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Correia I, Oliveira C, Reis A, Guimarães AR, Aveiro S, Domingues P, Bezerra AR, Vitorino R, Moura G, Santos MAS. A proteogenomic pipeline for the analysis of protein biosynthesis errors in the human pathogen Candida albicans. Mol Cell Proteomics 2024:100818. [PMID: 39047911 DOI: 10.1016/j.mcpro.2024.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/20/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
Candida albicans is a diploid pathogen known for its ability to live as a commensal fungus in healthy individuals, but causing both superficial infections and disseminated candidiasis in immunocompromised patients where it is associated with high morbidity and mortality. Its success in colonizing the human host is attributed to a wide range of virulence traits that modulate interactions between the host and the pathogen, such as optimal growth rate at 37 ºC, the ability to switch between yeast and hyphal forms and a remarkable genomic and phenotypic plasticity. A fascinating aspect of its biology is a prominent heterogeneous proteome that arises from frequent genomic rearrangements, high allelic variation, and high levels of amino acid misincorporations in proteins. This leads to increased morphological and physiological phenotypic diversity of high adaptive potential, but the scope of such protein mistranslation is poorly understood due to technical difficulties in detecting and quantifying amino acid misincorporation events in complex protein samples. We have developed and optimized mass spectrometry and bioinformatics pipelines capable of identifying rare amino acid misincorporation events at the proteome level. We have also analysed the proteomic profile of an engineered C. albicans strain that exhibits high level of leucine misincorporation at protein CUG sites and employed an in vivo quantitative gain-of-function fluorescence reporter system to validate our LC-MS/MS data. C. albicans misincorporates amino acids above the background level at protein sites of diverse codons, particularly at CUG, confirming our previous data on the quantification of leucine incorporation at single CUG sites of recombinant reporter proteins, but increasing misincorporation of Leucine at these sites does not alter the translational fidelity of the other codons. These findings indicate that the C. albicans statistical proteome exceeds prior estimates, suggesting that its highly plastic phenome may also be modulated by environmental factors due to translational ambiguity.
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Affiliation(s)
- Inês Correia
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal.
| | - Carla Oliveira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Ana Rita Guimarães
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Susana Aveiro
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Pedro Domingues
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ana Rita Bezerra
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Gabriela Moura
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal; Multidisciplinary Institute of Ageing (MIA-Portugal), University of Coimbra, Coimbra, Portugal.
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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Snashall CM, Sutton CW, Faro LL, Ceresa C, Ploeg R, Shaheed SU. Comparison of in-gel and in-solution proteolysis in the proteome profiling of organ perfusion solutions. Clin Proteomics 2023; 20:51. [PMID: 37968584 PMCID: PMC10648346 DOI: 10.1186/s12014-023-09440-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/25/2023] [Indexed: 11/17/2023] Open
Abstract
PURPOSE The organ perfusion solution (perfusate), collected at clinically and temporally significant stages of the organ preservation and transplantation process, provides a valuable insight into the biological status of an organ over time and prior to reperfusion (transplantation) in the recipient. The objective of this study was to assess two bottom-up proteomics workflows for the extraction of tryptic peptides from the perfusate. EXPERIMENTAL DESIGN Two different kinds of perfusate samples from kidney and liver trials were profiled using liquid chromatography-mass spectrometry (LC-MS/MS). The preparation of clean peptide mixtures for downstream analysis was performed considering different aspects of sample preparation; protein estimation, enrichment, in-gel and urea-based in-solution digestion. RESULTS In-solution digestion of perfusate allowed identification of the highest number of peptides and proteins with greater sequence coverage and higher confidence data in kidney and liver perfusate. Key pathways identified by gene ontology analysis included complement, coagulation and antioxidant pathways, and a number of biomarkers previously linked to ischemia-reperfusion injury were also observed in perfusate. CONCLUSIONS This study showed that in-solution digestion is a more efficient method for LC-MS/MS analysis of kidney and liver organ perfusion solutions. This method is also quicker and easier than in-gel digestion, allowing for greater sample throughput, with fewer opportunities for experimental error or peptide loss.
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Affiliation(s)
- Corinna M Snashall
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Chris W Sutton
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Letizia Lo Faro
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Carlo Ceresa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Rutger Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Leiden University Medical Centre, Leiden University, Leiden, Netherlands
- Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Sadr Ul Shaheed
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- NHSBT Oxford Blood Donor Centre John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9BQ, UK.
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Gautam P, Pandey AK, Gupta A, Dubey SK. Microcosm-omics centric investigation reveals elevated bacterial degradation of imidacloprid. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121402. [PMID: 36889658 DOI: 10.1016/j.envpol.2023.121402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/25/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Imidacloprid, a broad-spectrum insecticide, is widely used against aphids and other sucking insects. As a result, its toxic effect is becoming apparent in non-targeted organisms. In-situ bioremediation of residual insecticide from the environment utilizing efficient microbes would be helpful in reducing its load. In the present work, in-depth genomics, proteomics, bioinformatics, and metabolomics analyses were employed to reveal the potential of Sphingobacterium sp. InxBP1 for in-situ degradation of imidacloprid. The microcosm study revealed ∼79% degradation with first-order kinetics (k = 0.0726 day-1). Genes capable of mediating oxidative degradation of imidacloprid and subsequent decarboxylation of intermediates were identified in the bacterial genome. Proteome analysis demonstrated significant overexpression of the enzymes coded by these genes. Bioinformatic analysis revealed significant affinity and binding of the identified enzymes for their respective substrates (the degradation pathway intermediates). The nitronate monooxygenase (K7A41 01745), amidohydrolase (K7A41 03835 and K7A41 07535), FAD-dependent monooxygenase (K7A41 12,275), and ABC transporter enzymes (K7A41 05325, and K7A41 05605) were found to be effective in facilitating the transport and intracellular degradation of imidacloprid. The metabolomic study identified the pathway intermediates and validated the proposed mechanism and functional role of the identified enzymes in degradation. Thus, the present investigation provides an efficient imidacloprid degrading bacterial species as evidenced by its genetic attributes which can be utilized or further improved to develop technologies for in-situ remediation.
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Affiliation(s)
- Pallavi Gautam
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, 284128, India
| | - Ankush Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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Kumari M, Pradhan UK, Joshi R, Punia A, Shankar R, Kumar R. In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. BMC PLANT BIOLOGY 2021; 21:604. [PMID: 34937558 PMCID: PMC8693493 DOI: 10.1186/s12870-021-03394-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Picrorhiza kurroa Royle ex Benth. being a rich source of phytochemicals, is a promising high altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages. RESULTS We were able to identify 5186 protein accessions (FDR < 1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RNA binding proteins (RBPs) and post-translational modifications (PTMs), particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development. CONCLUSIONS This report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.
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Affiliation(s)
- Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upendra Kumar Pradhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
- Present address: ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, 110012, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ravi Shankar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Bickner AN, Champion MM, Hummon AB, Bruening ML. Electroblotting through a tryptic membrane for LC-MS/MS analysis of proteins separated in electrophoretic gels. Analyst 2021; 145:7724-7735. [PMID: 33000802 DOI: 10.1039/d0an01380c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Digestion of proteins separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) remains a popular method for protein identification using mass-spectrometry based proteomics. Although robust and routine, the in-gel digestion procedure is laborious and time-consuming. Electroblotting to a capture membrane prior to digestion reduces preparation steps but requires on-membrane digestion that yields fewer peptides than in-gel digestion. This paper develops direct electroblotting through a trypsin-containing membrane to a capture membrane to simplify extraction and digestion of proteins separated by SDS-PAGE. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the extracted peptides. Analysis of peptides from different capture membrane pieces shows that electrodigestion does not greatly disturb the spatial resolution of a standard protein mixture separated by SDS-PAGE. Electrodigestion of an Escherichia coli (E. coli) cell lysate requires four hours of total sample preparation and results in only 13% fewer protein identifications than in-gel digestion, which can take 24 h. Compared to simple electroblotting and protein digestion on a poly(vinylidene difluoride) (PVDF) capture membrane, adding a trypsin membrane to the electroblot increases the number of protein identifications by 22%. Additionally, electrodigestion experiments using capture membranes coated with polyelectrolyte layers identify a higher fraction of small proteolytic peptides than capture on PVDF or in-gel digestion.
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Affiliation(s)
- A N Bickner
- Department of Chemistry and Biochemistry University of Notre Dame, Notre Dame, Indiana 46556, USA.
