Departamento de Ciencia Y Tecnología de Los Alimentos, Facultad de Farmacia, Universidad de Concepción. Barrio Universitario S/N, Concepción, Chile
| | - Karem Henriquez-Aedo
- Laboratorio de Biotecnología Y Genética de Alimentos, Departamento de Ciencia Y Tecnología de Los Alimentos, Facultad de Farmacia, Universidad de Concepción. Barrio Universitario S/N, Concepción, Chile
- Laboratorio de Alimentos Funcionales, Centro de Biotecnología, Universidad de Concepción. Barrio Universitario S/N, Concepción, Chile
| | - Ricardo Salazar
- Laboratorio de Electroquímica del Medio Ambiente, LEQMA, Departamento de Química de Los Materiales, Universidad de Santiago de Chile, USACH, Casilla 40, C.P. 33, Av. Libertador Bernardo O’Higgins, 3363, Estación Central, Santiago, Chile
| | - Miguel Herrero
- Instituto de Investigación en Ciencias de La Alimentación CIAL (CSIC-UAM), Calle Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - Mario Aranda
- Laboratorio de Investigación en Fármacos Y Alimentos, Departamento de Farmacia, Facultad de Química Y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna Casilla 306, Correo 22, 4860 Macul, Santiago, Chile
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13
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Zhang S, Di Y, Yao J, Wang Y, Shu H, Yan G, Zhang L, Lu H. Mass defect-based carbonyl activated tags (mdCATs) for multiplex data-independent acquisition proteome quantification. Chem Commun (Camb) 2021; 57:737-740. [DOI: 10.1039/d0cc06493a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A novel eight-plex mass-defect-based carbonyl activated tag (mdCAT) has been designed for DIA quantification for the first time.
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Affiliation(s)
- Siwen Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Yi Di
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Jun Yao
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Yingjie Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - Hong Shu
- Department of Clinical Laboratory
- Cancer Hospital of Guangxi Medical University
- Nanning
- China
| | - Guoquan Yan
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research
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14
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Biggi S, Bassani GA, Vincoli V, Peroni D, Bonaldo V, Biagiotti M, Belli R, Alessandrino A, Biasini E, Freddi G. Characterization of Physical, Mechanical, and Biological Properties of SilkBridge Nerve Conduit after Enzymatic Hydrolysis. ACS APPLIED BIO MATERIALS 2020; 3:8361-8374. [PMID: 35019608 DOI: 10.1021/acsabm.0c00613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The in vitro degradation profile and the cytotoxicity of the degradation products of a silk fibroin (SF)-based nerve conduit (SilkBridge), with a complex three-layered wall architecture comprising both native and regenerated (electrospun) fibers, are reported. The bacterial protease type XIV from Streptomyces griseus was used as a hydrolytic agent at three different enzyme/substrate ratios (1:8, 1:80, and 1:800 w/w) to account for the different susceptibility to degradation of the native and regenerated components. The incubation time was extended up to 91 days. At fixed time points, the remaining device, the insoluble debris, and the incubation buffers containing soluble degradation products were separated and analyzed. The electrospun fibers forming the inner and outer layers of the conduit wall were almost completely degraded within 10 days of incubation at an enzyme/substrate ratio of 1:80 w/w. The progression of degradation was highlighted by the emergence of zones of erosion and discontinuity along the electrospun fibers, weakening of the electrospun layers, and decrease in resistance to compressive stress. Native SF microfibers forming the middle layer of the conduit wall displayed a higher resistance to enzymatic degradation. When incubated at an enzyme/substrate ratio of 1:8 w/w, the weight decreased gradually over the incubation time as a consequence of fiber erosion and fragmentation. Analogously, the tensile properties markedly decreased. Both spectroscopic and thermal analyses confirmed the gradual increase in the crystalline character of the fibers. The incubation buffers containing the soluble degradation products were subjected to cytotoxicity testing with human HEK293 cells and mouse neuroblastoma N2a cells. No detrimental effects on cell viability were observed, suggesting that the degradation products do not retain any toxic property. Finally, the mass spectrometry analysis of degradation products showed that the SF polypeptides recovered in the incubation buffers were representative of the aminoacidic sequence of the fibroin light chain and of the highly repetitive fibroin heavy chain, indicating that virtually the entire sequence of the fibroin protein constituent of SilkBridge was degraded.
