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Silva CJ, Erickson-Beltran ML. General Method of Quantifying the Extent of Methionine Oxidation in the Prion Protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:255-263. [PMID: 36608322 DOI: 10.1021/jasms.2c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The normal cellular prion protein (PrPC) and its infectious conformer, PrPSc, possess a disproportionately greater amount of methionines than would be expected for a typical mammalian protein. The thioether of methionine can be readily oxidized to the corresponding sulfoxide, which means that oxidation of methionine can be used to map the surface of the conformation of PrPC or PrPSc, as covalent changes are retained after denaturation. We identified a set of peptides (TNMK, MLGSAMSR, LLGSAMSR, PMIHFGNDWEDR, ENMNR, ENMYR, IMER, MMER, MIER, VVEQMCVTQYQK, and VVEQMCITQYQR) that contains every methionine in sheep, cervid, mouse, and bank vole PrP. Each is the product of a tryptic digestion and is suitable for a multiple reaction monitoring (MRM) based analysis. The peptides chromatograph well. The oxidized and unoxidized peptides containing one methionine readily separate. The unoxidized, two singly oxidized, and doubly oxidized forms of the MLGSAMSR and MMER peptides are also readily distinguishable. This approach can be used to determine the surface exposure of each methionine by measuring its oxidation after reaction with added hydrogen peroxide.
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Affiliation(s)
- Christopher J Silva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan Street, Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan Street, Albany, California 94710, United States
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Silva CJ, Erickson-Beltran ML, Dynin IC. Quantifying the Role of Lysine in Prion Replication by Nano-LC Mass Spectrometry and Bioassay. Front Bioeng Biotechnol 2020; 8:562953. [PMID: 33072723 PMCID: PMC7542330 DOI: 10.3389/fbioe.2020.562953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/24/2020] [Indexed: 11/26/2022] Open
Abstract
Prions propagate by a template driven process, inducing the normal cellular isoform (PrPC) to adopt the prion (PrPSc) conformation. In PrPC, the positions of lysines are highly conserved and strongly influence prion propagation. In this study, covalent modification was used to quantitate the role of lysines in the PrPSc template that drives prion replication. The ε-amino group of lysines in the PrPSc (hamster-adapted scrapie Sc237) template was acetylated by either acetic anhydride (Ac2O) or the N-hydroxysuccinimide ester of acetic acid (Ac-NHS). The extent of lysine acetylation in PrPSc was quantitated by mass spectrometry or Western blot-based analysis. Identical samples were bioassayed to quantitate the loss of infectivity associated with lysine acetylation. The reduction of infectivity at the highest reagent concentration was approximately 90% (∼10-fold). Ten of the eleven prion lysines were acetylated to a greater extent (25−400-fold) than the observed loss of infectivity. Only one lysine, at position 220 (K220), had a reactivity that is consistent with the loss of infectivity. Although lysines are highly conserved and play a crucial role in converting PrPC into the PrPSc conformation, once that conformation is adopted, the lysines present in the PrPSc template play only a limited role in prion replication. In principle, this approach could be used to clarify the role of other amino acids in the replication of prions and other prion-like protein misfolding diseases.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
| | - Melissa L Erickson-Beltran
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
| | - Irina C Dynin
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, United States
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Liu P, Guo L, Mao H, Gu Z. Serum proteomics analysis reveals the thermal fitness of crossbred dairy buffalo to chronic heat stress. J Therm Biol 2020; 89:102547. [PMID: 32364989 DOI: 10.1016/j.jtherbio.2020.102547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 12/11/2022]
Abstract
Chronic heat stress (CHS) reduces the production efficiency of the buffalo dairy industry. Relatively low-abundance proteins with particular functions in biological processes are changed by CHS. The present study aimed to quantify the differences in low-abundance proteins of crossbred dairy buffaloes under CHS and thermal-neutral (TN) conditions. With label-free quantification, 344 low-abundance proteins were identified in serum. Of these, 17 differentially expressed low-abundance proteins with known functions were detected, and six of the differentially expressed proteins related to heat stress were validated with parallel reaction monitoring. Lipase (LPL), glutathione peroxidase 3 (GPX3), cathelicidin-2 (CATHL2), ceruloplasmin (CP), and hemoglobin subunit alpha 1 (HBA1) cooperatively played roles in the thermal fitness of dairy buffalo by decreasing heat production and increasing blood oxygen delivery. Also, dairy buffaloes may adapt to CHS and hypoxia with high levels of RBCs, HBA1 and CP to increase blood oxygen delivery capacity.