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Chan QWT, Rogalski J, Moon KM, Foster LJ. The application of forensic proteomics to identify an unknown snake venom in a deceased toddler. Forensic Sci Int 2021; 323:110820. [PMID: 33984813 DOI: 10.1016/j.forsciint.2021.110820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Proteomics is the global analysis of proteins in a sample, and its methodologies are commonly applied in life science research. Despite its wide applicability however, proteomics is rarely used as a tool in criminal investigations. Here we present a case where the technique provided key evidence in a case that involved the death of a two-year old girl. The defendant was known to keep exotic snakes, including several venomous species, which led the coroner to probe whether there could be snake venom in the blood of the deceased. One major challenge of the investigation was the overwhelming presence of several blood proteins, such as apolipoprotein and complement proteins, which hinders the detection of less abundant analytes. In a counter-acting strategy, a combination of immunodepletion and fractionation methods was used; the sample was then submitted to tandem mass spectrometry for peptide identification. Using this strategy, 15,000 peptides could be sequenced. However, the subsequent challenge was to differentiate between human and snake proteins, given the genetic similarities that are shared by the two vertebrate species. After a thorough bioinformatics search and manual inspection, we found that<1% of the sequenced peptides could be matched unequivocally to snake proteins, including a well-known venom component, phospholipase A2. This evidence, in part, led to a court-issued search warrant of the defendant's home, followed by his arrest and an eventual guilty plea with formal sentencing to 18 months in prison. The work outlined here is an example of how proteomics technology can help to expand the toolkit for molecular forensics.
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Affiliation(s)
- Queenie W T Chan
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC V6T 1Z4, Canada
| | - Jason Rogalski
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC V6T 1Z4, Canada
| | - Kyung-Mee Moon
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC V6T 1Z4, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry & Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC V6T 1Z4, Canada.
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Nilo-Poyanco R, Moraga C, Benedetto G, Orellana A, Almeida AM. Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening. BMC Genomics 2021; 22:17. [PMID: 33413072 PMCID: PMC7788829 DOI: 10.1186/s12864-020-07299-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening. RESULTS To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O'Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively. CONCLUSIONS Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.
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Affiliation(s)
- Ricardo Nilo-Poyanco
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide, 5750, Huechuraba, Chile
| | - Carol Moraga
- Université Claude Bernard Lyon 1, 69622, Villeurbanne, France
- Inria Grenoble Rhône-Alpes, 38334, Montbonnot, France
| | - Gianfranco Benedetto
- Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, República 330, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, República 330, Santiago, Chile
- Center for Genome Regulation, Blanco Encalada, 2085, Santiago, Chile
| | - Andrea Miyasaka Almeida
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide, 5750, Huechuraba, Chile.
- Escuela de Agronomía, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide, 5750, Huechuraba, Chile.
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Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122453. [PMID: 33279813 DOI: 10.1016/j.jchromb.2020.122453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/29/2022]
Abstract
Shotgun proteomics is a high-throughput technology which has been developed with the aim of investigating the maximum number of proteins in cells in a given experiment. However, protein discovery and data generation vary in depth and coverage when different technical strategies are selected. In this study, three different sample preparation approaches, and peptide or protein fractionation methods, were applied to identify and quantify proteins from log-phase yeast lysate: sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), filter-aided sample preparation coupled with gas phase fractionation (FASP-GPF), and FASP - high pH reversed phase fractionation (HpH). Fractions were initially analyzed and compared using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS) employing data dependent acquisition on a linear ion trap instrument. The number of fractions and analytical replicates was adjusted so that each experiment used a similar amount of mass spectrometric instrument time. A second set of experiments was performed, comparing FASP-GPF, SDS-PAGE and FASP-HpH using a Q Exactive Orbitrap mass spectrometer. Compared with results from the linear ion trap mass spectrometer, the use of a Q Exactive Orbitrap mass spectrometer enabled a substantial increase in protein identifications, and an even greater increase in peptide identifications. This shows that the main advantage of using the higher resolution instrument is in increased proteome coverage. A total of 1035, 1357 and 2134 proteins were separately identified by FASP-GPF, SDS-PAGE and FASP-HpH. Combining results from the Orbitrap experiments, there were a total of 2269 proteins found, with 94% of them identified using the FASP-HpH method. Therefore, the FASP-HpH method is the optimal choice among these approaches, when applied to this type of sample.
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Affiliation(s)
- Liting Deng
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - David C L Handler
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Dylan H Multari
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
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Deducing the presence of proteins and proteoforms in quantitative proteomics. Nat Commun 2018; 9:2320. [PMID: 29899466 PMCID: PMC5998138 DOI: 10.1038/s41467-018-04411-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/27/2018] [Indexed: 11/20/2022] Open
Abstract
The human genome harbors just 20,000 genes suggesting that the variety of possible protein products per gene plays a significant role in generating functional diversity. In bottom-up proteomics peptides are mapped back to proteins and proteoforms to describe a proteome; however, accurate quantitation of proteoforms is challenging due to incomplete protein sequence coverage and mapping ambiguities. Here, we demonstrate that a new software tool called ProteinClusterQuant (PCQ) can be used to deduce the presence of proteoforms that would have otherwise been missed, as exemplified in a proteomic comparison of two fly species, Drosophilamelanogaster and D. virilis. PCQ was used to identify reduced levels of serine/threonine protein kinases PKN1 and PKN4 in CFBE41o− cells compared to HBE41o− cells and to elucidate that shorter proteoforms of full-length caspase-4 and ephrin B receptor are differentially expressed. Thus, PCQ extends current analyses in quantitative proteomics and facilitates finding differentially regulated proteins and proteoforms. An accurate quantitation of different proteoforms remains challenging due to incomplete protein sequence coverage in mass spectrometry datasets. Here the authors describe a method to facilitate the discovery of proteoforms that may otherwise not be considered due to incomplete protein coverage or ambiguities in mapping peptides back to proteins.
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Boyatzis AE, Bringans SD, Piggott MJ, Duong MN, Lipscombe RJ, Arthur PG. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation. J Proteome Res 2017; 16:2004-2015. [DOI: 10.1021/acs.jproteome.6b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Amber E. Boyatzis
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Matthew J. Piggott
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Marisa N. Duong
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Peter G. Arthur
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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13
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Pisano M, Palomba A, Tanca A, Pagnozzi D, Uzzau S, Addis MF, Dettori MA, Fabbri D, Palmieri G, Rozzo C. Protein expression changes induced in a malignant melanoma cell line by the curcumin analogue compound D6. BMC Cancer 2016; 16:317. [PMID: 27192978 PMCID: PMC4870815 DOI: 10.1186/s12885-016-2362-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background We have previously demonstrated that the hydroxylated biphenyl compound D6 (3E,3′E)-4,4′-(5,5′,6,6′-tetramethoxy-[1,1′-biphenyl]-3,3′-diyl)bis(but-3-en-2-one), a structural analogue of curcumin, exerts a strong antitumor activity on melanoma cells both in vitro and in vivo. Although the mechanism of action of D6 is yet to be clarified, this compound is thought to inhibit cancer cell growth by arresting the cell cycle in G2/M phase, and to induce apoptosis through the mitochondrial intrinsic pathway. To investigate the changes in protein expression induced by exposure of melanoma cells to D6, a differential proteomic study was carried out on D6-treated and untreated primary melanoma LB24Dagi cells. Methods Proteins were fractionated by SDS-PAGE and subjected to in gel digestion. The peptide mixtures were analyzed by liquid chromatography coupled with tandem mass spectrometry. Proteins were identified and quantified using database search and spectral counting. Proteomic data were finally uploaded into the Ingenuity Pathway Analysis software to find significantly modulated networks and pathways. Results Analysis of the differentially expressed protein profiles revealed the activation of a strong cellular stress response, with overexpression of several HSPs and stimulation of ubiquitin-proteasome pathways. These were accompanied by a decrease of protein synthesis, evidenced by downregulation of proteins involved in mRNA processing and translation. These findings are consistent with our previous results on gene expression profiling in melanoma cells treated with D6. Conclusions Our findings confirm that the curcumin analogue D6 triggers a strong stress response in melanoma cells, turning down majority of cell functions and finally driving cells to apoptosis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2362-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Pisano
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Antonio Palomba
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy.,Biosistema Scrl, Sassari, Italy
| | - Alessandro Tanca
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy
| | - Daniela Pagnozzi
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy
| | - Sergio Uzzau
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy
| | | | - Maria Antonietta Dettori
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Davide Fabbri
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Carla Rozzo
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy.