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Affiliation(s)
- Silvia Biggi
- Dulbecco Telethon Laboratory of Prions and Amyloids, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | | | | | - Daniele Peroni
- Mass Spectrometry (MS) Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | - Valerio Bonaldo
- Dulbecco Telethon Laboratory of Prions and Amyloids, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | - Marco Biagiotti
- Silk Biomaterials Srl, Via Cavour 2, 22074 Lomazzo, Co, Italy
| | - Romina Belli
- Mass Spectrometry (MS) Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | | | - Emiliano Biasini
- Dulbecco Telethon Laboratory of Prions and Amyloids, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | - Giuliano Freddi
- Silk Biomaterials Srl, Via Cavour 2, 22074 Lomazzo, Co, Italy
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15
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Calvano CD, Rigante ECL, Cataldi TRI, Sabbatini L. In Situ Hydrogel Extraction with Dual-Enzyme Digestion of Proteinaceous Binders: the Key for Reliable Mass Spectrometry Investigations of Artworks. Anal Chem 2020; 92:10257-10261. [PMID: 32648736 DOI: 10.1021/acs.analchem.0c01898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel strategy based on in situ dual-enzyme digestion of paint layer proteinaceous binders is introduced for faster and more confident identification, resulting in a bottom-up proteomics approach by MALDI-TOF mass spectrometry (MS). In situ sampling/extraction of proteinaceous binders using small pieces of a hydrophilic gel, previously loaded with trypsin and chymotrypsin proteolytic enzymes, was successfully exploited. Along with minimal invasiveness, the synergy of both enzymes was very useful to increase the number of annotated peptide peaks with their corresponding amino acid sequence by database search and subsequent MALDI-TOF/TOF analysis. The protocol was initially aimed at enhancing the identification of egg-based binders and then validated on fresh and aged model pictorial layers; an increased protein coverage was significantly attained regardless of the used painting binders. Optical microscope images and spectrophotocolorimetry analysis evidenced that the painting layers were not damaged or altered because of contact/sampling without leaving hydrogel residues. The proposed protocol was successfully applied on a painted altarpiece "Assumption of the Virgin" dated to the XVI century and on an angel statue of the Nativity crib dated to the XII century, both from Altamura's Cathedral (Apulia, Italy). The occurrence of various protein binders of animal origin was easily and reliably ascertained.
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16
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Lin Z, Ren Y, Shi Z, Zhang K, Yang H, Liu S, Hao P. Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8733. [PMID: 32031715 DOI: 10.1002/rcm.8733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
UNLABELLED High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation. METHODS In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry. RESULTS Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol. CONCLUSIONS The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol.
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Affiliation(s)
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhaomei Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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17
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Tiruvayipati S, Wolfgeher D, Yue M, Duan F, Andrade J, Jiang H, Schuger L. Variability in protein cargo detection in technical and biological replicates of exosome-enriched extracellular vesicles. PLoS One 2020; 15:e0228871. [PMID: 32119684 PMCID: PMC7051218 DOI: 10.1371/journal.pone.0228871] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
Exosomes are extracellular vesicles (EVs) of ~20-200 nm diameter that shuttle DNAs, RNAs, proteins and other biomolecules between cells. The large number of biomolecules present in exosomes demands the frequent use of high-throughput analysis. This, in turn, requires technical replicates (TRs), and biological replicates (BRs) to produce accurate results. As the number and abundance of identified biomolecules varies between replicates (Rs), establishing the replicate variability predicted for the event under study is essential in determining the number of Rs required. Although there have been few reports of replicate variability in high throughput biological data, none of them focused on exosomes. Herein, we determined the replicate variability in protein profiles found in exosomes released from 3 lung adenocarcinoma cell lines, H1993, A549 and H1975. Since exosome isolates are invariably contaminated by a small percentage of ~200-300 nm microvesicles, we refer to our samples as exosome-enriched EVs (EE-EVs). We generated BRs of EE-EVs from each cell line, and divided each group into 3 TRs. All Rs were analyzed by liquid chromatography/mass spectrometry (LC/MS/MS) and customized bioinformatics and biostatistical workflows (raw data available via ProteomeXchange: PXD012798). We found that the variability among TRs as well as BRs, was largely qualitative (protein present or absent) and higher among BRs. By contrast, the quantitative (protein abundance) variability was low, save for the H1975 cell line where the quantitative variability was significant. Importantly, our replicate strategy identified 90% of the most abundant proteins, thereby establishing the utility of our approach.
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Affiliation(s)
- Suma Tiruvayipati
- Biological Sciences Division, Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Don Wolfgeher
- Proteomics Core Laboratory, Cummings Life Science Center, The University of Chicago, Chicago, Illinois, United States of America
| | - Ming Yue
- Biological Sciences Division, Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - FangFang Duan
- Biological Sciences Division, Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Jorge Andrade
- The Center for Research Informatics, The University of Chicago, Chicago, Illinois, United States of America
| | - Hui Jiang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucia Schuger
- Biological Sciences Division, Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
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18
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Doellinger J, Schneider A, Hoeller M, Lasch P. Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction. Mol Cell Proteomics 2020; 19:209-222. [PMID: 31754045 PMCID: PMC6944244 DOI: 10.1074/mcp.tir119.001616] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.
