1
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
2
|
Nickerson JL, Gagnon H, Wentzell PD, Doucette AA. Assessing the precision of a detergent-assisted cartridge precipitation workflow for non-targeted quantitative proteomics. Proteomics 2024; 24:e2300339. [PMID: 38299459 DOI: 10.1002/pmic.202300339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024]
Abstract
Detergent-based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent-based workflow for quantitative proteomics, we herein evaluate the precision of a bottom-up sample preparation strategy incorporating cartridge-based protein precipitation with organic solvent to deplete SDS. The variance of data-independent acquisition (SWATH-MS) data was isolated from sample preparation error by modelling the variance as a function of peptide signal intensity. Our SDS-assisted cartridge workflow yield a coefficient of variance (CV) of 13%-14%. By comparison, conventional (detergent-free) in-solution digestion increased the CV to 50%; in-gel digestion provided lower CVs between 14% and 20%. By filtering peptides predicting to display lower precision, we further enhance the validity of data in global comparative proteomics. These results demonstrate the detergent-based precipitation workflow is a reliable approach for in depth, label-free quantitative proteome analysis.
Collapse
Affiliation(s)
| | - Hugo Gagnon
- PhenoSwitch Bioscience Inc., Sherbrooke, Quebec, Canada
| | - Peter D Wentzell
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
3
|
Lopez-Pedrera C, Oteros R, Ibáñez-Costa A, Luque-Tévar M, Muñoz-Barrera L, Barbarroja N, Chicano-Gálvez E, Marta-Enguita J, Orbe J, Velasco F, Perez-Sanchez C. The thrombus proteome in stroke reveals a key role of the innate immune system and new insights associated with its etiology, severity, and prognosis. J Thromb Haemost 2023; 21:2894-2907. [PMID: 37100394 DOI: 10.1016/j.jtha.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Nowadays little is known about the molecular profile of the occluding thrombus of patients with ischemic stroke. OBJECTIVES To analyze the proteomic profile of thrombi in patients who experienced an ischemic stroke in order to gain insights into disease pathogenesis. METHODS Thrombi from an exploratory cohort of patients who experienced a stroke were obtained by thrombectomy and analyzed by sequential window acquisition of all theoretical spectra-mass spectrometry. Unsupervised k-means clustering analysis was performed to stratify patients who experienced a stroke. The proteomic profile was associated with both the neurological function (National Institute of Health Stroke Scale [NIHSS]) and the cerebral involvement (Alberta Stroke Program Early CT Score [ASPECTS]) prior to thrombectomy and the clinical status of patients at 3 months using the modified Rankin Scale. In an independent cohort of 210 patients who experienced a stroke, the potential role of neutrophils in stroke severity was interrogated. RESULTS Proteomic analysis identified 580 proteins in thrombi, which were stratified into 4 groups: hemostasis, proteasome and neurological diseases, structural proteins, and innate immune system and neutrophils. The thrombus proteome identified 3 clusters of patients with distinctive severity, prognosis, and etiology of the stroke. A protein signature clearly distinguished atherothrombotic and cardioembolic strokes. Several proteins were significantly correlated with the severity of the stroke (NIHSS and ASPECTS). Functional proteomic analysis highlighted the prominent role of neutrophils in stroke severity. This was in line with the association of neutrophil activation markers and count with NIHSS, ASPECTS, and the modified Rankin Scale score 90 days after the event. CONCLUSION The use of sequential window acquisition of all theoretical spectra-mass spectrometry in thrombi from patients who experienced an ischemic stroke has provided new insights into pathways and players involved in its etiology, severity, and prognosis. The prominent role of the innate immune system identified might pave the way for the development of new biomarkers and therapeutic approaches in this disease.
Collapse
Affiliation(s)
- Chary Lopez-Pedrera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain.
| | - Rafael Oteros
- Diagnostic and Therapeutic Neuroradiology Unit, Reina Sofia Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Rheumatology Service, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain; Department of Cell Biology, Immunology and Physiology, Agrifood Campus of International Excellence, University of Córdoba, ceiA3, Córdoba, Spain
| | - María Luque-Tévar
- Rheumatology Service, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Laura Muñoz-Barrera
- Rheumatology Service, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Nuria Barbarroja
- Rheumatology Service, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain; Cobiomic Bioscience SL, EBT University of Córdoba/IMIBIC, Córdoba, Spain
| | - Eduardo Chicano-Gálvez
- IMIBIC Mass Spectrometry and Molecular Imaging Unit, Maimonides Biomedical Research Institute of Córdoba, Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain
| | - Juan Marta-Enguita
- Atherothrombosis-Laboratory, Cardiovascular Diseases Program, CIMA-Universidad Navarra, IdiSNA, Pamplona, Spain; Neurology Department, Hospital Universitario Navarra, Pamplona, Spain; RICORS-ICTUS, Instituto Salud Carlos III, Madrid, Spain
| | - Josune Orbe
- Atherothrombosis-Laboratory, Cardiovascular Diseases Program, CIMA-Universidad Navarra, IdiSNA, Pamplona, Spain; RICORS-ICTUS, Instituto Salud Carlos III, Madrid, Spain
| | - Francisco Velasco
- Department of Medicine, University of Córdoba, Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
| | - Carlos Perez-Sanchez
- Rheumatology Service, Maimonides Institute of Biomedical Research of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, Córdoba, Spain; Department of Cell Biology, Immunology and Physiology, Agrifood Campus of International Excellence, University of Córdoba, ceiA3, Córdoba, Spain; Cobiomic Bioscience SL, EBT University of Córdoba/IMIBIC, Córdoba, Spain. https://twitter.com/carlosps85
| |
Collapse
|
4
|
Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi. Curr Issues Mol Biol 2022; 44:2069-2088. [PMID: 35678669 PMCID: PMC9164042 DOI: 10.3390/cimb44050140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022] Open
Abstract
An important step in the proteomic analysis of missing proteins is the use of a wide range of tissues, optimal extraction, and the processing of protein material in order to ensure the highest sensitivity in downstream protein detection. This work describes a purification protocol for identifying low-abundance proteins in human chorionic villi using the proposed “1DE-gel concentration” method. This involves the removal of SDS in a short electrophoresis run in a stacking gel without protein separation. Following the in-gel digestion of the obtained holistic single protein band, we used the peptide mixture for further LC–MS/MS analysis. Statistically significant results were derived from six datasets, containing three treatments, each from two tissue sources (elective or missed abortions). The 1DE-gel concentration increased the coverage of the chorionic villus proteome. Our approach allowed the identification of 15 low-abundance proteins, of which some had not been previously detected via the mass spectrometry of trophoblasts. In the post hoc data analysis, we found a dubious or uncertain protein (PSG7) encoded on human chromosome 19 according to neXtProt. A proteomic sample preparation workflow with the 1DE-gel concentration can be used as a prospective tool for uncovering the low-abundance part of the human proteome.