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14
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Barkla BJ, Vera-Estrella R, Raymond C. Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins. BMC PLANT BIOLOGY 2016; 16:110. [PMID: 27160145 PMCID: PMC4862212 DOI: 10.1186/s12870-016-0797-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/02/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Epidermal bladder cells (EBC) are large single-celled, specialized, and modified trichomes found on the aerial parts of the halophyte Mesembryanthemum crystallinum. Recent development of a simple but high throughput technique to extract the contents from these cells has provided an opportunity to conduct detailed single-cell-type analyses of their molecular characteristics at high resolution to gain insight into the role of these cells in the salt tolerance of the plant. RESULTS In this study, we carry out large-scale complementary quantitative proteomic studies using both a label (DIGE) and label-free (GeLC-MS) approach to identify salt-responsive proteins in the EBC extract. Additionally we perform an ionomics analysis (ICP-MS) to follow changes in the amounts of 27 different elements. Using these methods, we were able to identify 54 proteins and nine elements that showed statistically significant changes in the EBC from salt-treated plants. GO enrichment analysis identified a large number of transport proteins but also proteins involved in photosynthesis, primary metabolism and Crassulacean acid metabolism (CAM). Validation of results by western blot, confocal microscopy and enzyme analysis helped to strengthen findings and further our understanding into the role of these specialized cells. As expected EBC accumulated large quantities of sodium, however, the most abundant element was chloride suggesting the sequestration of this ion into the EBC vacuole is just as important for salt tolerance. CONCLUSIONS This single-cell type omics approach shows that epidermal bladder cells of M. crystallinum are metabolically active modified trichomes, with primary metabolism supporting cell growth, ion accumulation, compatible solute synthesis and CAM. Data are available via ProteomeXchange with identifier PXD004045.
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Affiliation(s)
- Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.
| | - Rosario Vera-Estrella
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, MOR, México
| | - Carolyn Raymond
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
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15
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Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJC, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC. Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. J Proteome Res 2015; 15:691-706. [PMID: 26653538 PMCID: PMC4779376 DOI: 10.1021/acs.jproteome.5b00859] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation (source code is available from http://homepages.uc.edu/~wang2x7/Research.htm ). From these assessments, we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61 to 93% of the time. When comparing across different instruments and quantitative technologies, using multiple replicates, differential genes were reproduced by other data sets from 67 to 99% of the time. Projecting gene differences to biological pathways and networks increased the degree of similarity. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.
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Affiliation(s)
| | - Xia Wang
- Department of Mathematical Sciences, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Karl R Clauser
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | - Philipp Mertins
- Proteomics Platform, Broad Institute of MIT and Harvard , Cambridge, Massachusetts 02142, United States
| | | | | | | | | | | | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Sherri R Davies
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Matthew J C Ellis
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Shunqiang Li
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - R Reid Townsend
- Department of Medicine, Washington University , St. Louis, Missouri 63110, United States
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Karen A Ketchum
- Enterprise Science and Computing, Inc. , Rockville, Maryland 20850, United States
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute , Bethesda, Maryland 20892, United States
| | - Tao Liu
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Sangtae Kim
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Jason E McDermott
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Samuel H Payne
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Vladislav A Petyuk
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Karin D Rodland
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Richard D Smith
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Feng Yang
- Division of Biological Sciences, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Daniel W Chan
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Bai Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Hui Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Zhen Zhang
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
| | - Jian-Ying Zhou
- JHMI and Division of Clinical Chemistry, Johns Hopkins University , Baltimore, Maryland 21231, United States
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16
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Geddes JMH, Croll D, Caza M, Stoynov N, Foster LJ, Kronstad JW. Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A. BMC Microbiol 2015; 15:206. [PMID: 26453029 PMCID: PMC4600298 DOI: 10.1186/s12866-015-0532-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/25/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The pathogenic yeast Cryptococcus neoformans causes life-threatening meningoencephalitis in individuals suffering from HIV/AIDS. The cyclic-AMP/protein kinase A (PKA) signal transduction pathway regulates the production of extracellular virulence factors in C. neoformans, but the influence of the pathway on the secretome has not been investigated. In this study, we performed quantitative proteomics using galactose-inducible and glucose-repressible expression of the PKA1 gene encoding the catalytic subunit of PKA to identify regulated proteins in the secretome. METHODS The proteins in the supernatants of cultures of C. neoformans were precipitated and identified using liquid chromatography-coupled tandem mass spectrometry. We also employed multiple reaction monitoring in a targeted approach to identify fungal proteins in samples from macrophages after phagocytosis of C. neoformans cells, as well as from the blood and bronchoalveolar fluid of infected mice. RESULTS We identified 61 secreted proteins and found that changes in PKA1 expression influenced the extracellular abundance of five proteins, including the Cig1 and Aph1 proteins with known roles in virulence. We also observed a change in the secretome profile upon induction of Pka1 from proteins primarily involved in catabolic and metabolic processes to an expanded set that included proteins for translational regulation and the response to stress. We further characterized the secretome data using enrichment analysis and by predicting conventional versus non-conventional secretion. Targeted proteomics of the Pka1-regulated proteins allowed us to identify the secreted proteins in lysates of phagocytic cells containing C. neoformans, and in samples from infected mice. This analysis also revealed that modulation of PKA1 expression influences the intracellular survival of cryptococcal cells upon phagocytosis. CONCLUSIONS Overall, we found that the cAMP/PKA pathway regulates specific components of the secretome including proteins that affect the virulence of C. neoformans. The detection of secreted cryptococcal proteins from infected phagocytic cells and tissue samples suggests their potential utility as biomarkers of infection. The proteomics data are available via ProteomeXchange with identifiers PXD002731 and PASS00736.
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Affiliation(s)
- Jennifer M H Geddes
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Daniel Croll
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Mélissa Caza
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Nikolay Stoynov
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Leonard J Foster
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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17
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Yakovleva ME, Welinder C, Sugihara Y, Pawłowski K, Rezeli M, Wieslander E, Malm J, Marko-Varga G. Workflow for large-scale analysis of melanoma tissue samples. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G. In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J Proteome Res 2015; 14:3441-51. [PMID: 26155874 DOI: 10.1021/acs.jproteome.5b00486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered to be "missing" proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these missing proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C-HPP teams (chromosomes 5, 10, 16, and 19) has joined forces to devise new strategies to identify missing proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low-complexity samples derived from IVTT. The optimized assays are then applied to identify missing proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of 18 missing proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
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Affiliation(s)
- Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ákos Végvári
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Justin Saul
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Jin G Park
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Ji Qiu
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Michael Syring
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Patrick Pirrotte
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Konstantinos Petritis
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States.,Pathology Research, Phoenix Children's Hospital , 1919 East Thomas Road, Phoenix, Arizona 85016, United States
| | - Tony J Tegeler
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Meraj Aziz
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | | | | | | | | | | | | | - Concha Gil
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Felipe Clemente
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Maria Luisa Hernaez
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Fernando J Corrales
- Center for Applied Medical Research (CIMA), University of Navarra, PRB2-ProteoRed-ISCIII, IDISNA, Ciberhed , 31008 Pamplona, Spain
| | - Carol L Nilsson
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen , Postbox 7804, N-5009 Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Postbox 1400, 5021 Bergen, Norway
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - György Marko-Varga
- First Department of Surgery, Tokyo Medical University , 6-7-1 Nishishinjuku Shinjuku-ku, 160-0023 Tokyo, Japan
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19
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Proteomic profiling of nipple aspirate fluid (NAF): Exploring the complementarity of different peptide fractionation strategies. J Proteomics 2015; 117:86-94. [PMID: 25638022 DOI: 10.1016/j.jprot.2015.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 12/15/2014] [Accepted: 01/16/2015] [Indexed: 12/20/2022]
Abstract
UNLABELLED NAF is a breast fluid that is closely related to the tumor microenvironment and a valuable sample for studying breast cancer. To perform an in-depth proteomic analysis of this sample, aliquots of a single NAF digest were analyzed by the following peptide-centric fractionation strategies: a) 30-cm reversed-phase (RP) column on-line with an LTQ-Orbitrap XL; b) off-line strong cation-exchange (SCX) column; and c) pI-based OFFGEL fractionation. All fractions from approaches (b) and (c) were further analyzed on a 10-cm RP column hyphenated to the same mass spectrometer. The RP-30cm, SCX/RP-10cm, and OFFGEL/RP-10cm approaches identified 1676, 2930, and 3240 peptides, which corresponded to 193, 390 and 528 proteins, respectively. In our cumulative dataset, 4466 distinct NAF peptides corresponded to a total of 557 proteins, of which only 34% were identified by all three approaches. No exclusive protein identification was associated to the RP-30cm approach, while SCX/RP-10cm and OFFGEL/RP-10cm contributed to 28 and 166 exclusive identifications, respectively. Each approach provided additional information related to energy metabolism (fermentation process/carbohydrate biosynthesis). In conclusion, the pre-fractionation platforms used were complementary for the comprehensive characterization of NAF and our work provides methodological information for future quantitative cancer-related NAF sample studies. BIOLOGICAL SIGNIFICANCE High-resolution peptide separation is a sine qua non condition for achieving extensive proteome coverage. Various techniques have been employed to improve peptide fractionation prior to LC-MS/MS, thus allowing a comprehensive characterization of complex biological samples. Although fractionation efficiency is very sample-dependent, this issue is commonly overlooked, and a "cookbook" approach is routinely used during this critical step. The present study provides a systematic comparison of analytical information needed for the successful large-scale differential proteomic analysis of NAF samples from breast cancer patients, a precious and volume-limited biological sample. It reinforces the importance of optimizing sample-specific fractionation protocols for information retrieval from mass spectrometric analysis.