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Affiliation(s)
- Ping Liu
- Yunnan Agricultural University, Black dargon pool, China.
| | - Lulu Guo
- Yunnan Agricultural University, Black dargon pool, China.
| | - Huaming Mao
- Yunnan Agricultural University, Black dargon pool, China.
| | - Zhaobing Gu
- Yunnan Agricultural University, Black dargon pool, China.
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Silva CJ, Erickson-Beltran ML, Duque Velásquez C, Aiken JM, McKenzie D. A General Mass Spectrometry-Based Method of Quantitating Prion Polymorphisms from Heterozygous Chronic Wasting Disease-Infected Cervids. Anal Chem 2019; 92:1276-1284. [PMID: 31815434 DOI: 10.1021/acs.analchem.9b04449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chronic wasting disease (CWD) is the only prion disease naturally transmitted among farmed and free-ranging cervids (deer, elk, moose, etc.). These diseases are always fatal and have long asymptomatic incubation periods. By 2019, CWD-infected cervids had been detected in 26 states, three Canadian provinces, South Korea, Norway, Finland, and Sweden. Prions (PrPSc) replicate by inducing a normal cellular prion protein (PrPC) to adopt the prion conformation. This prion templated conformational conversion is influenced by PrPC polymorphisms. Cervid PrPC contains at least 20 different polymorphic sites. By using chymotrypsin, trypsin, or trypsin followed by chymotrypsin to digest denatured cervid PrP, 19 peptides suitable for multiple reaction monitoring (MRM)-based analysis and spanning positions 30-51, 61-112, and 114-231 of cervid PrP were identified. Ten of these peptides span polymorphism-containing regions of cervid PrP. The other nine contain no polymorphisms, so they can be used as internal standards. Calibration curves relating the area ratios of MRM signals from polymorphism-containing peptides to appropriate internal standard peptides were linear and had excellent correlation coefficients. Samples from heterozygous (G96/S96) white-tailed deer orally dosed with CWD from homozygous (G96/G96) deer were analyzed. The G96 polymorphism comprised 75 ± 5% of the total PrP from the G96/S96 heterozygotes. Heterozygous animals facilitate conversion of different PrPC polymorphisms into PrPSc. This approach can be used to quantitate the relative amounts of the polymorphisms present in other animal species and even humans.
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Affiliation(s)
- Christopher J Silva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture , Agricultural Research Service , 800 Buchanan Street , Albany , California 94710 , United States of America
| | - Melissa L Erickson-Beltran
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture , Agricultural Research Service , 800 Buchanan Street , Albany , California 94710 , United States of America
| | - Camilo Duque Velásquez
- University of Alberta , Centre for Prions and Protein Folding Diseases , 114 Brain and Aging Research Building , Edmonton , Alberta T6G 2M8 , Canada
| | - Judd M Aiken
- University of Alberta , Centre for Prions and Protein Folding Diseases , 114 Brain and Aging Research Building , Edmonton , Alberta T6G 2M8 , Canada
| | - Debbie McKenzie
- University of Alberta , Centre for Prions and Protein Folding Diseases , 114 Brain and Aging Research Building , Edmonton , Alberta T6G 2M8 , Canada
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Jiang L, Meng F, Qiu Z, Zhang K, Ding Y, Li H, Ren Y, Yu P, Peng J. Comparison of UPLC-MS/MS-based targeted quantitation and conventional quantitative methods for the analysis of MRP1 expression in tumor cell lines. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1109:10-18. [DOI: 10.1016/j.jchromb.2019.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/13/2018] [Accepted: 01/06/2019] [Indexed: 10/27/2022]
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A novel photoelectrochemical immunosensor for prion protein based on CdTe quantum dots and glucose oxidase. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.09.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Silva CJ. Food Forensics: Using Mass Spectrometry To Detect Foodborne Protein Contaminants, as Exemplified by Shiga Toxin Variants and Prion Strains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8435-8450. [PMID: 29860833 DOI: 10.1021/acs.jafc.8b01517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Food forensicists need a variety of tools to detect the many possible food contaminants. As a result of its analytical flexibility, mass spectrometry is one of those tools. Use of the multiple reaction monitoring (MRM) method expands its use to quantitation as well as detection of infectious proteins (prions) and protein toxins, such as Shiga toxins. The sample processing steps inactivate prions and Shiga toxins; the proteins are digested with proteases to yield peptides suitable for MRM-based analysis. Prions are detected by their distinct physicochemical properties and differential covalent modification. Shiga toxin analysis is based on detecting peptides derived from the five identical binding B subunits comprising the toxin. 15N-labeled internal standards are prepared from cloned proteins. These examples illustrate the power of MRM, in that the same instrument can be used to safely detect and quantitate protein toxins, prions, and small molecules that might contaminate our food.