Collapse
|
5
|
Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens. Clin Proteomics 2022; 19:10. [PMID: 35501693 PMCID: PMC9063121 DOI: 10.1186/s12014-022-09346-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
Objectives Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins. Methods Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS). Results Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09346-0.
Collapse
|
6
|
Vowinckel J, Hartl J, Marx H, Kerick M, Runggatscher K, Keller MA, Mülleder M, Day J, Weber M, Rinnerthaler M, Yu JSL, Aulakh SK, Lehmann A, Mattanovich D, Timmermann B, Zhang N, Dunn CD, MacRae JI, Breitenbach M, Ralser M. The metabolic growth limitations of petite cells lacking the mitochondrial genome. Nat Metab 2021; 3:1521-1535. [PMID: 34799698 PMCID: PMC7612105 DOI: 10.1038/s42255-021-00477-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022]
Abstract
Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.
Collapse
Affiliation(s)
- Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Biognosys AG, Schlieren, Switzerland
| | - Johannes Hartl
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Hans Marx
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Martin Kerick
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Parasitology and Biomedicine 'López-Neyra' (IPBLN, CSIC), Granada, Spain
| | - Kathrin Runggatscher
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Manuela Weber
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Simran Kaur Aulakh
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Andrea Lehmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics and Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Nianshu Zhang
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Molecular Biology and Genetics, Koç University, İstanbul, Turkey
| | - James I MacRae
- Metabolomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Biochemistry, Berlin, Germany.
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
| |
Collapse
|
7
|
Xin JW, Chai ZX, Zhang CF, Zhang Q, Zhu Y, Cao HW, YangJi C, Chen XY, Jiang H, Zhong JC, Ji QM. Differences in proteomic profiles between yak and three cattle strains provide insights into molecular mechanisms underlying high-altitude adaptation. J Anim Physiol Anim Nutr (Berl) 2021; 106:485-493. [PMID: 34494310 DOI: 10.1111/jpn.13629] [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: 12/03/2020] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 01/22/2023]
Abstract
Yaks display unique properties of the lung and heart, enabling their adaptation to high-altitude environments, but the underlying molecular mechanisms are still largely unknown. In the present study, the proteome differences in lung and heart tissues were compared between yak (Bos grunniens) and three cattle strains (Bos taurus, Holstein, Sanjiang and Tibetan cattle) using the sequential window acquisition of all theoretical mass spectra/data-independent acquisition (SWATH/DIA) proteomic method. In total, 51,755 peptides and 7215 proteins were identified. In the lung tissue, there were 162, 310 and 118 differential abundance proteins (DAPs) in Tibetan, Holstein and Sanjiang cattle compared to yak respectively. In the heart tissue, there were 71, 57 and 78 DAPs in Tibetan, Holstein and Sanjiang cattle compared to yak respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the DAPs were enriched for the retinol metabolism and toll-like receptor categories in lung tissue. The changes in these two pathways may regulate hypoxia-induced factor and immune function in yaks. Moreover, DAPs in heart tissues were enriched for cardiac muscle contraction, Huntington's disease, chemical carcinogenesis and drug metabolism-cytochrome P450. Further exploration indicated that yaks may alter cardiac function through regulation of type 2 ryanodine receptor (RyR2) and Ca2+ -release channels. The present results are useful to further develop an understanding of the mechanisms underlying adaptation of animals to high-altitude conditions.
Collapse
Affiliation(s)
- Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhi-Xin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Cidan YangJi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Xiao-Ying Chen
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Hui Jiang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Jin-Cheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiu-Mei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China.,Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| |
Collapse
|
8
|
Messner CB, Demichev V, Bloomfield N, Yu JSL, White M, Kreidl M, Egger AS, Freiwald A, Ivosev G, Wasim F, Zelezniak A, Jürgens L, Suttorp N, Sander LE, Kurth F, Lilley KS, Mülleder M, Tate S, Ralser M. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol 2021; 39:846-854. [PMID: 33767396 PMCID: PMC7611254 DOI: 10.1038/s41587-021-00860-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.