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20
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Siljamäki P, Varmanen P, Kankainen M, Sukura A, Savijoki K, Nyman TA. Comparative exoprotein profiling of different Staphylococcus epidermidis strains reveals potential link between nonclassical protein export and virulence. J Proteome Res 2014; 13:3249-61. [PMID: 24840314 DOI: 10.1021/pr500075j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Staphylococcus epidermidis (SE) includes commensal and pathogenic strains capable of infecting humans and animals. This study reports global exoproteome profiling of bovine mastitis strain PM221 and two human strains, commensal-type ATCC12228 and sepsis-associated RP62A. We identified 451, 395, and 518 proteins from culture supernatants of PM221, ATCC12228, and RP62A, respectively. Comparison of the identified exoproteomes revealed several strain-specific differences related to secreted antigens and adhesins, higher virulence capability for RP62A, and similarities between the PM221 and RP62A exoproteomes. The majority of the identified proteins (∼80%) were predicted to be cytoplasmic, including proteins known to be associated in membrane vesicles (MVs) in Staphylococcus aureus and immunogenic/adhesive moonlighting proteins. Enrichment of MV fractions from culture supernatants and analysis of their protein composition indicated that this nonclassical protein secretion pathway was being exploited under the conditions used and that there are strain-specific differences in nonclassical protein export. In addition, several predicted cell-surface proteins were identified in the culture media. In summary, the present study is the first in-depth exoproteome analysis of SE highlighting strain-specific factors able to contribute to virulence and adaptation.
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Affiliation(s)
- Pia Siljamäki
- Department of Food and Environmental Sciences, ‡Institute of Biotechnology, and §Department of Veterinary Biosciences, University of Helsinki , FI-00014 Helsinki, Finland
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21
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Becher D, Bernhardt J, Fuchs S, Riedel K. Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics 2014; 13:2895-909. [PMID: 23894095 DOI: 10.1002/pmic.201300095] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/03/2013] [Accepted: 05/13/2013] [Indexed: 11/06/2022]
Abstract
Soil- and litter-borne microorganisms vitally contribute to biogeochemical cycles. However, changes in environmental parameters but also human interferences may alter species composition and elicit alterations in microbial activities. Soil and litter metaproteomics, implying the assignment of soil and litter proteins to specific phylogenetic and functional groups, has a great potential to provide essential new insights into the impact of microbial diversity on soil ecosystem functioning. This article will illuminate challenges and perspectives of current soil and litter metaproteomics research, starting with an introduction to an appropriate experimental design and state-of-the-art proteomics methodologies. This will be followed by a summary of important studies aimed at (i) the discovery of the major biotic drivers of leaf litter decomposition, (ii) metaproteomics analyses of rhizosphere-inhabiting microbes, and (iii) global approaches to study bioremediation processes. The review will be closed by a brief outlook on future developments and some concluding remarks, which should assist the reader to develop successful concepts for soil and litter metaproteomics studies.
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Affiliation(s)
- Dörte Becher
- Ernst-Moritz-Arndt-University of Greifswald, Institute of Microbiology, Greifswald, Germany
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22
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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23
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Krey JF, Wilmarth PA, Shin JB, Klimek J, Sherman NE, Jeffery ED, Choi D, David LL, Barr-Gillespie PG. Accurate label-free protein quantitation with high- and low-resolution mass spectrometers. J Proteome Res 2013; 13:1034-1044. [PMID: 24295401 DOI: 10.1021/pr401017h] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free quantitation of proteins analyzed by tandem mass spectrometry uses either integrated peak intensity from the parent-ion mass analysis (MS1) or features from fragment-ion analysis (MS2), such as spectral counts or summed fragment-ion intensity. We directly compared MS1 and MS2 quantitation by analyzing human protein standards diluted into Escherichia coli extracts on an Orbitrap mass spectrometer. We found that summed MS2 intensities were nearly as accurate as integrated MS1 intensities, and both outperformed MS2 spectral counting in accuracy and linearity. We compared these results to those obtained from two low-resolution ion-trap mass spectrometers; summed MS2 intensities from LTQ and LTQ Velos instruments were similar in accuracy to those from the Orbitrap. Data from all three instruments are available via ProteomeXchange with identifier PXD000602. Abundance measurements using MS1 or MS2 intensities had limitations, however. While measured protein concentration was on average well-correlated with the known concentration, there was considerable protein-to-protein variation. Moreover, not all human proteins diluted to a mole fraction of 10(-3) or lower were detected, with a strong falloff below 10(-4) mole fraction. These results show that MS1 and MS2 intensities are simple measures of protein abundance that are on average accurate but should be limited to quantitation of proteins of intermediate to higher fractional abundance.
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Affiliation(s)
- Jocelyn F Krey
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR
| | - Phillip A Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Jung-Bum Shin
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR
| | - John Klimek
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR
| | - Nicholas E Sherman
- W.M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, VA
| | - Erin D Jeffery
- W.M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, VA
| | - Dongseok Choi
- Department of Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR
| | - Larry L David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR.,Proteomics Shared Resource, Oregon Health & Science University, Portland, OR
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR
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Haga A, Ogawara Y, Kubota D, Kitabayashi I, Murakami Y, Kondo T. Interactomic approach for evaluating nucleophosmin-binding proteins as biomarkers for Ewing's sarcoma. Electrophoresis 2013; 34:1670-8. [PMID: 23483572 DOI: 10.1002/elps.201200661] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/21/2013] [Accepted: 01/29/2013] [Indexed: 02/02/2023]
Abstract
Nucleophosmin (NPM) is a novel prognostic biomarker for Ewing's sarcoma. To evaluate the prognostic utility of NPM, we conducted an interactomic approach to characterize the NPM protein complex in Ewing's sarcoma cells. A gene suppression assay revealed that NPM promoted cell proliferation and the invasive properties of Ewing's sarcoma cells. FLAG-tag-based affinity purification coupled with liquid chromatography-tandem mass spectrometry identified 106 proteins in the NPM protein complex. The functional classification suggested that the NPM complex participates in critical biological events, including ribosome biogenesis, regulation of transcription and translation, and protein folding, that are mediated by these proteins. In addition to JAK1, a candidate prognostic biomarker for Ewing's sarcoma, the NPM complex, includes 11 proteins known as prognostic biomarkers for other malignancies. Meta-analysis of gene expression profiles of 32 patients with Ewing's sarcoma revealed that 6 of 106 were significantly and independently associated with survival period. These observations suggest a functional role as well as prognostic value of these NPM complex proteins in Ewing's sarcoma. Further, our study suggests the potential applications of interactomics in conjunction with meta-analysis for biomarker discovery.