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Affiliation(s)
- Joerg Doellinger
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany.
| | - Andy Schneider
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Marcell Hoeller
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
| | - Peter Lasch
- Robert Koch-Institute, Centre for Biological Threats and Special Pathogens, Proteomics and Spectroscopy (ZBS6), Berlin, Germany
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19
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Maillet N. Rapid Peptides Generator: fast and efficient in silico protein digestion. NAR Genom Bioinform 2019; 2:lqz004. [PMID: 33575558 PMCID: PMC7671371 DOI: 10.1093/nargab/lqz004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/27/2019] [Accepted: 09/07/2019] [Indexed: 11/14/2022] Open
Abstract
Recent developments in mass spectrometry techniques used in proteomics and proteogenomics have led to a constantly increasing interest in proteases. These proteases are used in different mass spectrometry analyses requiring protein digestions. To perform such digestions, one or multiple proteases are used. Few software exist that predict cleavage sites of proteases and simulate in silico digestions. In this work, Rapid Peptides Generator (RPG), a new software developed in order to predict proteases-induced cleavage sites on sequences, is presented. RPG offers extra features and overcomes most issues of existing software in different ways. First, for each generated peptide, RPG gives its sequence, length and estimation of mass, measurements already provided by other software, as well as the peptide’s isoelectric point. Moreover, contrary to existing software that limit the option of proteases to be used to a predefined list, users of RPG are able to easily define new proteases using a simple yet powerful grammar. This feature allows users to stay up-to-date to new or more specific proteases available on the market and optimizes time and effort before the actual mass spectrometry experiment. RPG is freely available through the well established package management system ‘pip’ and follows the standards for software development.
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Affiliation(s)
- Nicolas Maillet
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
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20
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Hakobyan A, Schneider MB, Liesack W, Glatter T. Efficient Tandem LysC/Trypsin Digestion in Detergent Conditions. Proteomics 2019; 19:e1900136. [DOI: 10.1002/pmic.201900136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/22/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Anna Hakobyan
- Research group of Methanotrophic Bacteria, and Environmental Genomics/TranscriptomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
| | - Martin Bernd Schneider
- Core Facility for Mass Spectrometry and ProteomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
- Genomics and Proteomics Core FacilityGerman Cancer Research Center Im Neuenheimer Feld 580 D‐69120 Heidelberg Germany
| | - Werner Liesack
- Research group of Methanotrophic Bacteria, and Environmental Genomics/TranscriptomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
- Center for Synthetic Microbiology (SYNMIKRO)Philipps‐Universität Marburg Karl‐von‐Frisch‐Str. 16 D‐35043 Marburg Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and ProteomicsMax Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10 D‐35043 Marburg Germany
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21
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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Chen Y, Doud E, Stone T, Xin L, Hong W, Li Y. Rapid global characterization of immunoglobulin G1 following oxidative stress. MAbs 2019; 11:1089-1100. [PMID: 31156028 PMCID: PMC6748588 DOI: 10.1080/19420862.2019.1625676] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although peroxide and leachable metal-induced chemical modifications are among the most important quality attributes in bioprocess development, there is no mainstream characterization method covering all common modifications theoretically possible on therapeutic proteins that also gives consistent results quickly. Here, we describe a method for rapid and consistent global characterization of leachable metals- or peroxide-stressed immunoglobulin (Ig) G1 monoclonal antibodies (mAbs). Using two independent protease digestions, data-independent acquisition and data-dependent acquisition liquid chromatography high-resolution mass spectrometry, we monitored 55 potential chemical modifications on trastuzumab, a humanized IgG1 mAb. Processing templates including all observed peptides were developed on Skyline to consistently monitor all modifications throughout the stress conditions for both enzymatic digestions. The Global Characterization Data Processing Site, a universal automated data processing application, was created to batch process data, plot modification trends for peptides, generate sortable and downloadable modification tables, and produce Jmol code for three-dimensional structural models of the analyzed protein. In total, 53 sites on the mAb were found to be modified. Oxidation rates generally increased with the peroxide concentration, while leachable metals alone resulted in lower rates of modifications but more oxidative degradants. Multiple chemical modifications were found on IgG1 surfaces known to interact with FcɣRIII, complement protein C1q, and FcRn, potentially affecting activity. The combination of Skyline templates and the Global Characterization Data Processing Site results in a universally applicable assay allowing users to batch process numerous modifications. Applying this new method to stability studies will promote a broader and deeper understanding of stress modifications on therapeutic proteins.
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Affiliation(s)
- Yao Chen
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Emma Doud
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Todd Stone
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Lun Xin
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Wei Hong
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Yunsong Li
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
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23
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Clark DJ, Hu Y, Schnaubelt M, Fu Y, Ponce S, Chen SY, Zhou Y, Shah P, Zhang H. Simple Tip-Based Sample Processing Method for Urinary Proteomic Analysis. Anal Chem 2019; 91:5517-5522. [PMID: 30924636 PMCID: PMC6512789 DOI: 10.1021/acs.analchem.8b05234] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mass spectrometry-based urinary proteomics is one of the most attractive strategies to discover proteins for diagnosis, prognosis, monitoring, or prediction of therapeutic responses of urological diseases involving the kidney, prostate, and bladder; however, interfering compounds found in urine necessitate sample preparation strategies that are currently not suitable for urinary proteomics in the clinical setting. Herein, we describe the C4-tip method, comprising a simple, automated strategy utilizing a reverse-phase resin tip-based format and "on-tip" digestion to examine the urine proteome. We first determined the optimal conditions for protein isolation and protease digestion on the C4-tip using the standard protein bovine fetuin. Next, we applied the C4-tip method to urinary proteomics, identifying a total of 813 protein groups using LC-MS/MS, with identified proteins from the C4-tip method displaying a similar distribution of gene ontology (GO) cellular component assignments compared to identified proteins from an ultrafiltration preparation method. Finally, we assessed the reproducibility of the C4-tip method, revealing a high Spearman correlation R-value for shared proteins identified across all tips. Together, we have shown the C4-tip method to be a simple, robust method for high-throughput analysis of the urinary proteome by mass spectrometry in the clinical setting.