Collapse
Affiliation(s)
- Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Jason S L Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Matthew White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Marco Kreidl
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Linda Jürgens
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| |
Collapse
|
9
|
Root L, Campo A, MacNiven L, Con P, Cnaani A, Kültz D. A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus. Mol Ecol Resour 2021; 21:2486-2503. [PMID: 34101993 DOI: 10.1111/1755-0998.13445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/30/2021] [Accepted: 06/01/2021] [Indexed: 12/31/2022]
Abstract
Interactions of organisms with their environment are complex and environmental regulation at different levels of biological organization is often nonlinear. Therefore, the genotype to phenotype continuum requires study at multiple levels of organization. While studies of transcriptome regulation are now common for many species, quantitative studies of environmental effects on proteomes are needed. Here we report the generation of a data-independent acquisition (DIA) assay library that enables simultaneous targeted proteomics of thousands of Oreochromis niloticus kidney proteins using a label- and gel-free workflow that is well suited for ecologically relevant field samples. We demonstrate the usefulness of this DIA assay library by discerning environmental effects on the kidney proteome of O. niloticus. Moreover, we demonstrate that the DIA assay library approach generates data that are complimentary rather than redundant to transcriptomic data. Transcript and protein abundance differences in kidneys of tilapia acclimated to freshwater and brackish water (25 g/kg) were correlated for 2114 unique genes. A high degree of non-linearity in salinity-dependent regulation of transcriptomes and proteomes was revealed suggesting that the regulation of O. niloticus renal function by environmental salinity relies heavily on post-transcriptional mechanisms. The application of functional enrichment analyses using STRING and KEGG to DIA assay data sets is demonstrated by identifying myo-inositol metabolism, antioxidant and xenobiotic functions, and signalling mechanisms as key elements controlled by salinity in tilapia kidneys. The DIA assay library resource presented here can be adopted for other tissues and other organisms to study proteome dynamics during changing ecological contexts.
Collapse
Affiliation(s)
- Larken Root
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| | - Aurora Campo
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Leah MacNiven
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| | - Pazit Con
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California Davis, Davis, CA, USA
| |
Collapse
|
10
|
León-Vaz A, Romero LC, Gotor C, León R, Vigara J. Effect of cadmium in the microalga Chlorella sorokiniana: A proteomic study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111301. [PMID: 32949933 DOI: 10.1016/j.ecoenv.2020.111301] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Cadmium is one of the most common heavy metals in contaminated aquatic environments and one of the most toxic contaminants for phytoplankton. Nevertheless, there are not enough studies focused on the effect of this metal in algae. Through a proteomic approach, this work shows how Cd can alter the growth, cell morphology and metabolism of the microalga Chlorella sorokiniana. Using the sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS), we concluded that exposure of Chlorella sorokiniana to 250 μM Cd2+ for 40 h caused downregulation of different metabolic pathways, such as photosynthesis, oxidative phosphorylation, glycolysis, TCA cycle and ribosomal proteins biosynthesis. However, photorespiration, antioxidant enzymes, gluconeogenesis, starch catabolism, and biosynthesis of glutamate, cysteine, glycine and serine were upregulated, under the same conditions. Finally, exposure to Cd also led to changes in the metabolism of carotenoids and lipids. In addition, the high tolerance of Chlorella sorokiniana to Cd points to this microalga as a potential microorganism to be used in bioremediation processes.
Collapse
Affiliation(s)
- Antonio León-Vaz
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 210071, Huelva, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Seville. Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Seville. Spain
| | - Rosa León
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 210071, Huelva, Spain
| | - Javier Vigara
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 210071, Huelva, Spain.
| |
Collapse
|
11
|
León-Vaz A, Romero LC, Gotor C, León R, Vigara J. Dataset for proteomic analysis of Chlorella sorokiniana cells under cadmium stress. Data Brief 2020; 33:106544. [PMID: 33294530 PMCID: PMC7695938 DOI: 10.1016/j.dib.2020.106544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/03/2022] Open
Abstract
Cadmium is one of the most hazardous heavy metal for aquatic environments and one of the most toxic contaminants for phytoplankton. This work provides the dataset associated with the research publication “Effect of cadmium in the microalga Chlorella sorokiniana: a proteomic study” [1]. This dataset describes a proteomic approach, based on the sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS), derived from exposure of Chlorella sorokiniana to 250 µM Cd2+ for 40 h, showing the proteins that are up- or downregulated. The processing of data included the identification of the Chlamydomonas reinhardtii protein sequences equivalent to the corresponding of Chlorella sorokiniana sequences obtained, which made possible to use KEGG Database. MS and MS/MS information, and quantitative data were deposited PRIDE public repository under accession number PXD015932.