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Affiliation(s)
- Ayako Haga
- Division of Pharmaco-proteomics, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
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Merali S, Barrero CA, Bowler RP, Chen DE, Criner G, Braverman A, Litwin S, Yeung A, Kelsen SG. Analysis of the plasma proteome in COPD: Novel low abundance proteins reflect the severity of lung remodeling. COPD 2013; 11:177-89. [PMID: 24111704 DOI: 10.3109/15412555.2013.831063] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The search for COPD biomarkers has largely employed a targeted approach that focuses on plasma proteins involved in the systemic inflammatory response and in lung injury and repair. This proof of concept study was designed to test the idea that an open, unbiased, in-depth proteomics approach could identify novel, low abundance plasma proteins i.e., ng/mL concentration, which could serve as potential biomarkers. Differentially expressed proteins were identified in a discovery group with severe COPD (FEV1 <45% predicted; n = 10). Subjects with normal lung function matched for age, sex, ethnicity and smoking history served as controls (n = 10). Pooled plasma from each group was exhaustively immunodepleted of abundant proteins, d separated by 1-D gel electrophoresis and extensively fractionated prior to LC-tandem mass spectroscopy (GeLC-MS). Thirty one differentially expressed proteins were identified in the discovery group including markers of lung defense against oxidant stress, alveolar macrophage activation, and lung tissue injury and repair. Four of the 31 proteins (i.e., GRP78, soluble CD163, IL1AP and MSPT9) were measured in a separate verification group of 80 subjects with varying COPD severity by immunoassay. All 4 were significantly altered in COPD and 2 (GRP78 and soluble CD163) correlated with both FEV1 and the extent of emphysema. In-depth, plasma proteomic analysis identified a group of novel, differentially expressed, low abundance proteins that reflect known pathogenic mechanisms and the severity of lung remodeling in COPD. These proteins may also prove useful as COPD biomarkers.
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Affiliation(s)
- Salim Merali
- 1Department of Biochemistry, Temple University School of Medicine , Philadelphia, PA , USA
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26
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Weston LA, Bauer KM, Hummon AB. Comparison of bottom-up proteomic approaches for LC-MS analysis of complex proteomes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2013; 5:10.1039/C3AY40853A. [PMID: 24288579 PMCID: PMC3839868 DOI: 10.1039/c3ay40853a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Discovery-based proteomic studies aim to answer important biological questions by identifying as many proteins as possible. In order to accomplish this lofty goal, an effort must be placed on determining an optimal workflow that maximizes protein identifications. In this study, we compare protein extraction, digestion and fractionation methods for bottom-up proteomics using a human colon cancer cell line as our model system. Four different buffers for protein extraction, two digestion approaches, as well as three sample fractionation methods were evaluated in order to determine an accessible workflow that gives maximal protein identifications. Samples comparing these workflows were analyzed via UPLC paired with tandem MS on a Q-Exactive mass spectrometer. Our goal is to determine an optimal workflow to enable users to maximize protein identifications. Our results show that an increased number of confident protein identifications are attained with a filter-aided digestion approach as compared to an in-solution digestion. Overall SDS-PAGE fractionation leads to higher numbers of identifications than SCX SpinTip and reverse phased cartridge platforms. The novel aspect of this work is the comparison of two readily available, offline platforms for fractionation in reference to a traditional technique, SDS-PAGE.
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Affiliation(s)
| | | | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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27
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Sample loading influences studies comparing isoelectric focusing vs. strong cation exchange peptide fractionation. J Chromatogr A 2013; 1307:207-8. [DOI: 10.1016/j.chroma.2013.06.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/26/2013] [Accepted: 06/30/2013] [Indexed: 01/28/2023]
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28
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Ma C, Zhao X, Han H, Tong W, Zhang Q, Qin P, Chang C, Peng B, Ying W, Qian X. N-linked glycoproteome profiling of human serum using tandem enrichment and multiple fraction concatenation. Electrophoresis 2013; 34:2440-50. [DOI: 10.1002/elps.201200662] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/05/2013] [Accepted: 03/08/2013] [Indexed: 11/08/2022]
Affiliation(s)
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Huanhuan Han
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Wei Tong
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Qi Zhang
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Peibin Qin
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Cheng Chang
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Bo Peng
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
| | - Wantao Ying
- State Key Laboratory of Proteomics; Beijing Proteome Research Center; Beijing Institute of Radiation Medicine; Beijing; P. R. China
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29
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Lukic N, Visentin R, Delhaye M, Frossard JL, Lescuyer P, Dumonceau JM, Farina A. An integrated approach for comparative proteomic analysis of human bile reveals overexpressed cancer-associated proteins in malignant biliary stenosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:1026-33. [PMID: 23872482 DOI: 10.1016/j.bbapap.2013.06.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/21/2013] [Accepted: 06/28/2013] [Indexed: 12/18/2022]
Abstract
Proteomics is a key tool in the identification of new bile biomarkers for differentiating malignant and nonmalignant biliary stenoses. Unfortunately, the complexity of bile and the presence of molecules interfering with protein analysis represent an obstacle for quantitative proteomic studies in bile samples. The simultaneous need to introduce purification steps and minimize the use of pre-fractionation methods inevitably leads to protein loss and limited quantifications. This dramatically reduces the chance of identifying new potential biomarkers. In the present study, we included differential centrifugation as a preliminary step in a quantitative proteomic workflow involving iTRAQ labeling, peptide fractionation by OFFGEL electrophoresis and LC-MS/MS, to compare protein expression in bile samples collected from patients with malignant or nonmalignant biliary stenoses. A total of 1267 proteins were identified, including a set of 322 newly described bile proteins, mainly belonging to high-density cellular fractions. The subsequent comparative analysis led to a 5-fold increase in the number of quantified proteins over previously published studies and highlighted 104 proteins overexpressed in malignant samples. Finally, immunoblot verifications performed on a cohort of 8 malignant (pancreatic adenocarcinoma, n=4; cholangiocarcinoma, n=4) and 5 nonmalignant samples (chronic pancreatitis, n=3; biliary stones, n=2) confirmed the results of proteomic analysis for three proteins: olfactomedin-4, syntenin-2 and Ras-related C3 botulinum toxin substrate 1. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Natalija Lukic
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland
| | - Rémy Visentin
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland
| | - Myriam Delhaye
- Department of Gastroenterology, Erasme Hospital, Free University of Brussels, Brussels BE-1070, Belgium
| | - Jean-Louis Frossard
- Division of Gastroenterology and Hepatology, Geneva University Hospitals, Geneva CH-1211, Switzerland
| | - Pierre Lescuyer
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland; Clinical Proteomics Laboratory, Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva CH-1211, Switzerland
| | - Jean-Marc Dumonceau
- Division of Gastroenterology and Hepatology, Geneva University Hospitals, Geneva CH-1211, Switzerland
| | - Annarita Farina
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, Geneva University, Geneva CH-1211, Switzerland.
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30
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León IR, Schwämmle V, Jensen ON, Sprenger RR. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics 2013; 12:2992-3005. [PMID: 23792921 DOI: 10.1074/mcp.m112.025585] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods.
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Affiliation(s)
- Ileana R León
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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31
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Yadeta KA, Elmore JM, Coaker G. Advancements in the analysis of the Arabidopsis plasma membrane proteome. FRONTIERS IN PLANT SCIENCE 2013; 4:86. [PMID: 23596451 PMCID: PMC3622881 DOI: 10.3389/fpls.2013.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/22/2013] [Indexed: 05/09/2023]
Abstract
The plasma membrane (PM) regulates diverse processes essential to plant growth, development, and survival in an ever-changing environment. In addition to maintaining normal cellular homeostasis and plant nutrient status, PM proteins perceive and respond to a myriad of environmental cues. Here we review recent advances in the analysis of the plant PM proteome with a focus on the model plant Arabidopsis thaliana. Due to membrane heterogeneity, hydrophobicity, and low relative abundance, analysis of the PM proteome has been a special challenge. Various experimental techniques to enrich PM proteins and different protein and peptide separation strategies have facilitated the identification of thousands of integral and membrane-associated proteins. Numerous classes of proteins are present at the PM with diverse biological functions. PM microdomains have attracted much attention. However, it still remains a challenge to characterize these cell membrane compartments. Dynamic changes in the PM proteome in response to different biotic and abiotic stimuli are highlighted. Future prospects for PM proteomics research are also discussed.
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Affiliation(s)
- Koste A. Yadeta
- Department of Plant Pathology, University of California DavisDavis, CA, USA
| | - J. Mitch Elmore
- Department of Plant Pathology, University of California DavisDavis, CA, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California DavisDavis, CA, USA
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32
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Zhao F, Wu Y, Guo L, Li X, Han J, Chen Y, Ge Y. Using proteomics platform to develop a potential immunoassay method of royal jelly freshness. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-1939-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Kranenburg O, Emmink BL, Knol J, van Houdt WJ, Rinkes IHMB, Jimenez CR. Proteomics in studying cancer stem cell biology. Expert Rev Proteomics 2013; 9:325-36. [PMID: 22809210 DOI: 10.1586/epr.12.24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and how these are affected by cancer-specific genetic alterations and by treatment. Proteomics is emerging as a powerful tool to identify the signaling complexes and pathways that control multi- and pluri-potency and SC differentiation. Here, the authors review the novel insights that these studies have provided and present a comprehensive strategy for the use of proteomics in studying cancer SC biology.
