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Stachniuk A, Trzpil A, Czeczko R, Nowicki Ł, Ziomkowska M, Fornal E. Absolute quantification of targeted rabbit liver- and meat tissue-specific peptide markers in highly processed food products. Food Chem 2024; 438:138069. [PMID: 38007955 DOI: 10.1016/j.foodchem.2023.138069] [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: 09/07/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
A highly sensitive and selective method for the simultaneous absolute quantification of peptides unique to rabbit meat- and liver-specific tissue was developed using liquid chromatography - triple quadrupole mass spectrometry. Two rabbit skeletal muscle-specific peptides (SSVFVADPK and PHSHPALTPEQK), three rabbit liver tissue-specific peptides (FNLEALVTHTLPFEK, AILNYVANK, and TELAEPTSTR) and one peptide specific to both rabbit offal and skeletal muscle tissue (AFFGHYLYEVAR) were monitored. Analyses were performed using peptides labelled with stable isotopes (13C and 15N) as internal standards. Fifteen food samples containing rabbit meat and/or liver were analysed to verify compliance of the rabbit meat and liver composition with product labelling. One sample was adulterated with undeclared rabbit liver. The limit of detection and limit of quantification for the selected peptides of interest were in the range of 0.17 to 0.35 ng/mg and 0.57 to 1.17 ng/mg, respectively. The method may be useful for the determination of rabbit meat and liver tissue in highly processed food samples.
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Affiliation(s)
- Anna Stachniuk
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland.
| | - Alicja Trzpil
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Renata Czeczko
- Department of Chemistry, University of Live Sciences in Lublin, ul. Akademicka 15, 20-950 Lublin, Poland
| | - Łukasz Nowicki
- Altium International Sp. z o.o, ul. Puławska 303, 02-785 Warszawa, Poland
| | | | - Emilia Fornal
- Department of Bioanalytics, Medical University of Lublin, ul. Jaczewskiego 8b, 20-090 Lublin, Poland
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Degliesposti G. Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:41-57. [PMID: 38507199 DOI: 10.1007/978-3-031-52193-5_4] [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: 03/22/2024]
Abstract
The characterization of a protein complex by mass spectrometry can be conducted at different levels. Initial steps regard the qualitative composition of the complex and subunit identification. After that, quantitative information such as stoichiometric ratios and copy numbers for each subunit in a complex or super-complex is acquired. Peptide-based LC-MS/MS offers a wide number of methods and protocols for the characterization of protein complexes. This chapter concentrates on the applications of peptide-based LC-MS/MS for the qualitative, quantitative, and structural characterization of protein complexes focusing on subunit identification, determination of stoichiometric ratio and number of subunits per complex as well as on cross-linking mass spectrometry and hydrogen/deuterium exchange as methods for the structural investigation of the biological assemblies.
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Abstract
Targeted proteomics detects proteins of interest with high sensitivity, quantitative accuracy, and reproducibility. In a targeted proteomics assay, surrogate peptides are generated by proteolytic digestion of target proteins and selected reaction monitoring (SRM) assays are developed to quantify these peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this report, we describe the details of quantitative analysis of target protein in cells and tissue samples.
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Affiliation(s)
- Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, China.
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University, Nanjing, China
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Calderón-Celis F, Encinar JR, Sanz-Medel A. Standardization approaches in absolute quantitative proteomics with mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:715-737. [PMID: 28758227 DOI: 10.1002/mas.21542] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 05/10/2023]
Abstract
Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers. However, the physico-chemical environment of the analyte species affects strongly the ionization efficiency in most mass spectrometry (MS) types, which thereby require the use of specially designed standardization approaches to provide absolute quantifications. Most common of such approaches nowadays include (i) the use of stable isotope-labeled peptide standards, isotopologues to the target proteotypic peptides expected after tryptic digestion of the target protein; (ii) use of stable isotope-labeled protein standards to compensate for sample preparation, sample loss, and proteolysis steps; (iii) isobaric reagents, which after fragmentation in the MS/MS analysis provide a final detectable mass shift, can be used to tag both analyte and standard samples; (iv) label-free approaches in which the absolute quantitative data are not obtained through the use of any kind of labeling, but from computational normalization of the raw data and adequate standards; (v) elemental mass spectrometry-based workflows able to provide directly absolute quantification of peptides/proteins that contain an ICP-detectable element. A critical insight from the Analytical Chemistry perspective of the different standardization approaches and their combinations used so far for absolute quantitative MS-based (molecular and elemental) proteomics is provided in this review.