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Affiliation(s)
- Christopher J Silva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service , United States Department of Agriculture , Albany , California 94710 , United States
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Li X, Li J, Zhu C, Zhang X, Chen J. A new electrochemical immunoassay for prion protein based on hybridization chain reaction with hemin/G-quadruplex DNAzyme. Talanta 2018; 182:292-298. [PMID: 29501155 DOI: 10.1016/j.talanta.2018.01.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/22/2018] [Accepted: 01/30/2018] [Indexed: 11/29/2022]
Abstract
In this work, a new electrochemical immunosensor was developed for prion protein assay based on hybridization chain reaction (HCR) with hemin/G-quadruplex DNAzyme for signal amplification. In this amplification system, the hemin/G-quadruplex DNAzyme simultaneously mimicked the biocatalytic functions for H2O2 reduction and L-cysteine oxidation. In the presence of L-cysteine, the hemin/G-quadruplex catalyzed the oxidation of L-cysteine to L-cystine. At the same time, H2O2 was produced under the oxygen condition. Then, the hemin/G-quadruplex could quickly catalyze the reduction of H2O2, mimicking the catalytic performance of horseradish peroxidase (HRP). Under the optimal conditions, the immunosensor showed a wide linear response range from 0.5 pg/mL to 100 ng/mL with the low detection limit of 0.38 pg/mL (3σ). By changing the specific antibody, this strategy could be easily extended to detect the infectious isoform of prion (PrPSc) and other proteins. Based on its good analytical performance, the developed method shows great potential applications in diagnosis of prion diseases at presymptomatic stage and bioanalysis.
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Affiliation(s)
- Xiaoyu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Junjing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Caixia Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaohua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Jinhua Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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Li J, Yan X, Li X, Zhang X, Chen J. A new electrochemical immunosensor for sensitive detection of prion based on Prussian blue analogue. Talanta 2017; 179:726-733. [PMID: 29310300 DOI: 10.1016/j.talanta.2017.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/27/2017] [Accepted: 12/02/2017] [Indexed: 11/28/2022]
Abstract
Based on Co-Co Prussian blue analogue (Co-Co PBA), a novel immunosensor has been developed for sensitive detection of prion protein (PrPC). Gold nanoparticles (AuNPs)-modified Co-Co PBA nanocubes (PBA-AuNPs) worked as a support of the antibody (Ab2) of PrPC to obtain Ab2-PBA-AuNPs composite and also as the signal source for PrPC assay. When PrPC existed, Ab2-PBA-AuNPs could be introduced to the surface of another antibody of PrPC (Ab1) modified AuNPs/GC electrode (the gold nanoparticles-modified glassy carbon electrode) through specific antigen-antibody interaction between PrPC and its antibodies to form the Ab1-PrPC-Ab2 sandwich structure. With the help of KOH aqueous solution, PBA generated a large DPV response. The response peak currents were linear with the logarithmic values of the concentration of PrPC in the range from 0.075pgmL-1 to 100pgmL-1 with the detection limit of 0.014pgmL-1. Also, the immunosensor showed good selectivity and reproducibility. Based on the simple sensing structure and good analytical performance, the developed immunosensor may have promising applications in practical assay of infectious isoform of prion (PrPSc) and other proteins by simply changing the related antibody.