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Affiliation(s)
- Onno Kranenburg
- Department of Surgery, University Medical Center Utrecht, Heidelberglaan 100, 3584CX, The Netherlands.
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34
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Tabb DL. Quality assessment for clinical proteomics. Clin Biochem 2012; 46:411-20. [PMID: 23246537 DOI: 10.1016/j.clinbiochem.2012.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/01/2012] [Accepted: 12/03/2012] [Indexed: 12/21/2022]
Abstract
Proteomics has emerged from the labs of technologists to enter widespread application in clinical contexts. This transition, however, has been hindered by overstated early claims of accuracy, concerns about reproducibility, and the challenges of handling batch effects properly. New efforts have produced sets of performance metrics and measurements of variability that establish sound expectations for experiments in clinical proteomics. As researchers begin incorporating these metrics in a quality by design paradigm, the variability of individual steps in experimental pipelines will be reduced, regularizing overall outcomes. This review discusses the evolution of quality assessment in 2D gel electrophoresis, mass spectrometry-based proteomic profiling, tandem mass spectrometry-based protein inventories, and proteomic quantitation. Taken together, the advances in each of these technologies are establishing databases that will be increasingly useful for decision-making in clinical experimentation.
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Affiliation(s)
- David L Tabb
- Department of Biomedical Informatics, Vanderbilt University, USA.
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35
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Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Giri AP, Gupta VS. Proteome profiling of flax (Linum usitatissimum) seed: characterization of functional metabolic pathways operating during seed development. J Proteome Res 2012; 11:6264-76. [PMID: 23153172 DOI: 10.1021/pr300984r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Flax (Linum usitatissimum L.) seeds are an important source of food and feed due to the presence of various health promoting compounds, making it a nutritionally and economically important plant. An in-depth analysis of the proteome of developing flax seed is expected to provide significant information with respect to the regulation and accumulation of such storage compounds. Therefore, a proteomic analysis of seven seed developmental stages (4, 8, 12, 16, 22, 30, and 48 days after anthesis) in a flax variety, NL-97 was carried out using a combination of 1D-SDS-PAGE and LC-MSE methods. A total 1716 proteins were identified and their functional annotation revealed that a majority of them were involved in primary metabolism, protein destination, storage and energy. Three carbon assimilatory pathways appeared to operate in flax seeds. Reverse transcription quantitative PCR of selected 19 genes was carried out to understand their roles during seed development. Besides storage proteins, methionine synthase, RuBisCO and S-adenosylmethionine synthetase were highly expressed transcripts, highlighting their importance in flax seed development. Further, the identified proteins were mapped onto developmental seed specific expressed sequence tag (EST) libraries of flax to obtain transcriptional evidence and 81% of them had detectable expression at the mRNA level. This study provides new insights into the complex seed developmental processes operating in flax.
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Affiliation(s)
- Vitthal T Barvkar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
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36
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Abstract
Protein compositional data can address nutritional, packaging, origin/authenticity, processing history, safety and other quality questions. Such data has been time-consuming and expensive to generate until recently but “protein analysis on a chip” systems are now available that can analyze a complex food sample in a few minutes and do not require great protein analytical expertise. We review some of the main new approaches with examples of their application and discuss their advantages and disadvantages.
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Affiliation(s)
- Filomena Nazzaro
- Institute of Food Science, ISA-CNR, Via Roma 64, Avellino 83100, Italy; (F.F.); (A.D.L.); (R.C.)
- Author to whom correspondence should be addressed; ; Tel.:+39-0825299102; Fax: +39-0825781585
| | - Pierangelo Orlando
- Institute of Protein Biochemistry, IBP-CNR, Via P. Castellino 121, Napoli 80124, Italy;
| | - Florinda Fratianni
- Institute of Food Science, ISA-CNR, Via Roma 64, Avellino 83100, Italy; (F.F.); (A.D.L.); (R.C.)
| | - Aldo Di Luccia
- Institute of Food Science, ISA-CNR, Via Roma 64, Avellino 83100, Italy; (F.F.); (A.D.L.); (R.C.)
- Department of Food Science, University of Foggia, Via Napoli 25, Foggia 71100, Italy
| | - Raffaele Coppola
- Institute of Food Science, ISA-CNR, Via Roma 64, Avellino 83100, Italy; (F.F.); (A.D.L.); (R.C.)
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37
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Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting. J Proteomics 2012; 77:561-76. [PMID: 23043969 DOI: 10.1016/j.jprot.2012.09.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/17/2012] [Accepted: 09/22/2012] [Indexed: 11/22/2022]
Abstract
In this study, a Veterinary Department repository composed by paired formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FrFr) sets of the same tissues, routinely archived in the typical conditions of a clinical setting, was exploited to perform a comparative evaluation of the results generated by GeLC-MS/MS (1-DE followed by in-gel digestion and LC-MS/MS) and spectral counting with the two types of archival samples. Therefore, two parallel differential proteomic studies were performed using 3 canine mammary carcinomas and 3 normal controls in a paired fashion (6 FrFr and 6 FFPE in total). As a result, the FrFr and FFPE differential proteomic datasets exhibited fair consistency in differential expression trends, according to protein molecular function, cellular localization, networks, and pathways. However, FFPE samples were globally slightly less informative, especially concerning the high-MW subproteome. As a further investigation, new insights into the molecular aspects of protein fixation and retrieval were obtained. In conclusion, archival FFPE samples can be reliably used for differential proteomics studies employing a spectral counting GeLC-MS/MS approach, although some typical biases need to be taken into account, and FrFr specimens (when available) should still be considered as the gold standard for clinical proteomics.
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38
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Thiede B, Koehler CJ, Strozynski M, Treumann A, Stein R, Zimny-Arndt U, Schmid M, Jungblut PR. High resolution quantitative proteomics of HeLa cells protein species using stable isotope labeling with amino acids in cell culture(SILAC), two-dimensional gel electrophoresis(2DE) and nano-liquid chromatograpohy coupled to an LTQ-OrbitrapMass spectrometer. Mol Cell Proteomics 2012; 12:529-38. [PMID: 23033477 DOI: 10.1074/mcp.m112.019372] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein separation. Therefore, we combined stable isotope labeling with amino acids in cell culture of controls and apoptotic HeLa cells with 2-DE and the subsequent analysis of tryptic peptides via nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer to obtain quantitative data using the methods with the highest resolving power on all levels of the proteomics workflow. More than 1,200 proteins with more than 2,700 protein species were identified and quantified from 816 Coomassie Brilliant Blue G-250 stained 2-DE spots. About half of the proteins were identified and quantified only in single 2-DE spots. The majority of spots revealed one to five proteins; however, in one 2-DE spot, up to 23 proteins were identified. Only half of the 2-DE spots represented a dominant protein with more than 90% of the whole protein amount. Consequently, quantification based on staining intensities in 2-DE gels would in approximately half of the spots be imprecise, and minor components could not be quantified. These problems are circumvented by quantification using stable isotope labeling with amino acids in cell culture. Despite challenges, as shown in detail for lamin A/C and vimentin, the quantitative changes of protein species can be detected. The combination of 2-DE with high-resolution nano-liquid chromatography-mass spectrometry allowed us to identify proteomic changes in apoptotic cells that would be unobservable using any of the other previously employed proteomic workflows.
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Affiliation(s)
- Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Gaustadalleen 21, 0349 Oslo, Norway.
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39
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Yang F, Shen Y, Camp DG, Smith RD. High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev Proteomics 2012; 9:129-34. [PMID: 22462785 DOI: 10.1586/epr.12.15] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Orthogonal high-resolution separations are critical for attaining improved analytical dynamic range and protein coverage in proteomic measurements. High-pH reversed-phase liquid chromatography (RPLC), followed by fraction concatenation, affords better peptide analysis than conventional strong cation-exchange chromatography applied for 2D proteomic analysis. For example, concatenated high-pH RPLC increased identification of peptides (by 1.8-fold) and proteins (by 1.6-fold) in shotgun proteomics analyses of a digested human protein sample. Additional advantages of high-pH RPLC with fraction concatenation include improved protein sequence coverage, simplified sample processing and reduced sample losses, making this an attractive alternative to strong cation-exchange chromatography in conjunction with second-dimension low-pH RPLC for 2D proteomics analyses.