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Affiliation(s)
- David J. Clark
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Yi Fu
- The Bradley Department of Electrical and Computer Engineering Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Shao-Yung Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21231, United States
| | - Yangying Zhou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Punit Shah
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
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25
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Ma F, Liu F, Xu W, Li L. Surfactant and Chaotropic Agent Assisted Sequential Extraction/On-Pellet Digestion (SCAD) for Enhanced Proteomics. J Proteome Res 2018; 17:2744-2754. [PMID: 29923408 PMCID: PMC6171104 DOI: 10.1021/acs.jproteome.8b00197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As a popular sample preparation approach, filter-aided sample preparation (FASP) has been widely used in proteomic analysis. However, several limitations have been noted, including sample loss during filtration, repetitive centrifugation steps, and the possibility of breakage of filtration membrane. Extraction bias among different sample preparation strategies presents another challenge. To overcome these limitations and address remaining challenges, we developed a novel surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion (SCAD) protocol. The new strategy resulted in higher protein yield and improved peptide recovery and protein coverage compared to two conventional sample preparation methods (FASP and urea). In combination of three strategies, more than 10,000 distinct protein groups were identified with 1% FDR from MDA-MB-231 cells without any prefractionation. This in-depth proteome analysis was accomplished by optimization of protein extraction, enzymatic digestion, LC gradient, and peptide sequencing method. Ingenuity Pathways Analysis (IPA) of proteins exclusively identified in SCAD revealed several crucial signaling pathways that regulate breast cancer progression. SCAD also enabled an unbiased extraction of different categories of proteins (membrane, intracellular, nuclear) associated with tumorigenesis, which integrates the advantages of FASP and urea extraction. This novel strategy expedites comprehensive protein identification, which is applicable for biomarker discovery in various types of cancers.
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Affiliation(s)
- Fengfei Ma
- School of Pharmacy, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin‒Madison, Madison, Wisconsin 53706, United States
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China
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26
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Betancourt LH, Sanchez A, Pla I, Kuras M, Zhou Q, Andersson R, Marko-Varga G. Quantitative Assessment of Urea In-Solution Lys-C/Trypsin Digestions Reveals Superior Performance at Room Temperature over Traditional Proteolysis at 37 °C. J Proteome Res 2018; 17:2556-2561. [PMID: 29812944 DOI: 10.1021/acs.jproteome.8b00228] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Urea-containing buffer solutions are generally used in proteomic studies to aid protein denaturation and solubilization during cell and tissue lysis. It is well-known, however, that urea can lead to carbamylation of peptides and proteins and, subsequently, incomplete digestion of proteins. By the use of cells and tissues that had been lysed with urea, different solution digestion strategies were quantitatively assessed. In comparison with traditional proteolysis at 37 °C, urea in-solution digestion performed at room temperature improved peptide and protein identification and quantitation and had a minimum impact on miscleavage rates. Furthermore, the signal intensities and the number of carbamylated and pyroglutamic acid-modified peptides decreased. Overall, this led to a reduction in the negative effects often observed for such modifications. Data are available via ProteomeXchange with identifier PXD009426.