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Affiliation(s)
- Junjing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoxia Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoyu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaohua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
| | - Jinhua Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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Josić D, Peršurić Ž, Rešetar D, Martinović T, Saftić L, Kraljević Pavelić S. Use of Foodomics for Control of Food Processing and Assessing of Food Safety. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 81:187-229. [PMID: 28317605 DOI: 10.1016/bs.afnr.2016.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Food chain, food safety, and food-processing sectors face new challenges due to globalization of food chain and changes in the modern consumer preferences. In addition, gradually increasing microbial resistance, changes in climate, and human errors in food handling remain a pending barrier for the efficient global food safety management. Consequently, a need for development, validation, and implementation of rapid, sensitive, and accurate methods for assessment of food safety often termed as foodomics methods is required. Even though, the growing role of these high-throughput foodomic methods based on genomic, transcriptomic, proteomic, and metabolomic techniques has yet to be completely acknowledged by the regulatory agencies and bodies. The sensitivity and accuracy of these methods are superior to previously used standard analytical procedures and new methods are suitable to address a number of novel requirements posed by the food production sector and global food market.
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Affiliation(s)
- D Josić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia.
| | - Ž Peršurić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - D Rešetar
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - T Martinović
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - L Saftić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
| | - S Kraljević Pavelić
- University of Rijeka, Centre for High-Throughput Technologies, Radmile Matejčić 2, Rijeka, Croatia
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Silva CJ, Erickson-Beltran ML, Hui C, Badiola JJ, Nicholson EM, Requena JR, Bolea R. Quantitating PrP Polymorphisms Present in Prions from Heterozygous Scrapie-Infected Sheep. Anal Chem 2016; 89:854-861. [PMID: 27936597 DOI: 10.1021/acs.analchem.6b03822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scrapie is a prion (PrPSc) disease of sheep. The incubation period of sheep scrapie is strongly influenced by polymorphisms at positions 136, 154, and 171 of a sheep's normal cellular prion protein (PrPC). Chymotrypsin was used to digest sheep recombinant PrP to identify a set of characteristic peptides [M132LGSXMSRPL141 (X = A or V), Y153XENMY158 (X,= H or R), and Y166RPVDXY172 (X = H, K, Q, or R)] that could be used to detect and quantitate polymorphisms at positions 136, 154, and 171 of sheep PrPC or PrPSc. These peptides were used to develop a multiple reaction monitoring method (MRM) to detect the amounts of a particular polymorphism in a sample of PrPSc isolated from sheep heterozygous for their PrPC proteins. The limit of detection for these peptides was less than 50 attomole. Spinal cord tissue from heterozygous (ARQ/VRQ or ARH/ARQ) scrapie-infected Rasa Aragonesa sheep was analyzed using this MRM method. Both sets of heterozygotes show the presence of both polymorphisms in PrPSc. This was true for samples containing both proteinase K (PK)-sensitive and PK-resistant PrPSc and samples containing only the PK-resistant PrPSc. These results show that heterozygous animals contain PrPSc that is composed of significant amounts of both PrP polymorphisms.