Collapse
Affiliation(s)
- Antonio León-Vaz
- Laboratory of Biochemistry. Faculty of Experimental Sciences. Marine International Campus of Excellence and REMSMA. University of Huelva, 210071 Huelva, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis. Consejo Superior de Investigaciones Científicas and Universidad de Sevilla. Avenida Américo Vespucio, 49. 41092 Seville. Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis. Consejo Superior de Investigaciones Científicas and Universidad de Sevilla. Avenida Américo Vespucio, 49. 41092 Seville. Spain
| | - Rosa León
- Laboratory of Biochemistry. Faculty of Experimental Sciences. Marine International Campus of Excellence and REMSMA. University of Huelva, 210071 Huelva, Spain
| | - Javier Vigara
- Laboratory of Biochemistry. Faculty of Experimental Sciences. Marine International Campus of Excellence and REMSMA. University of Huelva, 210071 Huelva, Spain
| |
Collapse
|
12
|
Suchacki KJ, Morton NM, Vary C, Huesa C, Yadav MC, Thomas BJ, Turban S, Bunger L, Ball D, Barrios-Llerena ME, Guntur AR, Khavandgar Z, Cawthorn WP, Ferron M, Karsenty G, Murshed M, Rosen CJ, MacRae VE, Millán JL, Farquharson C. PHOSPHO1 is a skeletal regulator of insulin resistance and obesity. BMC Biol 2020; 18:149. [PMID: 33092598 PMCID: PMC7584094 DOI: 10.1186/s12915-020-00880-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/25/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The classical functions of the skeleton encompass locomotion, protection and mineral homeostasis. However, cell-specific gene deletions in the mouse and human genetic studies have identified the skeleton as a key endocrine regulator of metabolism. The bone-specific phosphatase, Phosphatase, Orphan 1 (PHOSPHO1), which is indispensable for bone mineralisation, has been recently implicated in the regulation of energy metabolism in humans, but its role in systemic metabolism remains unclear. Here, we probe the mechanism underlying metabolic regulation by analysing Phospho1 mutant mice. RESULTS Phospho1-/- mice exhibited improved basal glucose homeostasis and resisted high-fat-diet-induced weight gain and diabetes. The metabolic protection in Phospho1-/- mice was manifested in the absence of altered levels of osteocalcin. Osteoblasts isolated from Phospho1-/- mice were enriched for genes associated with energy metabolism and diabetes; Phospho1 both directly and indirectly interacted with genes associated with glucose transport and insulin receptor signalling. Canonical thermogenesis via brown adipose tissue did not underlie the metabolic protection observed in adult Phospho1-/- mice. However, the decreased serum choline levels in Phospho1-/- mice were normalised by feeding a 2% choline rich diet resulting in a normalisation in insulin sensitivity and fat mass. CONCLUSION We show that mice lacking the bone mineralisation enzyme PHOSPHO1 exhibit improved basal glucose homeostasis and resist high-fat-diet-induced weight gain and diabetes. This study identifies PHOSPHO1 as a potential bone-derived therapeutic target for the treatment of obesity and diabetes.
Collapse
Affiliation(s)
- Karla J Suchacki
- Roslin Institute, R(D)SVS, University of Edinburgh, Edinburgh, Scotland, UK. .,Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK.
| | - Nicholas M Morton
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Calvin Vary
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Carmen Huesa
- Roslin Institute, R(D)SVS, University of Edinburgh, Edinburgh, Scotland, UK.,MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, Scotland, UK
| | - Manisha C Yadav
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Benjamin J Thomas
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Sophie Turban
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Lutz Bunger
- Scottish Rural College, Edinburgh, Scotland, UK
| | - Derek Ball
- Medical Sciences and Nutrition, School of Medicine, University of Aberdeen, Aberdeen, Scotland, UK
| | | | - Anyonya R Guntur
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Zohreh Khavandgar
- Department of Medicine and Faculty of Dentistry, McGill University, Montreal, Canada
| | - William P Cawthorn
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Mathieu Ferron
- Molecular Physiology Research Unit, Institut de recherches cliniques de Montréal, Montreal, Canada
| | - Gérard Karsenty
- Department of Genetics and Development, Columbia University Medical Center, New York, USA
| | - Monzur Murshed
- Department of Medicine and Faculty of Dentistry, McGill University, Montreal, Canada
| | - Clifford J Rosen
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Vicky E MacRae
- Roslin Institute, R(D)SVS, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jose Luis Millán
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA
| | - Colin Farquharson
- Roslin Institute, R(D)SVS, University of Edinburgh, Edinburgh, Scotland, UK
| |
Collapse
|
13
|
Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
Collapse
Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| |
Collapse
|
14
|
Bouchal P, Schubert OT, Faktor J, Capkova L, Imrichova H, Zoufalova K, Paralova V, Hrstka R, Liu Y, Ebhardt HA, Budinska E, Nenutil R, Aebersold R. Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Rep 2020; 28:832-843.e7. [PMID: 31315058 PMCID: PMC6656695 DOI: 10.1016/j.celrep.2019.06.046] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 03/06/2019] [Accepted: 06/12/2019] [Indexed: 01/10/2023] Open
Abstract
Accurate classification of breast tumors is vital for patient management decisions and enables more precise cancer treatment. Here, we present a quantitative proteotyping approach based on sequential windowed acquisition of all theoretical fragment ion spectra (SWATH) mass spectrometry and establish key proteins for breast tumor classification. The study is based on 96 tissue samples representing five conventional breast cancer subtypes. SWATH proteotype patterns largely recapitulate these subtypes; however, they also reveal varying heterogeneity within the conventional subtypes, with triple negative tumors being the most heterogeneous. Proteins that contribute most strongly to the proteotype-based classification include INPP4B, CDK1, and ERBB2 and are associated with estrogen receptor (ER) status, tumor grade status, and HER2 status. Although these three key proteins exhibit high levels of correlation with transcript levels (R > 0.67), general correlation did not exceed R = 0.29, indicating the value of protein-level measurements of disease-regulated genes. Overall, this study highlights how cancer tissue proteotyping can lead to more accurate patient stratification. Proteotyping of 96 breast tumors by SWATH mass spectrometry Three key proteins for breast tumor classification Varying degrees of heterogeneity within conventional breast cancer subtypes Generally modest correlation between protein and transcript levels in tumor tissue
Collapse
Affiliation(s)
- Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology, Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jakub Faktor
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Lenka Capkova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Imrichova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic; Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Karolina Zoufalova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Vendula Paralova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Roman Hrstka
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Yansheng Liu
- Department of Pharmacology, Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, USA
| | - Holger Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland; Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Eva Budinska
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic; Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Rudolf Nenutil
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
15
|
iPS-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient In Vitro Cell Migration Stimulation. Cells 2020; 9:cells9081803. [PMID: 32751289 PMCID: PMC7463559 DOI: 10.3390/cells9081803] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
The most challenging aspect of secondary progressive multiple sclerosis (SPMS) is the lack of efficient regenerative response for remyelination, which is carried out by the endogenous population of adult oligoprogenitor cells (OPCs) after proper activation. OPCs must proliferate and migrate to the lesion and then differentiate into mature oligodendrocytes. To investigate the OPC cellular component in SPMS, we developed induced pluripotent stem cells (iPSCs) from SPMS-affected donors and age-matched controls (CT). We confirmed their efficient and similar OPC differentiation capacity, although we reported SPMS-OPCs were transcriptionally distinguishable from their CT counterparts. Analysis of OPC-generated conditioned media (CM) also evinced differences in protein secretion. We further confirmed SPMS-OPC CM presented a deficient capacity to stimulate OPC in vitro migration that can be compensated by exogenous addition of specific components. Our results provide an SPMS-OPC cellular model and encouraging venues to study potential cell communication deficiencies in the progressive form of multiple sclerosis (MS) for future treatment strategies.