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Affiliation(s)
- Lazaro Hiram Betancourt
- Division of Clinical Protein Science and Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , SE-221 84 Lund , Sweden
| | - Aniel Sanchez
- Division of Clinical Protein Science and Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , SE-221 84 Lund , Sweden
| | - Indira Pla
- Division of Clinical Protein Science and Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , SE-221 84 Lund , Sweden
| | - Magdalena Kuras
- Division of Clinical Protein Science and Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , SE-221 84 Lund , Sweden
| | - Qimin Zhou
- Department of Clinical Sciences Lund (Surgery) , Lund University, and Skåne University Hospital , SE-221 84 Lund , Sweden
| | - Roland Andersson
- Department of Clinical Sciences Lund (Surgery) , Lund University, and Skåne University Hospital , SE-221 84 Lund , Sweden
| | - Gyorgy Marko-Varga
- Division of Clinical Protein Science and Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , SE-221 84 Lund , Sweden.,First Department of Surgery , Tokyo Medical University , Shinjuku-ku , Tokyo 160-8402 , Japan
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27
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Dahabiyeh LA. The discovery of protein biomarkers in pre-eclampsia: the promising role of mass spectrometry. Biomarkers 2018; 23:609-621. [DOI: 10.1080/1354750x.2018.1474257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lina A. Dahabiyeh
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman, Jordan
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Anekthanakul K, Hongsthong A, Senachak J, Ruengjitchatchawalya M. SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database. BMC Bioinformatics 2018; 19:149. [PMID: 29678128 PMCID: PMC5910554 DOI: 10.1186/s12859-018-2143-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/03/2018] [Indexed: 12/22/2022] Open
Abstract
Background Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo. In this study, we developed an efficient computational method, SpirPep, which offers many advantages over the currently available tools. Results The SpirPep web application tool is a one-stop analysis and visualization facility to assist bioactive peptide discovery. The tool is equipped with 15 customized enzymes and 1–3 miscleavage options, which allows in silico digestion of protein sequences encoded by protein-coding genes from single, multiple, or genome-wide scaling, and then directly classifies the peptides by bioactivity using an in-house database that contains bioactive peptides collected from 13 public databases. With this tool, the resulting peptides are categorized by each selected enzyme, and shown in a tabular format where the peptide sequences can be tracked back to their original proteins. The developed tool and webpages are coded in PHP and HTML with CSS/JavaScript. Moreover, the tool allows protein-peptide alignment visualization by Generic Genome Browser (GBrowse) to display the region and details of the proteins and peptides within each parameter, while considering digestion design for the desirable bioactivity. SpirPep is efficient; it takes less than 20 min to digest 3000 proteins (751,860 amino acids) with 15 enzymes and three miscleavages for each enzyme, and only a few seconds for single enzyme digestion. Obviously, the tool identified more bioactive peptides than that of the benchmarked tool; an example of validated pentapeptide (FLPIL) from LC-MS/MS was demonstrated. The web and database server are available at http://spirpepapp.sbi.kmutt.ac.th. Conclusion SpirPep, a web-based bioactive peptide discovery application, is an in silico-based tool with an overview of the results. The platform is a one-stop analysis and visualization facility; and offers advantages over the currently available tools. This tool may be useful for further bioactivity analysis and the quantitative discovery of desirable peptides. Electronic supplementary material The online version of this article (10.1186/s12859-018-2143-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Krittima Anekthanakul
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Apiradee Hongsthong
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi, 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Jittisak Senachak
- Biochemical Engineering and Pilot Plant Research and Development Unit, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi, 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Marasri Ruengjitchatchawalya
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand. .,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, 10150, Thailand.
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29
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Yan Z, Yan R. Exploring the Potential of Data-Independent Acquisition Proteomics Using Untargeted All-Ion Quantitation: Application to Tumor Subtype Diagnosis. Anal Chem 2018. [PMID: 29522333 DOI: 10.1021/acs.analchem.7b03920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Maximizing the recovery of meaningful biological information can facilitate proteomics-guided early detection and precise treatment of diseases. However, the conventional protein and peptide level targeted quantification of untargeted data independent acquisition (DIA) such as sequential window acquisition of all theoretical spectra (SWATH) is not necessarily descriptive of all information. Untargeted all-ion quantification theoretically could retrieve more features in SWATH digital maps by circumventing the initial identification process but is intrinsically susceptible to errors because of the extreme complexity of proteome samples and the poor selectivity of a single ion. In this study, we optimized and applied the untargeted all-ion quantification of SWATH data to differentiate tumor subtypes. Large peptides and low abundant peptides benefited more from untargeted all-ion quantification. Top-ranked significant ions were linked to their corresponding ion envelops, where multiple correlated ions were used for measurement and only ion envelopes containing at least three ions with consistent intensity ratio were kept as refined differentiating features. Multivariate statistical analysis revealed that for the tested data set, the refined markers discovered by untargeted SWATH analysis showed comparable diagnostic power to protein and peptide markers. Limitations and benefits of the approach are further discussed.