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Affiliation(s)
- Christopher J Silva
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Colleen Hui
- Produce Safety & Microbiology Research Unit, Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service , Albany, California 94710, United States
| | - Juan José Badiola
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza Spain
| | - Eric M Nicholson
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service , Ames, Iowa 50010, United States
| | - Jesús R Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS , Santiago de Compostela, 15782 Spain
| | - Rosa Bolea
- Veterinary Faculty, Centro de Investigación en Encefalopatías y Enfermedades Transmisibles Emergentes (CIEETE), Universidad de Zaragoza , 50013, Zaragoza Spain
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Yu P, Zhang X, Xiong E, Zhou J, Li X, Chen J. A label-free and cascaded dual-signaling amplified electrochemical aptasensing platform for sensitive prion assay. Biosens Bioelectron 2016; 85:471-478. [PMID: 27208480 DOI: 10.1016/j.bios.2016.05.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/26/2016] [Accepted: 05/13/2016] [Indexed: 01/18/2023]
Abstract
Prion proteins, as an important biomarker of prion disease, are responsible for the transmissible spongiform encephalopathies (a group of fatal neurodegenerative diseases). Hence, the sensitive detection of prion protein is very essential for biological studies and medical diagnostics. In this paper, a novel label-free and cascaded dual-signaling amplified electrochemical strategy was developed for sensitive and selective analysis of cellular prion protein (PrP(C)). The recognition elements included double-stranded DNA consisted of PrP(C)-binding aptamer (DNA1) and its partially complementary DNA (DNA2), and ordered mesoporous carbon probe (OMCP) fabricated by sealing the electroactive ferrocenecarboxylic acid (Fc) into its inner pores and then using single-stranded DNA (DNA3) as the gatekeeper. In the presence of PrP(C), DNA1 could bind the target protein and free DNA2. More importantly, DNA2 could hybridize with DNA3 to form a rigid duplex DNA and thus triggered the exonuclease III (Exo III) cleavage process to realize the DNA2 recycling, accompanied by opening more biogates and releasing more Fc. The released Fc could be further used as a competitive guest of β-cyclodextrin (β-CD) to displace the Rhodamine B (RhB) on the electrode. As a result, an amplified oxidation peak current of Fc (RhB) increased (decreased) with the increase of PrP(C) concentration. When "ΔI=ΔIFc+|ΔIRhB|" (ΔIFc and ΔIRhB were the change values of the oxidation peak currents of Fc and RhB, respectively.) was used as the response signal for quantitative determination of PrP(C), the detection limit was 7.6fM (3σ), which was much lower than that of the most reported methods for PrP(C) assay. This strategy provided a simple and sensitive approach for the detection of PrP(C) and has a great potential for bioanalysis, disease diagnostics, and clinical biomedicine applications.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaohua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
| | - Erhu Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Jiawan Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Xiaoyu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Jinhua Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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Defining the wheat gluten peptide fingerprint via a discovery and targeted proteomics approach. J Proteomics 2016; 147:156-168. [PMID: 26994601 DOI: 10.1016/j.jprot.2016.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 03/02/2016] [Accepted: 03/08/2016] [Indexed: 11/24/2022]
Abstract
UNLABELLED Accurate, reliable and sensitive detection methods for gluten are required to support current EU regulations. The enforcement of legislative levels requires that measurement results are comparable over time and between methods. This is not a trivial task for gluten which comprises a large number of protein targets. This paper describes a strategy for defining a set of specific analytical targets for wheat gluten. A comprehensive proteomic approach was applied by fractionating wheat gluten using RP-HPLC (reversed phase high performance liquid chromatography) followed by a multi-enzymatic digestion (LysC, trypsin and chymotrypsin) with subsequent mass spectrometric analysis. This approach identified 434 peptide sequences from gluten. Peptides were grouped based on two criteria: unique to a single gluten protein sequence; contained known immunogenic and toxic sequences in the context of coeliac disease. An LC-MS/MS method based on selected reaction monitoring (SRM) was developed on a triple quadrupole mass spectrometer for the specific detection of the target peptides. The SRM based screening approach was applied to gluten containing cereals (wheat, rye, barley and oats) and non-gluten containing flours (corn, soy and rice). A unique set of wheat gluten marker peptides were identified and are proposed as wheat specific markers. SIGNIFICANCE The measurement of gluten in processed food products in support of regulatory limits is performed routinely. Mass spectrometry is emerging as a viable alternative to ELISA based methods. Here we outline a set of peptide markers that are representative of gluten and consider the end user's needs in protecting those with coeliac disease. The approach taken has been applied to wheat but can be easily extended to include other species potentially enabling the MS quantification of different gluten containing species from the identified markers.