Collapse
|
16
|
Barkovits K, Pacharra S, Pfeiffer K, Steinbach S, Eisenacher M, Marcus K, Uszkoreit J. Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition. Mol Cell Proteomics 2020; 19:181-197. [PMID: 31699904 PMCID: PMC6944235 DOI: 10.1074/mcp.ra119.001714] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/17/2019] [Indexed: 12/14/2022] Open
Abstract
Currently data-dependent acquisition (DDA) is the method of choice for mass spectrometry-based proteomics discovery experiments, but data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirements to perform a DIA analysis is the availability of suitable spectral libraries for peptide identification and quantification. Several studies were performed addressing the evaluation of spectral library performance for protein identification in DIA measurements. But so far only few experiments estimate the effect of these libraries on the quantitative level.In this work we created a gold standard spike-in sample set with known contents and ratios of proteins in a complex protein matrix that allowed a detailed comparison of DIA quantification data obtained with different spectral library approaches. We used in-house generated sample-specific spectral libraries created using varying sample preparation approaches and repeated DDA measurement. In addition, two different search engines were tested for protein identification from DDA data and subsequent library generation. In total, eight different spectral libraries were generated, and the quantification results compared with a library free method, as well as a default DDA analysis. Not only the number of identifications on peptide and protein level in the spectral libraries and the corresponding DIA analysis results was inspected, but also the number of expected and identified differentially abundant protein groups and their ratios.We found, that while libraries of prefractionated samples were generally larger, there was no significant increase in DIA identifications compared with repetitive non-fractionated measurements. Furthermore, we show that the accuracy of the quantification is strongly dependent on the applied spectral library and whether the quantification is based on peptide or protein level. Overall, the reproducibility and accuracy of DIA quantification is superior to DDA in all applied approaches.Data has been deposited to the ProteomeXchange repository with identifiers PXD012986, PXD012987, PXD012988 and PXD014956.
Collapse
Affiliation(s)
- Katalin Barkovits
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
| | - Sandra Pacharra
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
| | - Kathy Pfeiffer
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
| | - Simone Steinbach
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
| | - Martin Eisenacher
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany
| | - Katrin Marcus
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany.
| | - Julian Uszkoreit
- Ruhr University Bochum, Faculty of Medicine, Medizinisches Proteom-Center, Bochum, Germany.
| |
Collapse
|
17
|
López-Sánchez LM, Jiménez-Izquierdo R, Peñarando J, Mena R, Guil-Luna S, Toledano M, Conde F, Villar C, Díaz C, Ortea I, De la Haba-Rodríguez JR, Aranda E, Rodríguez-Ariza A. SWATH-based proteomics reveals processes associated with immune evasion and metastasis in poor prognosis colorectal tumours. J Cell Mol Med 2019; 23:8219-8232. [PMID: 31560832 PMCID: PMC6850959 DOI: 10.1111/jcmm.14693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/25/2019] [Accepted: 08/25/2019] [Indexed: 01/02/2023] Open
Abstract
Newly emerged proteomic methodologies, particularly data‐independent acquisition (DIA) analysis–related approaches, would improve current gene expression–based classifications of colorectal cancer (CRC). Therefore, this study was aimed to identify protein expression signatures using SWATH‐MS DIA and targeted data extraction, to aid in the classification of molecular subtypes of CRC and advance in the diagnosis and development of new drugs. For this purpose, 40 human CRC samples and 7 samples of healthy tissue were subjected to proteomic and bioinformatic analysis. The proteomic analysis identified three different molecular CRC subtypes: P1, P2 and P3. Significantly, P3 subtype showed high agreement with the mesenchymal/stem‐like subtype defined by gene expression signatures and characterized by poor prognosis and survival. The P3 subtype was characterized by decreased expression of ribosomal proteins, the spliceosome, and histone deacetylase 2, as well as increased expression of osteopontin, SERPINA 1 and SERPINA 3, and proteins involved in wound healing, acute inflammation and complement pathway. This was also confirmed by immunodetection and gene expression analyses. Our results show that these tumours are characterized by altered expression of proteins involved in biological processes associated with immune evasion and metastasis, suggesting new therapeutic options in the treatment of this aggressive type of CRC.
Collapse
Affiliation(s)
- Laura M López-Sánchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Jon Peñarando
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Rafael Mena
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Silvia Guil-Luna
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Toledano
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Francisco Conde
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carlos Villar
- Unidad de Gestión Clínica de Anatomía Patológica, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - César Díaz
- Unidad de Gestión Clínica de Cirugía General y del Aparato Digestivo, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Ignacio Ortea
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Juan R De la Haba-Rodríguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Enrique Aranda
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Unidad de Gestión Clínica de Oncología Médica, Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| |
Collapse
|
18
|
Gao SH, Ho JY, Fan L, Nouwens A, Hoelzle RD, Schulz B, Guo J, Zhou J, Yuan Z, Bond PL. A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:625-633. [PMID: 30974354 DOI: 10.1016/j.scitotenv.2019.03.442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.