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Affiliation(s)
- Zhixiang Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences , University of Macau , Taipa, Macao , China.,Zhuhai UM Science & Technology Research Institute , Zhuhai 519080 , China
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences , University of Macau , Taipa, Macao , China.,Zhuhai UM Science & Technology Research Institute , Zhuhai 519080 , China
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30
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Mayfield AB, Chen YJ, Lu CY, Chen CS. Exploring the Environmental Physiology of the Indo-Pacific Reef Coral <em>Seriatopora hystrix</em> with Differential Proteomics. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/ojms.2018.82012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Achour B, Dantonio A, Niosi M, Novak JJ, Fallon JK, Barber J, Smith PC, Rostami-Hodjegan A, Goosen TC. Quantitative Characterization of Major Hepatic UDP-Glucuronosyltransferase Enzymes in Human Liver Microsomes: Comparison of Two Proteomic Methods and Correlation with Catalytic Activity. Drug Metab Dispos 2017; 45:1102-1112. [DOI: 10.1124/dmd.117.076703] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/31/2017] [Indexed: 01/29/2023] Open
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32
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Levernæs MCS, Broughton MN, Reubsaet L, Halvorsen TG. To elute or not to elute in immunocapture bottom-up LC–MS. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1055-1056:51-60. [DOI: 10.1016/j.jchromb.2017.03.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/03/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
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33
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Achour B, Al Feteisi H, Lanucara F, Rostami-Hodjegan A, Barber J. Global Proteomic Analysis of Human Liver Microsomes: Rapid Characterization and Quantification of Hepatic Drug-Metabolizing Enzymes. Drug Metab Dispos 2017; 45:666-675. [PMID: 28373266 DOI: 10.1124/dmd.116.074732] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/30/2017] [Indexed: 12/17/2022] Open
Abstract
Many genetic and environmental factors lead to interindividual variations in the metabolism and transport of drugs, profoundly affecting efficacy and toxicity. Precision dosing, that is, targeting drug dose to a well characterized subpopulation, is dependent on quantitative models of the profiles of drug-metabolizing enzymes (DMEs) and transporters within that subpopulation, informed by quantitative proteomics. We report the first use of ion mobility-mass spectrometry for this purpose, allowing rapid, robust, label-free quantification of human liver microsomal (HLM) proteins from distinct individuals. Approximately 1000 proteins were identified and quantified in four samples, including an average of 70 DMEs. Technical and biological variabilities were distinguishable, with technical variability accounting for about 10% of total variability. The biological variation between patients was clearly identified, with samples showing a range of expression profiles for cytochrome P450 and uridine 5'-diphosphoglucuronosyltransferase enzymes. Our results showed excellent agreement with previous data from targeted methods. The label-free method, however, allowed a fuller characterization of the in vitro system, showing, for the first time, that HLMs are significantly heterogeneous. Further, the traditional units of measurement of DMEs (pmol mg-1 HLM protein) are shown to introduce error arising from variability in unrelated, highly abundant proteins. Simulations of this variability suggest that up to 1.7-fold variation in apparent CYP3A4 abundance is artifactual, as are background positive correlations of up to 0.2 (Spearman correlation coefficient) between the abundances of DMEs. We suggest that protein concentrations used in pharmacokinetic predictions and scaling to in vivo clinical situations (physiologically based pharmacokinetics and in vitro-in vivo extrapolation) should be referenced instead to tissue mass.
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Affiliation(s)
- Brahim Achour
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester (B.A., H.A.F., A.R.-H., J.B.), Waters Corporation, Wilmslow, Cheshire East (F.L.), and Simcyp Limited (a Certara Company), Blades Enterprise Centre, Sheffield (A.R.-H.), United Kingdom
| | - Hajar Al Feteisi
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester (B.A., H.A.F., A.R.-H., J.B.), Waters Corporation, Wilmslow, Cheshire East (F.L.), and Simcyp Limited (a Certara Company), Blades Enterprise Centre, Sheffield (A.R.-H.), United Kingdom
| | - Francesco Lanucara
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester (B.A., H.A.F., A.R.-H., J.B.), Waters Corporation, Wilmslow, Cheshire East (F.L.), and Simcyp Limited (a Certara Company), Blades Enterprise Centre, Sheffield (A.R.-H.), United Kingdom
| | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester (B.A., H.A.F., A.R.-H., J.B.), Waters Corporation, Wilmslow, Cheshire East (F.L.), and Simcyp Limited (a Certara Company), Blades Enterprise Centre, Sheffield (A.R.-H.), United Kingdom
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester (B.A., H.A.F., A.R.-H., J.B.), Waters Corporation, Wilmslow, Cheshire East (F.L.), and Simcyp Limited (a Certara Company), Blades Enterprise Centre, Sheffield (A.R.-H.), United Kingdom
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34
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Casanovas A, Pinto-Llorente R, Carrascal M, Abian J. Large-Scale Filter-Aided Sample Preparation Method for the Analysis of the Ubiquitinome. Anal Chem 2017; 89:3840-3846. [DOI: 10.1021/acs.analchem.6b04804] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Albert Casanovas
- Proteomics
Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), E-08036 Barcelona, Spain
| | - Roberto Pinto-Llorente
- Proteomics
Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), E-08036 Barcelona, Spain
| | - Montserrat Carrascal
- Proteomics
Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), E-08036 Barcelona, Spain
| | - Joaquin Abian
- Proteomics
Laboratory CSIC/UAB, Institute of Biomedical Research of Barcelona, Spanish National Research Council (IIBB-CSIC/IDIBAPS), E-08036 Barcelona, Spain
- Autonomous University of Barcelona, E-08193 Bellaterra, Spain
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35
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Affiliation(s)
- Cristina Chiva
- Proteomics Unit, Centre de
Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de
Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
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36
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Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations. Clin Proteomics 2016; 13:18. [PMID: 27597813 PMCID: PMC5011338 DOI: 10.1186/s12014-016-9119-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/13/2016] [Indexed: 01/30/2023] Open
Abstract