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Affiliation(s)
- Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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40
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Lößner C, Wee S, Ler SG, Li RHX, Carney T, Blackstock W, Gunaratne J. Expanding the zebrafish embryo proteome using multiple fractionation approaches and tandem mass spectrometry. Proteomics 2012; 12:1879-82. [DOI: 10.1002/pmic.201100576] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christopher Lößner
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
| | - Sheena Wee
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
| | - Siok Ghee Ler
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
| | - Rachel H. X. Li
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
| | - Tom Carney
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
| | - Walter Blackstock
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR); Singapore Singapore
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41
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Cao Z, Tang HY, Wang H, Liu Q, Speicher DW. Systematic comparison of fractionation methods for in-depth analysis of plasma proteomes. J Proteome Res 2012; 11:3090-100. [PMID: 22536952 DOI: 10.1021/pr201068b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Discovery and validation of plasma biomarkers are quite challenging because of the high complexity and wide dynamic range of the plasma proteome. Current plasma protein profiling strategies usually use major protein immunodepletion and nanoLC-MS/MS as the first and final analytical steps, respectively, but additional fractionation is needed to detect and quantify low-abundance disease biomarkers. In this study, the performances of 1-D SDS-PAGE, peptide isoelectrofocusing, and peptide high pH reverse-phase chromatography for fractionation of immunodepleted human plasma were systematically compared by evaluating protein coverage, peptide resolution, and capacity to detect known low-abundance proteins. Trade-offs between increasing the number of fractions to improve proteome coverage and resulting decreases in throughput also were assessed. High pH reverse-phase HPLC exhibited the highest peptide resolution and yielded the best depth of analysis with detection of the largest number of known low-abundance proteins for a given level of fractionation. Another advantage of using high pH reverse-phase fractionation rather than 1-D SDS gels is that all fractionation steps except for abundant protein depletion occur at the peptide level, making this strategy more compatible with quantitative biomarker validation methods such as stable isotope dilution multiple reaction monitoring.
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Affiliation(s)
- Zhijun Cao
- Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute , Philadelphia, Pennsylvania, United States
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Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K. Gel-based and gel-free quantitative proteomics approaches at a glance. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:494572. [PMID: 23213324 PMCID: PMC3508552 DOI: 10.1155/2012/494572] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/12/2012] [Indexed: 05/06/2023]
Abstract
Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.
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Affiliation(s)
- Cosette Abdallah
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
| | - Eliane Dumas-Gaudot
- UMR Agroécologie INRA 1347/Agrosup/Université de Bourgogne, Pôle Interactions Plantes Microorganismes ERL 6300 CNRS, Boite Postal 86510, 21065 Dijon Cedex, France
| | - Jenny Renaut
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Kjell Sergeant
- Environment and Agro-Biotechnologies Department, Centre de Recherche Public-Gabriel Lippmann, 41 rue du Brill, 4422 Belvaux, Luxembourg
- *Kjell Sergeant:
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43
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Prasad TSK, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LDN, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A. Proteogenomic Analysis of Candida glabrata using High Resolution Mass Spectrometry. J Proteome Res 2011; 11:247-60. [DOI: 10.1021/pr200827k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Centre
of Excellence in Bioinformatics,
Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry -605 014, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- Amrita School of Biotechnology, Amrita University, Kollam -690 525, India
| | - H. C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
| | | | - Nirujogi Raja Sekhar
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Centre
of Excellence in Bioinformatics,
Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry -605 014, India
| | - Lakshmi Dhevi N. Selvan
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam -690 525, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam -690 525, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Babylakshmi Muthusamy
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Centre
of Excellence in Bioinformatics,
Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry -605 014, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Rajiv Gandhi University of Health Sciences, Jayanagar, Bangalore −560
041, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
- Amrita School of Biotechnology, Amrita University, Kollam -690 525, India
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore
-560 066, India
| | - Premendu P. Mathur
- Centre
of Excellence in Bioinformatics,
Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry -605 014, India
| | - Raju Ravikumar
- Department of
Neuromicrobiology, National Institute of Mental Health and Neuro Sciences, Bangalore -560029, India
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Sriranganadane D, Waridel P, Salamin K, Feuermann M, Mignon B, Staib P, Neuhaus JM, Quadroni M, Monod M. Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH. Proteomics 2011; 11:4422-33. [PMID: 21919205 DOI: 10.1002/pmic.201100234] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/18/2011] [Accepted: 08/29/2011] [Indexed: 02/04/2023]
Abstract
The dermatophytes are a group of closely related fungi which are responsible for the great majority of superficial mycoses in humans and animals. Among various potential virulence factors, their secreted proteolytic activity attracts a lot of attention. Most dermatophyte-secreted proteases which have so far been isolated in vitro are neutral or alkaline enzymes. However, inspection of the recently decoded dermatophyte genomes revealed many other hypothetical secreted proteases, in particular acidic proteases similar to those characterized in Aspergillus spp. The validation of such genome predictions instigated the present study on two dermatophyte species, Microsporum canis and Arthroderma benhamiae. Both fungi were found to grow well in a protein medium at acidic pH, accompanied by extracellular proteolysis. Shotgun MS analysis of secreted protein revealed fundamentally different protease profiles during fungal growth in acidic versus neutral pH conditions. Most notably, novel dermatophyte-secreted proteases were identified at acidic pH such as pepsins, sedolisins and acidic carboxypeptidases. Therefore, our results not only support genome predictions, but demonstrate for the first time the secretion of acidic proteases by dermatophytes. Our findings also suggest the existence of different pathways of protein degradation into amino acids and short peptides in these highly specialized pathogenic fungi.
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Affiliation(s)
- Dev Sriranganadane
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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45
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Makawita S, Smith C, Batruch I, Zheng Y, Rückert F, Grützmann R, Pilarsky C, Gallinger S, Diamandis EP. Integrated proteomic profiling of cell line conditioned media and pancreatic juice for the identification of pancreatic cancer biomarkers. Mol Cell Proteomics 2011; 10:M111.008599. [PMID: 21653254 PMCID: PMC3205865 DOI: 10.1074/mcp.m111.008599] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 05/19/2011] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer is one of the leading causes of cancer-related deaths, for which serological biomarkers are urgently needed. Most discovery-phase studies focus on the use of one biological source for analysis. The present study details the combined mining of pancreatic cancer-related cell line conditioned media and pancreatic juice for identification of putative diagnostic leads. Using strong cation exchange chromatography, followed by LC-MS/MS on an LTQ-Orbitrap mass spectrometer, we extensively characterized the proteomes of conditioned media from six pancreatic cancer cell lines (BxPc3, MIA-PaCa2, PANC1, CAPAN1, CFPAC1, and SU.86.86), the normal human pancreatic ductal epithelial cell line HPDE, and two pools of six pancreatic juice samples from ductal adenocarcinoma patients. All samples were analyzed in triplicate. Between 1261 and 2171 proteins were identified with two or more peptides in each of the cell lines, and an average of 521 proteins were identified in the pancreatic juice pools. In total, 3479 nonredundant proteins were identified with high confidence, of which ∼ 40% were extracellular or cell membrane-bound based on Genome Ontology classifications. Three strategies were employed for identification of candidate biomarkers: (1) examination of differential protein expression between the cancer and normal cell lines using label-free protein quantification, (2) integrative analysis, focusing on the overlap of proteins among the multiple biological fluids, and (3) tissue specificity analysis through mining of publically available databases. Preliminary verification of anterior gradient homolog 2, syncollin, olfactomedin-4, polymeric immunoglobulin receptor, and collagen alpha-1(VI) chain in plasma samples from pancreatic cancer patients and healthy controls using ELISA, showed a significant increase (p < 0.01) of these proteins in plasma from pancreatic cancer patients. The combination of these five proteins showed an improved area under the receiver operating characteristic curve to CA19.9 alone. Further validation of these proteins is warranted, as is the investigation of the remaining group of candidates.