Collapse
Affiliation(s)
- Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jun Yuan Ho
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Amanda Nouwens
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Robert D Hoelzle
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Benjamin Schulz
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
| |
Collapse
|
19
|
Nybo T, Davies MJ, Rogowska-Wrzesinska A. Analysis of protein chlorination by mass spectrometry. Redox Biol 2019; 26:101236. [PMID: 31181457 PMCID: PMC6557747 DOI: 10.1016/j.redox.2019.101236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 01/04/2023] Open
Abstract
Chlorination of tyrosine is a commonly known effect/consequence of myeloperoxidase activity at sites of inflammation, and detection of 3-chlorotyrosine has been used as biomarker for inflammatory diseases. However, few studies have addressed site specific chlorination in proteins, and no methods for large scale chloroproteomics studies have yet been published. In this study, we present an optimized mass spectrometry based protocol to identify and quantify chlorinated peptides from single proteins modified by HOCl (100 and 500 μM, within estimated pathophysiological levels), at a high level of sensitivity and accuracy. Particular emphasis was placed on 1) sensitive and precise detection of modification sites, 2) the avoidance of loss or artefactual creation of modifications, 3) accurate quantification of peptide abundance and reduction of missing values problem, 4) monitoring the dynamics of modification in samples exposed to different oxidant concentrations and 5) development of guidelines for verification of chlorination sites assignment. A combination of an optimised sample preparation protocol, and improved data analysis approaches have allowed identification of 33 and 15 chlorination sites in laminin and fibronectin, respectively, reported in previous manuscripts [1,2]. The method was subsequently tested on murine basement membrane extract, which contains high levels of laminin in a complex mixture. Here, 10 of the major chlorination sites in laminin were recapitulated, highlighting the utility of the method in detecting damage in complex samples. An optimized mass spectrometry method is presented to detect protein chlorination. Reduction and alkylation leads to loss of chlorinated residues. Identification of modification sites in fibronectin and laminin induced by HOCl. Quantification of relative site occupancy (RSO) of chlorinated residues. Largest chloroproteomics dataset to date.
Collapse
Affiliation(s)
- Tina Nybo
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark; Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
| |
Collapse
|
20
|
Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS. Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules. J Proteome Res 2019; 18:2525-2534. [DOI: 10.1021/acs.jproteome.9b00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Jonathan G. Lees
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Ikrame Lazar
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Ido Livneh
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Manon Brunet
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| |
Collapse
|
21
|
Bernal-Bayard P, Álvarez C, Calvo P, Castell C, Roncel M, Hervás M, Navarro JA. The singular properties of photosynthetic cytochrome c 550 from the diatom Phaeodactylum tricornutum suggest new alternative functions. PHYSIOLOGIA PLANTARUM 2019; 166:199-210. [PMID: 30499233 DOI: 10.1111/ppl.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Cytochrome c550 is an extrinsic component in the luminal side of photosystem II (PSII) in cyanobacteria, as well as in eukaryotic algae from the red photosynthetic lineage including, among others, diatoms. We have established that cytochrome c550 from the diatom Phaeodactylum tricornutum can be obtained as a complete protein from the membrane fraction of the alga, although a C-terminal truncated form is purified from the soluble fractions of this diatom as well as from other eukaryotic algae. Eukaryotic cytochromes c550 show distinctive electrostatic features as compared with cyanobacterial cytochrome c550 . In addition, co-immunoseparation and mass spectrometry experiments, as well as immunoelectron microscopy analyses, indicate that although cytochrome c550 from P. tricornutum is mainly located in the thylakoid domain of the chloroplast - where it interacts with PSII - , it can also be found in the chloroplast pyrenoid, related with proteins linked to the CO2 concentrating mechanism and assimilation. These results thus suggest new alternative functions of this heme protein in eukaryotes.
Collapse
Affiliation(s)
- Pilar Bernal-Bayard
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Purificación Calvo
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Carmen Castell
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Mercedes Roncel
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| | - José A Navarro
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla and CSIC, Sevilla, Spain
| |
Collapse
|
22
|
Zelezniak A, Vowinckel J, Capuano F, Messner CB, Demichev V, Polowsky N, Mülleder M, Kamrad S, Klaus B, Keller MA, Ralser M. Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts. Cell Syst 2018; 7:269-283.e6. [PMID: 30195436 PMCID: PMC6167078 DOI: 10.1016/j.cels.2018.08.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
A challenge in solving the genotype-to-phenotype relationship is to predict a cell’s metabolome, believed to correlate poorly with gene expression. Using comparative quantitative proteomics, we found that differential protein expression in 97 Saccharomyces cerevisiae kinase deletion strains is non-redundant and dominated by abundance changes in metabolic enzymes. Associating differential enzyme expression landscapes to corresponding metabolomes using network models provided reasoning for poor proteome-metabolome correlations; differential protein expression redistributes flux control between many enzymes acting in concert, a mechanism not captured by one-to-one correlation statistics. Mapping these regulatory patterns using machine learning enabled the prediction of metabolite concentrations, as well as identification of candidate genes important for the regulation of metabolism. Overall, our study reveals that a large part of metabolism regulation is explained through coordinated enzyme expression changes. Our quantitative data indicate that this mechanism explains more than half of metabolism regulation and underlies the interdependency between enzyme levels and metabolism, which renders the metabolome a predictable phenotype. The proteome of kinase knockouts is dominated by enzyme abundance changes The enzyme expression profiles of kinase knockouts are non-redundant Metabolism is regulated by many expression changes acting in concert Machine learning accurately predicts the metabolome from enzyme abundance