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Silva CJ, Erickson-Beltran ML, Dynin IC. Covalent Surface Modification of Prions: A Mass Spectrometry-Based Means of Detecting Distinctive Structural Features of Prion Strains. Biochemistry 2016; 55:894-902. [PMID: 26786805 DOI: 10.1021/acs.biochem.5b01068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prions (PrP(Sc)) are molecular pathogens that are able to convert the isosequential normal cellular prion protein (PrP(C)) into a prion. The only demonstrated difference between PrP(C) and PrP(Sc) is conformational: they are isoforms. A given host can be infected by more than one kind or strain of prion. Five strains of hamster-adapted scrapie [Sc237 (=263K), drowsy, 139H, 22AH, and 22CH] and recombinant PrP were reacted with five different concentrations (0, 1, 5, 10, and 20 mM) of reagent (N-hydroxysuccinimide ester of acetic acid) that acetylates lysines. The extent of lysine acetylation was quantitated by mass spectrometry. The lysines in rPrP react similarly. The lysines in the strains react differently from one another in a given strain and react differently when strains are compared. Lysines in the C-terminal region of prions have different strain-dependent reactivity. The results are consistent with a recently proposed model for the structure of a prion. This model proposes that prions are composed of a four-rung β-solenoid structure comprised of four β-sheets that are joined by loops and turns of amino acids. Variation in the amino acid composition of the loops and β-sheet structures is thought to result in different strains of prions.
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Affiliation(s)
- Christopher J Silva
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
| | - Melissa L Erickson-Beltran
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
| | - Irina C Dynin
- Western Regional Research Center, United States Department of Agriculture , Albany, California 94710, United States
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Maaß S, Becher D. Methods and applications of absolute protein quantification in microbial systems. J Proteomics 2016; 136:222-33. [PMID: 26825536 DOI: 10.1016/j.jprot.2016.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/05/2016] [Accepted: 01/21/2016] [Indexed: 02/05/2023]
Abstract
In the last years the scientific community faced an increased need to provide high-quality data on the concentration of single proteins within a cell. Especially against the background of the fast evolving field of systems biology this does not only apply for a few proteins but preferably for the whole proteome of the organism. Therefore there has been a rapid development from pure identification of proteins via characterization of changes between different conditions by relative protein quantification towards determination of absolute protein amounts for hundreds of protein species in a cell. This review aims for discussion of different small-scale and large-scale approaches for absolute protein quantification in bacterial cells to picture biological processes and explore life in deeper detail. The presented advantages and limitations of various methods may provide interested researchers help to appraise available methods, select the most appropriate technique and avoid common pitfalls during determination of protein concentration in a complex sample.
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Affiliation(s)
- Sandra Maaß
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst Moritz Arndt Universität Greifswald, D-17487 Greifswald, Germany
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Abstract
Prion diseases are a heterogeneous class of fatal neurodegenerative disorders associated with misfolding of host cellular prion protein (PrP(C)) into a pathological isoform, termed PrP(Sc). Prion diseases affect various mammals, including humans, and effective treatments are not available. Prion diseases are distinguished from other protein misfolding disorders - such as Alzheimer's or Parkinson's disease - in that they are infectious. Prion diseases occur sporadically without any known exposure to infected material, and hereditary cases resulting from rare mutations in the prion protein have also been documented. The mechanistic underpinnings of prion and other neurodegenerative disorders remain poorly understood. Various proteomics techniques have been instrumental in early PrP(Sc) detection, biomarker discovery, elucidation of PrP(Sc) structure and mapping of biochemical pathways affected by pathogenesis. Moving forward, proteomics approaches will likely become more integrated into the clinical and research settings for the rapid diagnosis and characterization of prion pathogenesis.
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Affiliation(s)
- Roger A Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIH,NIAID, Hamilton, MT 59840, USA
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Silva CJ. Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure. Prion 2015; 8:42-50. [PMID: 24509645 DOI: 10.4161/pri.27891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP(C)) into a prion (PrP(Sc)). The information necessary for this conversion is contained in the conformation of PrP(Sc). Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10⁻¹⁸ mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP(Sc) and GPI-anchorless PrP(Sc). It has also been used to study the quaternary structure of the PrP(Sc) multimer. Small molecule reagents react differently with the same lysine in the PrP(C) conformation than in the PrP(Sc) conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP(Sc) without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.