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Affiliation(s)
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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Mohammed Y, Bhowmick P, Smith DS, Domanski D, Jackson AM, Michaud SA, Malchow S, Percy AJ, Chambers AG, Palmer A, Zhang S, Sickmann A, Borchers CH. PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues. Proteomics 2016; 17. [PMID: 27683069 DOI: 10.1002/pmic.201600210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/31/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Yassene Mohammed
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pallab Bhowmick
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Derek S Smith
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Dominik Domanski
- Molecular Pathology, JGH Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
| | - Angela M Jackson
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Sarah A Michaud
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
| | - Andrew J Percy
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Andrew G Chambers
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Andrea Palmer
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Suping Zhang
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
- Molecular Pathology, JGH Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH. Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600097] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/14/2016] [Accepted: 09/28/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Sarah A. Michaud
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Armando Jardim
- Institute of Parasitology; McGill University; Montreal QC Canada
| | - Nicholas J. Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Suping Zhang
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Center for Proteomics and Metabolomics; Leiden University Medical Center; ZA Leiden Netherlands
| | - Andrea L. Palmer
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Darryl B. Hardie
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Andre M. LeBlanc
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Lai X, Liangpunsakul S, Li K, Witzmann FA. Proteomic profiling of human sera for discovery of potential biomarkers to monitor abstinence from alcohol abuse. Electrophoresis 2015; 36:556-63. [PMID: 25475211 DOI: 10.1002/elps.201400319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/19/2014] [Accepted: 11/20/2014] [Indexed: 11/09/2022]
Abstract
Although numerous biomarkers or biomarker candidates have been discovered to detect levels of drinking and intervals of time after last drinking episode, only a few biomarkers have been applied to monitor abstinence in a longer interval (≥6 wks) from alcohol abuse. Considering sample sources, sensitivity, and specificity, new biomarkers from blood with better accuracy are needed. To address this, serum proteomic profiles were compared between pre- and post- treatment samples from subjects seeking treatment for alcohol abuse and dependence in an intensive 6 wk daily outpatient program using high-abundance plasma protein immunodepletion and LC-MS/MS techniques. Protein identification, quantification, candidate biomarker selection, and prioritization analyses were carried out. Among the 246 quantified serum proteins, abundance of 13 and 45 proteins in female and male subjects were significantly changed (p ≤ 0.05), respectively. Of these biomarker candidate proteins, 2 (female) and 8 (male) proteins were listed in category 1, with high area under the receiver operating characteristic curve, sensitivity, specificity, and fold change. In summary, several new biomarker candidates have been identified to monitor abstinence from alcohol abuse.
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Affiliation(s)
- Xianyin Lai
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, IN, USA; Department of Cellular & Integrative Physiology, Indiana University School of Medicine, IN, USA
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Absolute proteomic quantification of the activity state of proteases and proteolytic cleavages using proteolytic signature peptides and isobaric tags. J Proteomics 2013; 100:79-91. [PMID: 24060996 DOI: 10.1016/j.jprot.2013.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/29/2013] [Accepted: 09/13/2013] [Indexed: 01/25/2023]
Abstract
UNLABELLED Proteolytic processing alters the structure and function of a wide range of proteins in the proteome. We describe a method for the absolute quantification of proteolysis that is compatible with existing quantitative proteomic applications and could be applied on a protein-family wide scale. A tryptic peptide spanning a cleavage site differentiates this intact form of the protein from the corresponding semi-tryptic peptides of a protease cleaved protein. We term such proteomic signatures of specific proteolytic events "proteolytic signature peptides" (PSPs). By quantifying both the tryptic and semi-tryptic PSPs simultaneously with proteotypic peptides common to all forms of the protein both the relative and the absolute amounts of the intact and cleaved protein can be determined. Using synthetic PSP standards of cleavage sites in intact and cleaved proteins the absolute amounts of each form of the protein can be determined. The technique was demonstrated by the simultaneous identification and quantification of matrix metalloproteinase zymogens and their proteolytically activated forms in parallel with conventional absolute quantification of their TIMP inhibitors. For quantification we synthesized a pair of isobaric mass tags, we term CLIP-TRAQ, using C(13) labeled reagents that when fragmented during CID generate signature ions at 113.1 or 114.1 respectively. As an expandable platform this allows for the simultaneous identification of multiple proteins and their proteolytic state in complex proteomes on a family-wide scale in parallel with conventional proteomic analysis. This article is part of a Special Issue entitled: CNPN 2013. BIOLOGICAL SIGNIFICANCE Proteolysis is key to various biological processes and the activity and function of many proteins are dictated by their proteolytic state. The development of methods to quantify protein abundance in conjunction to determining their proteolytic state and hence activity is essential for the complete understanding of the processes for which proteolysis is involved. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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