Collapse
Affiliation(s)
- Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Biognosys AG, Schlieren, Switzerland
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Nicole Polowsky
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Stephan Kamrad
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Bernd Klaus
- Centre for Statistical Data Analysis, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Department of Biochemistry, Charité Universitaetsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
23
|
Lehmann R, Schmidt A, Pastuschek J, Müller MM, Fritzsche A, Dieterle S, Greb RR, Markert UR, Slevogt H. Comparison of sample preparation techniques and data analysis for the LC-MS/MS-based identification of proteins in human follicular fluid. Am J Reprod Immunol 2018; 80:e12994. [PMID: 29938851 DOI: 10.1111/aji.12994] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/23/2018] [Indexed: 12/20/2022] Open
Abstract
The proteomic analysis of complex body fluids by liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis requires the selection of suitable sample preparation techniques and optimal parameter settings in data analysis software packages to obtain reliable results. Proteomic analysis of follicular fluid, as a representative of a complex body fluid similar to serum or plasma, is difficult as it contains a vast amount of high abundant proteins and a variety of proteins with different concentrations. However, the accessibility of this complex body fluid for LC-MS/MS analysis is an opportunity to gain insights into the status, the composition of fertility-relevant proteins including immunological factors or for the discovery of new diagnostic and prognostic markers for, for example, the treatment of infertility. In this study, we compared different sample preparation methods (FASP, eFASP and in-solution digestion) and three different data analysis software packages (Proteome Discoverer with SEQUEST, Mascot and MaxQuant with Andromeda) combined with semi- and full-tryptic databank search options to obtain a maximum coverage of the follicular fluid proteome. We found that the most comprehensive proteome coverage is achieved by the eFASP sample preparation method using SDS in the initial denaturing step and the SEQUEST-based semi-tryptic data analysis. In conclusion, we have developed a fractionation-free methodical workflow for in depth LC-MS/MS-based analysis for the standardized investigation of human follicle fluid as an important representative of a complex body fluid. Taken together, we were able to identify a total of 1392 proteins in follicular fluid.
Collapse
Affiliation(s)
- Roland Lehmann
- Host Septomics Research Group, Jena University Hospital, Jena, Germany
| | - André Schmidt
- Department of Obstetrics, Placenta Lab, Jena University Hospital, Jena, Germany
| | - Jana Pastuschek
- Department of Obstetrics, Placenta Lab, Jena University Hospital, Jena, Germany
| | - Mario M Müller
- Host Septomics Research Group, Jena University Hospital, Jena, Germany
| | | | | | | | - Udo R Markert
- Department of Obstetrics, Placenta Lab, Jena University Hospital, Jena, Germany
| | - Hortense Slevogt
- Host Septomics Research Group, Jena University Hospital, Jena, Germany
| |
Collapse
|
24
|
Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements. J Proteomics 2018; 189:60-66. [PMID: 29605292 DOI: 10.1016/j.jprot.2018.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/12/2018] [Accepted: 03/27/2018] [Indexed: 12/17/2022]
Abstract
Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms data-dependent acquisition (DDA) in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple heterogeneous phosphopeptide-enriched samples and conclude that PRM shows a great promise in bacterial phosphoproteomics analyses where reproducible detection and quantification of a relatively small set of phosphopeptides is desired. SIGNIFICANCE: Bacterial phosphorylated peptides occur in low abundance compared to their unmodified counterparts, and are therefore rarely reproducibly detected in shotgun (DDA) proteomics measurements. Here we show that parallel reaction monitoring complements DDA analyses and makes detection of known, targeted phosphopeptides more reproducible. This will be of significance in replicated MS measurements that have a goal to reproducibly detect and quantify phosphopeptides of interest.
Collapse
|
25
|
Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition. Sci Rep 2018. [PMID: 29531254 PMCID: PMC5847575 DOI: 10.1038/s41598-018-22610-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Quantitative proteomics is key for basic research, but needs improvements to satisfy an increasing demand for large sample series in diagnostics, academia and industry. A switch from nanoflowrate to microflowrate chromatography can improve throughput and reduce costs. However, concerns about undersampling and coverage have so far hampered its broad application. We used a QTOF mass spectrometer of the penultimate generation (TripleTOF5600), converted a nanoLC system into a microflow platform, and adapted a SWATH regime for large sample series by implementing retention time- and batch correction strategies. From 3 µg to 5 µg of unfractionated tryptic digests that are obtained from proteomics-typical amounts of starting material, microLC-SWATH-MS quantifies up to 4000 human or 1750 yeast proteins in an hour or less. In the acquisition of 750 yeast proteomes, retention times varied between 2% and 5%, and quantified the typical peptide with 5–8% signal variation in replicates, and below 20% in samples acquired over a five-months period. Providing precise quantities without being dependent on the latest hardware, our study demonstrates that the combination of microflow chromatography and data-independent acquisition strategies has the potential to overcome current bottlenecks in academia and industry, enabling the cost-effective generation of precise quantitative proteomes in large scale.