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Trötschel C, Poetsch A. Current approaches and challenges in targeted absolute quantification of membrane proteins. Proteomics 2015; 15:915-29. [DOI: 10.1002/pmic.201400427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/05/2014] [Accepted: 12/05/2014] [Indexed: 01/08/2023]
Affiliation(s)
| | - Ansgar Poetsch
- Department of Plant Biochemistry; Ruhr-University Bochum; Bochum Germany
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Greer T, Lietz CB, Xiang F, Li L. Novel isotopic N,N-dimethyl leucine (iDiLeu) reagents enable absolute quantification of peptides and proteins using a standard curve approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:107-19. [PMID: 25377360 PMCID: PMC4276538 DOI: 10.1007/s13361-014-1012-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/20/2014] [Accepted: 09/23/2014] [Indexed: 05/23/2023]
Abstract
Absolute quantification of protein targets using liquid chromatography-mass spectrometry (LC-MS) is a key component of candidate biomarker validation. One popular method combines multiple reaction monitoring (MRM) using a triple quadrupole instrument with stable isotope-labeled standards (SIS) for absolute quantification (AQUA). LC-MRM AQUA assays are sensitive and specific, but they are also expensive because of the cost of synthesizing stable isotope peptide standards. While the chemical modification approach using mass differential tags for relative and absolute quantification (mTRAQ) represents a more economical approach when quantifying large numbers of peptides, these reagents are costly and still suffer from lower throughput because only two concentration values per peptide can be obtained in a single LC-MS run. Here, we have developed and applied a set of five novel mass difference reagents, isotopic N,N-dimethyl leucine (iDiLeu). These labels contain an amine reactive group, triazine ester, are cost effective because of their synthetic simplicity, and have increased throughput compared with previous LC-MS quantification methods by allowing construction of a four-point standard curve in one run. iDiLeu-labeled peptides show remarkably similar retention time shifts, slightly lower energy thresholds for higher-energy collisional dissociation (HCD) fragmentation, and high quantification accuracy for trypsin-digested protein samples (median errors <15%). By spiking in an iDiLeu-labeled neuropeptide, allatostatin, into mouse urine matrix, two quantification methods are validated. The first uses one labeled peptide as an internal standard to normalize labeled peptide peak areas across runs (<19% error), whereas the second enables standard curve creation and analyte quantification in one run (<8% error).
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Affiliation(s)
- Tyler Greer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Christopher B. Lietz
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Feng Xiang
- School of Pharmacy, University of Wisconsin-School of Madison, Madison, WI, 53705, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, United States
- School of Pharmacy, University of Wisconsin-School of Madison, Madison, WI, 53705, United States
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21
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Absolute quantification of endogenous angiotensin II levels in human plasma using ESI-LC-MS/MS. Clin Proteomics 2014; 11:37. [PMID: 25505856 PMCID: PMC4223748 DOI: 10.1186/1559-0275-11-37] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Angiotensin II acts as a peptide hormone and component of renin-angiotensin- system (RAS) regulating the blood pressure, and seems to be involved in renal and vascular disorders. There is no reliable quantification method for angiotensin II available until now and the angiotensin II plasma levels described in the literature are correspondingly strongly divergent. Therefore, we developed and validated a sensitive, selective and reliable LC-ESI-MS/MS method for absolute quantification of angiotensin II concentration in human plasma based on the AQUA strategy. METHODS Plasma samples were extracted using MAX Oasis cartridges and were subjected to a further immunoaffinity-purification using immobilized anti-angiotensin II antibodies in order to isolate endogenous angiotensin II. Stable isotope ((13)C- and (15) N-) labeled angiotensin II was used as an internal standard. The fractionated samples were analysed using LC-ESI-MS/MS. RESULTS The calibration curve was established in plasma in the concentration range 6-240 pM (r(2) > 0.999). The developed and validated method was successfully applied for quantification of endogenous angiotensin II in human plasma of healthy volunteers and chronic kidney disease (CKD-5D) patients. The mean plasma angiotensin II levels were found to be 18.4 ± 3.3 pM in healthy subjects and 64.5 ± 32.4 pM in CKD-5D patients (each n =9). CONCLUSION The LC-ESI-MS/MS-based method for quantification of angiotensin II levels in human plasma was successfully evaluated within the study. This method is applicable for clinical applications aiming at the validation of the impact of highly physiologically and pathophysiologically active angiotensin II.