Background Ebola virus like particles (EBOV VLPs, eVLPs), are produced by expressing the viral transmembrane glycoprotein (GP) and structural matrix protein VP40 in mammalian cells. When expressed, these proteins self-assemble and bud from ‘host’ cells displaying morphology similar to infectious virions. Several studies have shown that rodents and non-human primates vaccinated with eVLPs are protected from lethal EBOV challenge. The mucin-like domain of envelope glycoprotein GP1 serves as the major target for a productive humoral immune response. Therefore GP1 concentration is a critical quality attribute of EBOV vaccines and accurate measurement of the amount of GP1 present in eVLP lots is crucial to understanding variability in vaccine efficacy. Methods After production, eVLPs are characterized by determining total protein concentration and by western blotting, which only provides semi-quantitative information for GP1. Therefore, a liquid chromatography high resolution mass spectrometry (LC-HRMS) approach for accurately measuring GP1 concentration in eVLPs was developed. The method employs an isotope dilution strategy using four target peptides from two regions of the GP1 protein. Purified recombinant GP1 was generated to serve as an assay standard. GP1 quantitation in 5 eVLP lots was performed on an LTQ-Orbitrap Elite and the final quantitation was derived by comparing the relative response of 200 fmol AQUA peptide standards to the analyte response at 4 ppm. Results Conditions were optimized to ensure complete tryptic digestion of eVLP, however, persistent missed cleavages were observed in target peptides. Additionally, N-terminal truncated forms of the GP1 protein were observed in all eVLP lots, making peptide selection crucial. The LC-HRMS strategy resulted in quantitation of GP1 with a lower limit of quantitation of 1 fmol and an average percent coefficient of variation (CV) of 7.6 %. Unlike western blot values, the LC-HRMS quantitation of GP1 in 5 eVLP vaccine lots exhibited a strong linear relationship (positive correlation) with survival (after EBOV challenge) in mice. Conclusions This method provides a means to rapidly determine eVLP batch quality based upon quantitation of antigenic GP1. By monitoring variability in GP1 content, the eVLP production process can be optimized, and the total amount of GP1 needed to confer protection accurately determined. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9119-8) contains supplementary material, which is available to authorized users.
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37
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Wiśniewski JR. Quantitative Evaluation of Filter Aided Sample Preparation (FASP) and Multienzyme Digestion FASP Protocols. Anal Chem 2016; 88:5438-43. [PMID: 27119963 DOI: 10.1021/acs.analchem.6b00859] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Filter aided sample preparation (FASP) and related methods gain increasing popularity for proteomic sample preparation. Nevertheless, the originally published FASP method has been criticized by several authors, who reported low digestion performance. In this work, we re-evaluate FASP and the related multienzyme digestion (MED) FASP method. We use different types of animal tissues and cultured cells and test the performance of the method under various conditions. We analyze the protein to peptide conversion by assessing the yield of peptides, frequency of peptides with missed cleavage sites, and the reproducibility of FASP. We identify conditions allowing efficient protein processing with high peptide yields and demonstrate advantages of the two step digestion strategy over single step digestion with trypsin. In addition, we show that FASP outperforms in-solution cleavage strategies. Our results clearly demonstrate that the performance of digestion varies between different types of samples. We show that MED FASP in combination with the total protein approach provides highly reproducible protein abundance values. The presented data can be used as a guide for optimization of sample processing.
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Affiliation(s)
- Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany
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38
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Bienvenut WV, Giglione C, Meinnel T. Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition. Proteomics 2016; 15:2503-18. [PMID: 26017780 DOI: 10.1002/pmic.201500027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/14/2022]
Abstract
A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions, more than 1000 unique N-termini were identified with 56% showing initiator methionine removal. Additional modifications corresponded to partial or complete Nα-acetylation (10%) and N-formyl retention (5%). Among the proteins undergoing these N-terminal modifications, 140 unique N-termini from translocated membrane proteins were highlighted. The very early time-course impact of actinonin was followed after addition of bacteriostatic concentrations of the drug. Under these conditions, 26% of all proteins did not undergo deformylation any longer after 10 min, a value reaching more than 60% of all characterized proteins after 40 min of treatment. The N-formylation ratio measured on individual proteins increased with the same trend. Upon early PDF inhibition, two major categories of proteins retained their N-formyl group: a large number of inner membrane proteins and many proteins involved in protein synthesis including factors assisting the nascent chains in early cotranslational events. All MS data have been deposited in the ProteomeXchange with identifiers PXD001979, PXD002012 and PXD001983 (http://proteomecentral.proteomexchange.org/dataset/PXD001979, http://proteomecentral.proteomexchange.org/dataset/PXD002012 and http://proteomecentral.proteomexchange.org/dataset/PXD001983).
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
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39
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Techniques for quantitative LC–MS/MS analysis of protein therapeutics: advances in enzyme digestion and immunocapture. Bioanalysis 2016; 8:847-56. [DOI: 10.4155/bio.16.24] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
LC–MS/MS has been investigated to quantify protein therapeutics in biological matrices. The protein therapeutics is digested by an enzyme to generate surrogate peptide(s) before LC–MS/MS analysis. One challenge is isolating protein therapeutics in the presence of large number of endogenous proteins in biological matrices. Immunocapture, in which a capture agent is used to preferentially bind the protein therapeutics over other proteins, is gaining traction. The protein therapeutics is eluted for digestion and LC–MS/MS analysis. One area of tremendous potential for immunocapture-LC–MS/MS is to obtain quantitative data where ligand-binding assay alone is not sufficient, for example, quantitation of antidrug antibody complexes. Herein, we present an overview of recent advance in enzyme digestion and immunocapture applicable to protein quantitation.