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Affiliation(s)
- Shalini Makawita
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- §Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Chris Smith
- §Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Ihor Batruch
- ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Yingye Zheng
- ‖The Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Felix Rückert
- **Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Technical University of Dresden, Germany
| | - Robert Grützmann
- **Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Technical University of Dresden, Germany
| | - Christian Pilarsky
- **Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Technical University of Dresden, Germany
| | - Steven Gallinger
- ‡‡Zane Cohen Familial Gastrointestinal Cancer Registry and Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Eleftherios P. Diamandis
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- §Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
- ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
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Zhou F, Sikorski TW, Ficarro SB, Webber JT, Marto JA. Online nanoflow reversed phase-strong anion exchange-reversed phase liquid chromatography-tandem mass spectrometry platform for efficient and in-depth proteome sequence analysis of complex organisms. Anal Chem 2011; 83:6996-7005. [PMID: 21851055 PMCID: PMC3196608 DOI: 10.1021/ac200639v] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The dynamic range of protein expression in complex organisms coupled with the stochastic nature of discovery-driven tandem mass spectrometry (MS/MS) analysis continues to impede comprehensive sequence analysis and often provides only limited information for low-abundance proteins. High-performance fractionation of proteins or peptides prior to mass spectrometry analysis can mitigate these effects, though achieving an optimal combination of automation, reproducibility, separation peak capacity, and sample yield remains a significant challenge. Here we demonstrate an automated nanoflow 3-D liquid chromatography (LC)-MS/MS platform based on high-pH reversed phase (RP), strong anion exchange (SAX), and low-pH reversed phase (RP) separation stages for analysis of complex proteomes. We observed that RP-SAX-RP outperformed RP-RP for analysis of tryptic peptides derived from Escherichia coli and enabled identification of proteins present at a level of 50 copies per cell in Saccharomyces cerevisiae, corresponding to an estimated detection limit of 500 amol, from 40 μg of total lysate on a low-resolution 3-D ion trap mass spectrometer. A similar study performed on a LTQ-Orbitrap yielded over 4000 unique proteins from 5 μg of total yeast lysate analyzed in a single, 101 fraction RP-SAX-RP LC-MS/MS acquisition, providing an estimated detection limit of 65 amol for proteins expressed at 50 copies per cell.
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Affiliation(s)
- Feng Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
| | - Timothy W. Sikorski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
| | - Scott B. Ficarro
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115-6084
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
| | - James T. Webber
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115-6084
| | - Jarrod A. Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115-6084
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115-6084
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47
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Hughes CS, Radan L, Betts D, Postovit LM, Lajoie GA. Proteomic analysis of extracellular matrices used in stem cell culture. Proteomics 2011; 11:3983-91. [PMID: 21834137 DOI: 10.1002/pmic.201100030] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/26/2011] [Accepted: 06/08/2011] [Indexed: 01/02/2023]
Abstract
Numerous matrices for the growth of human embryonic stem cells (hESC) in vitro have been described. However, their exact composition is typically unknown. Information on the components of these matrices will aid in the development of a fully defined growth surface for hESCs. These matrices typically consist of mixture of proteins present in a wide range of abundance making their characterization challenging. In this study, we performed the proteomic analysis of five previously uncharacterized matrices: CellStart, Human Basement Membrane Extract (Human BME), StemXVivo, Bridge Human Extracellular Matrix (BridgeECM), and mouse embryonic fibroblast conditioned matrix (MEF-CMTX). Based on a proteomics protocol optimized using lysates from HeLa cells, we undertook the analysis of the five complex extracellular matrix (ECM) samples using a combination of strong anion and cation exchange chromatography and SDS-PAGE. For each of these matrices, we identify numerous proteins, indicating their complex nature. We also compared these results with a similar proteomics analysis of the growth matrix, Matrigel™. From these analyses, we observed that fibronectin is a primary component of nearly all hESC supportive matrices. This observation led to the investigation of the suitability of fibronectin as a defined ECM for the growth of hESCs. We found that fibronectin promotes the maintenance of pluripotent H9 and CA1 hESCs in an undifferentiated state using mTeSR1 medium. This finding validates the utility of characterizing matrices used for hESC growth in revealing ECM components required for culturing hESCs in a universally applicable defined system.
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Affiliation(s)
- Chris S Hughes
- Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
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48
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Xiang Y, Remily-Wood ER, Oliveira V, Yarde D, He L, Cheng JQ, Mathews L, Boucher K, Cubitt C, Perez L, Gauthier TJ, Eschrich SA, Shain KH, Dalton WS, Hazlehurst L, Koomen JM. Monitoring a nuclear factor-κB signature of drug resistance in multiple myeloma. Mol Cell Proteomics 2011; 10:M110.005520. [PMID: 21846842 DOI: 10.1074/mcp.m110.005520] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The emergence of acquired drug resistance results from multiple compensatory mechanisms acting to prevent cell death. Simultaneous monitoring of proteins involved in drug resistance is a major challenge for both elucidation of the underlying biology and development of candidate biomarkers for assessment of personalized cancer therapy. Here, we have utilized an integrated analytical platform based on SDS-PAGE protein fractionation prior to liquid chromatography coupled to multiple reaction monitoring mass spectrometry, a versatile and powerful tool for targeted quantification of proteins in complex matrices, to evaluate a well-characterized model system of melphalan resistance in multiple myeloma (MM). Quantitative assays were developed to measure protein expression related to signaling events and biological processes relevant to melphalan resistance in multiple myeloma, specifically: nuclear factor-κB subunits, members of the Bcl-2 family of apoptosis-regulating proteins, and Fanconi Anemia DNA repair components. SDS-PAGE protein fractionation prior to liquid chromatography coupled to multiple reaction monitoring methods were developed for quantification of these selected target proteins in amounts of material compatible with direct translation to clinical specimens (i.e. less than 50,000 cells). As proof of principle, both relative and absolute quantification were performed on cell line models of MM to compare protein expression before and after drug treatment in naïve cells and in drug resistant cells; these liquid chromatography-multiple reaction monitoring results are compared with existing literature and Western blots. The initial stage of a systems biology platform for examining drug resistance in MM has been implemented in cell line models and has been translated to MM cells isolated from a patient. The ultimate application of this platform could assist in clinical decision-making for individualized patient treatment. Although these specific assays have been developed to monitor MM, these techniques are expected to have broad applicability in cancer and other types of disease.
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Affiliation(s)
- Yun Xiang
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute University of South Florida, Tampa, FL 33612, USA
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49
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Savijoki K, Lietzén N, Kankainen M, Alatossava T, Koskenniemi K, Varmanen P, Nyman TA. Comparative Proteome Cataloging of Lactobacillus rhamnosus Strains GG and Lc705. J Proteome Res 2011; 10:3460-73. [DOI: 10.1021/pr2000896] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kirsi Savijoki
- Institute of Biotechnology, University of Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Niina Lietzén
- Institute of Biotechnology, University of Helsinki, Finland
| | | | - Tapani Alatossava
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | | | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, Finland
| | - Tuula A. Nyman
- Institute of Biotechnology, University of Helsinki, Finland
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50
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Remily-Wood ER, Liu RZ, Xiang Y, Chen Y, Thomas CE, Rajyaguru N, Kaufman LM, Ochoa JE, Hazlehurst L, Pinilla-Ibarz J, Lancet J, Zhang G, Haura E, Shibata D, Yeatman T, Smalley KSM, Dalton WS, Huang E, Scott E, Bloom GC, Eschrich SA, Koomen JM. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin Appl 2011; 5:383-96. [PMID: 21656910 DOI: 10.1002/prca.201000115] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/28/2011] [Accepted: 02/27/2011] [Indexed: 12/15/2022]
Abstract
PURPOSE The Quantitative Assay Database (QuAD), http://proteome.moffitt.org/QUAD/, facilitates widespread implementation of quantitative mass spectrometry in cancer biology and clinical research through sharing of methods and reagents for monitoring protein expression and modification. EXPERIMENTAL DESIGN Liquid chromatography coupled to multiple reaction monitoring (LC-MRM) mass spectrometry assays are developed using SDS-PAGE fractionated lysates from cancer cell lines. Pathway maps created using GeneGO Metacore provide the biological relationships between proteins and illustrate concepts for multiplexed analysis; each protein can be selected to examine assay development at the protein and peptide levels. RESULTS The coupling of SDS-PAGE and multiple reaction monitoring mass spectrometry screening has been used to detect 876 peptides from 218 cancer-related proteins in model systems including colon, lung, melanoma, leukemias, and myeloma, which has led to the development of 95 quantitative assays including stable-isotope-labeled peptide standards. Methods are published online and peptide standards are made available to the research community. Protein expression measurements for heat shock proteins, including a comparison with ELISA and monitoring response to the HSP90 inhibitor, 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin (17-DMAG), are used to illustrate the components of the QuAD and its potential utility. CONCLUSIONS AND CLINICAL RELEVANCE This resource enables quantitative assessment of protein components of signaling pathways and biological processes and holds promise for systematic investigation of treatment responses in cancer.
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