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Absolute quantification of protein NP24 in tomato fruit by liquid chromatography/tandem mass spectrometry using stable isotope-labelled tryptic peptide standard. Food Chem 2014; 173:238-42. [PMID: 25466018 DOI: 10.1016/j.foodchem.2014.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/30/2014] [Accepted: 10/02/2014] [Indexed: 01/15/2023]
Abstract
Protein NP24 is a thaumatin-like protein contained in tomato (Lycopersicon esculentum Mill.). This protein is reported to be a putative tomato allergen and is listed as a food allergen in Structural Database of Allergenic Proteins (SDAP). In this research, we developed the quantitative analysis of NP24 by employing the protein absolute quantification (AQUA) technology composed of stable isotope-labelled internal standard (SIIS) peptide (GQTWVINAPR[(13)C6,(15)N4]) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). A linear relationship (r(2)>0.99) was found throughout the concentration range (2.0-500 fmol/μL). The coefficients of variation (CVs) measured on each of the five days when NP24 contained in the tomato skin was analysed did not exceed 13%. Our developed assay of NP24 will contribute to the allergological examination of tomato and its derived products.
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24
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Trimpin S, Wang B, Lietz CB, Marshall DD, Richards AL, Inutan ED. New ionization processes and applications for use in mass spectrometry. Crit Rev Biochem Mol Biol 2013; 48:409-29. [DOI: 10.3109/10409238.2013.806887] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Clarke W, Rhea JM, Molinaro R. Challenges in implementing clinical liquid chromatography-tandem mass spectrometry methods--the light at the end of the tunnel. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:755-767. [PMID: 23832931 DOI: 10.1002/jms.3214] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 06/02/2023]
Abstract
The use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the clinical setting is a relatively new application. One of the significant barriers hampering the transition of LC-MS/MS from the research lab into a clinical setting is the uncertainty of how to successfully develop and validate a method that meets guidelines for clinical applications. Here, we have taken this seemingly overwhelming process and broken it into five general stages for consideration: assessing the clinical validity of a new LC-MS/MS assay, determination of feasibility, assay development, assay validation and post-implementation monitoring. Although various publications are available and serve as resources for determining development processes and acceptability criteria for specific LC-MS/MS assays, many of them are general recommendations or are specific to research applications that may not translate either practically or clinically. In this perspective special feature article, a resource is compiled that describes key differences between LC-MS/MS methods for research use versus clinical use. In addition, the challenges facing the expanding role of this technique in the clinical setting are discussed, including instrumentation/automation challenges, potential regulation of laboratory developed tests by the US Food and Drug Administration and standardization and harmonization of MS methods through the use of traceable materials and availability of guidance documents.
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Affiliation(s)
- William Clarke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:791985. [PMID: 23710360 PMCID: PMC3654371 DOI: 10.1155/2013/791985] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 02/06/2013] [Indexed: 12/21/2022]
Abstract
The receptor tyrosine kinase ErbB2 is a breast cancer biomarker whose posttranslational modifications (PTMs) are a key indicator of its activation. Quantifying the expression and PTMs of biomarkers such as ErbB2 by selected reaction monitoring (SRM) mass spectrometry has several limitations, including minimal coverage and extensive assay development time. Therefore, we assessed the utility of two high resolution, full scan mass spectrometry approaches, MS1 Filtering and SWATH MS2, for targeted ErbB2 proteomics. Endogenous ErbB2 immunoprecipitated from SK-BR-3 cells was in-gel digested with trypsin, chymotrypsin, Asp-N, or trypsin plus Asp-N in triplicate. Data-dependent acquisition with an AB SCIEX TripleTOF 5600 and MS1 Filtering data processing was used to assess peptide and PTM coverage as well as the reproducibility of enzyme digestion. Data-independent acquisition (SWATH) was also performed for MS2 quantitation. MS1 Filtering and SWATH MS2 allow quantitation of all detected analytes after acquisition, enabling the use of multiple proteases for quantitative assessment of target proteins. Combining high resolution proteomics with multiprotease digestion enabled quantitative mapping of ErbB2 with excellent reproducibility, improved amino acid sequence and PTM coverage, and decreased assay development time compared to typical SRM assays. These results demonstrate that high resolution quantitative proteomic approaches are an effective tool for targeted biomarker quantitation.
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