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40
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Bielow C, Mastrobuoni G, Kempa S. Proteomics Quality Control: Quality Control Software for MaxQuant Results. J Proteome Res 2015; 15:777-87. [PMID: 26653327 DOI: 10.1021/acs.jproteome.5b00780] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mass spectrometry-based proteomics coupled to liquid chromatography has matured into an automatized, high-throughput technology, producing data on the scale of multiple gigabytes per instrument per day. Consequently, an automated quality control (QC) and quality analysis (QA) capable of detecting measurement bias, verifying consistency, and avoiding propagation of error is paramount for instrument operators and scientists in charge of downstream analysis. We have developed an R-based QC pipeline called Proteomics Quality Control (PTXQC) for bottom-up LC-MS data generated by the MaxQuant software pipeline. PTXQC creates a QC report containing a comprehensive and powerful set of QC metrics, augmented with automated scoring functions. The automated scores are collated to create an overview heatmap at the beginning of the report, giving valuable guidance also to nonspecialists. Our software supports a wide range of experimental designs, including stable isotope labeling by amino acids in cell culture (SILAC), tandem mass tags (TMT), and label-free data. Furthermore, we introduce new metrics to score MaxQuant's Match-between-runs (MBR) functionality by which peptide identifications can be transferred across Raw files based on accurate retention time and m/z. Last but not least, PTXQC is easy to install and use and represents the first QC software capable of processing MaxQuant result tables. PTXQC is freely available at https://github.com/cbielow/PTXQC .
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Affiliation(s)
- Chris Bielow
- Max-Delbrück-Centrum for Molecular Medicine Berlin , Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Berlin Institute of Health , Kapelle-Ufer 2, 10117 Berlin, Germany
| | - Guido Mastrobuoni
- Max-Delbrück-Centrum for Molecular Medicine Berlin , Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Stefan Kempa
- Max-Delbrück-Centrum for Molecular Medicine Berlin , Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Berlin Institute of Health , Kapelle-Ufer 2, 10117 Berlin, Germany
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41
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Harwood MD, Achour B, Neuhoff S, Russell MR, Carlson G, Warhurst G. In Vitro-In Vivo Extrapolation Scaling Factors for Intestinal P-Glycoprotein and Breast Cancer Resistance Protein: Part I: A Cross-Laboratory Comparison of Transporter-Protein Abundances and Relative Expression Factors in Human Intestine and Caco-2 Cells. ACTA ACUST UNITED AC 2015; 44:297-307. [PMID: 26631742 DOI: 10.1124/dmd.115.067371] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022]
Abstract
Over the last 5 years the quantification of transporter-protein absolute abundances has dramatically increased in parallel to the expanded use of in vitro-in vivo extrapolation (IVIVE) and physiologically based pharmacokinetics (PBPK)-linked models, for decision-making in pharmaceutical company drug development pipelines and regulatory submissions. Although several research groups have developed laboratory-specific proteomic workflows, it is unclear if the large range of reported variability is founded on true interindividual variability or experimental variability resulting from sample preparation or the proteomic methodology used. To assess the potential for methodological bias on end-point abundance quantification, two independent laboratories, the University of Manchester (UoM) and Bertin Pharma (BPh), employing different proteomic workflows, quantified the absolute abundances of Na/K-ATPase, P-gp, and breast cancer resistance protein (BCRP) in the same set of biologic samples from human intestinal and Caco-2 cell membranes. Across all samples, P-gp abundances were significantly correlated (P = 0.04, Rs = 0.72) with a 2.4-fold higher abundance (P = 0.001) generated at UoM compared with BPh. There was a systematically higher BCRP abundance in Caco-2 cell samples quantified by BPh compared with UoM, but not in human intestinal samples. Consequently, a similar intestinal relative expression factor (REF), derived from distal jejunum and Caco-2 monolayer samples, between laboratories was found for P-gp. However, a 2-fold higher intestinal REF was generated by UoM (2.22) versus BPh (1.11). We demonstrate that differences in absolute protein abundance are evident between laboratories and they probably result from laboratory-specific methodologies relating to peptide choice.
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Affiliation(s)
- Matthew D Harwood
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Brahim Achour
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Sibylle Neuhoff
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Matthew R Russell
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Gordon Carlson
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Geoffrey Warhurst
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
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Strategies in protein sequencing and characterization: Multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry. Anal Chim Acta 2015; 854:106-17. [DOI: 10.1016/j.aca.2014.10.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/14/2022]
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Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. J Proteome Res 2014; 14:787-803. [PMID: 25495225 DOI: 10.1021/pr500834z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained under different experimental conditions. Here, we describe the design, synthesis, and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected either to favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion, and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements to large-scale biomarker screening in biomedical applications.
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