Collapse
|
26
|
Cardoso BR, Hare DJ, Bush AI, Li QX, Fowler CJ, Masters CL, Martins RN, Ganio K, Lothian A, Mukherjee S, Kapp EA, Roberts BR. Selenium Levels in Serum, Red Blood Cells, and Cerebrospinal Fluid of Alzheimer's Disease Patients: A Report from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL). J Alzheimers Dis 2018; 57:183-193. [PMID: 28222503 DOI: 10.3233/jad-160622] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Selenium (Se) protects cells against oxidative stress damage through a range of bioactive selenoproteins. Increased oxidative stress is a prominent feature of Alzheimer's disease (AD), and previous studies have shown that Se deficiency is associated with age-related cognitive decline. In this study, we assessed Se status in different biofluids from a subgroup of participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing. As Se in humans can either be an active component of selenoproteins or inactive via non-specific incorporation into other proteins, we used both size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) and tandem mass spectrometry to characterize selenoproteins in serum. We observed no differences in total Se concentration in serum or cerebrospinal fluid of AD subjects compared to mildly cognitively impairment patients and healthy controls. However, Se levels in erythrocytes were decreased in AD compared to controls. SEC-ICP-MS analysis revealed a dominant Se-containing fraction. This fraction was subjected to standard protein purification and a bottom-up proteomics approach to confirm that the abundant Se in the fraction was due, in part, to selenoprotein P. The lack of change in the Se level is at odds with our previous observations in a Brazilian population deficient in Se, and we attribute this to the Australian cohort being Se-replete.
Collapse
Affiliation(s)
- Bárbara R Cardoso
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, SP, Brazil
| | - Dominic J Hare
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, NSW, Australia
| | - Ashley I Bush
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Cooperative Research Centre for Mental Health, Parkville, VIC, Australia
| | - Qiao-Xin Li
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Christopher J Fowler
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ralph N Martins
- Edith Cowan University, School of Exercise, Biomedical and Health Sciences, Joondalup, WA, Australia
| | - Katherine Ganio
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Amber Lothian
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Cooperative Research Centre for Mental Health, Parkville, VIC, Australia
| | - Soumya Mukherjee
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - Eugene A Kapp
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Cooperative Research Centre for Mental Health, Parkville, VIC, Australia.,Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Blaine R Roberts
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.,Cooperative Research Centre for Mental Health, Parkville, VIC, Australia
| | | |
Collapse
|
27
|
Bruderer R, Bernhardt OM, Gandhi T, Xuan Y, Sondermann J, Schmidt M, Gomez-Varela D, Reiter L. Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results. Mol Cell Proteomics 2017; 16:2296-2309. [PMID: 29070702 PMCID: PMC5724188 DOI: 10.1074/mcp.ra117.000314] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/23/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence. 7739 proteins were identified in mouse tissues using 2-or-more peptides/protein and 8121 when including the 382 proteins that were identified based on a single peptide sequence. Missing values for proteins were within 0.3 to 2.1% and median coefficients of variation of 4.7 to 6.2% among technical triplicates. In very complex mixtures, we could quantify 10,780 proteins and 12,192 proteins when including the 1412 proteins that were identified based on a single peptide sequence. Using this optimized DIA, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in the murine somatosensory cortex 1-barrel field. This work shows that parallel mass spectrometry enables proteome profiling for discovery with high coverage, reproducibility, precision and scalability.
Collapse
Affiliation(s)
- Roland Bruderer
- From the ‡Biognosys, Wagistrasse 21, 8952 Schlieren, Switzerland
| | | | - Tejas Gandhi
- From the ‡Biognosys, Wagistrasse 21, 8952 Schlieren, Switzerland
| | - Yue Xuan
- §Thermo Fisher Scientific, 28199 Bremen, Germany
| | - Julia Sondermann
- ¶Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Goettingen, Germany
| | - Manuela Schmidt
- ¶Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Goettingen, Germany
| | - David Gomez-Varela
- ¶Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Goettingen, Germany
| | - Lukas Reiter
- From the ‡Biognosys, Wagistrasse 21, 8952 Schlieren, Switzerland.
| |
Collapse
|
28
|
Shan SW, Do CW, Lam TC, Kong RPW, Li KK, Chun KM, Stamer WD, To CH. New Insight of Common Regulatory Pathways in Human Trabecular Meshwork Cells in Response to Dexamethasone and Prednisolone Using an Integrated Quantitative Proteomics: SWATH and MRM-HR Mass Spectrometry. J Proteome Res 2017; 16:3753-3765. [PMID: 28920441 DOI: 10.1021/acs.jproteome.7b00449] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The molecular pathophysiology of corticosteroid-induced ocular hypertension (CIH) is not well understood. To determine the biological mechanisms of CIH, this study investigated protein expression profiles of human trabecular meshwork (hTM) cells in response to dexamethasone and prednisolone treatment. Both discovery-based sequential windowed data independent acquisition of the total high-resolution mass spectra (SWATH-MS) and targeted based high resolution multiple reaction monitoring (MRM-HR) confirmation were applied using a hybrid quadrupole-time-of-flight mass spectrometer. A comprehensive list of 1759 proteins (1% FDR) was generated from the hTM. Quantitative proteomics revealed 20 differentially expressed proteins (p-value ≤ 0.05 and fold-change ≥ 1.5 or ≤ 0.67) commonly induced by prednisolone and dexamethasone, both at 300 nM. These included connective tissue growth factor (CTGF) and thrombospondin-1 (THBS1), two proteins previously implicated in ocular hypertension, glaucoma, and the transforming growth factor-β pathway. Their gene expressions in response to corticosteroids were further confirmed using reverse-transcription polymerase chain reaction. Together with other novel proteins identified in the data sets, additional pathways implicated by these regulated proteins were the phosphatidylinositol 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway, integrin cell surface interaction, extracellular matrix (ECM) proteoglycans, and ECM-receptor interaction. Our results indicated that an integrated platform of SWATH-MS and MRM-HR allows high throughput identification and confirmation of novel and known corticosteroid-regulated proteins in trabecular meshwork cells, demonstrating the power of this technique in extending the current understanding of the pathogenesis of CIH.
Collapse
Affiliation(s)
- Sze Wan Shan
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University , Kowloon, Hong Kong, China
| | - Chi Wai Do
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University , Kowloon, Hong Kong, China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University , Kowloon, Hong Kong, China
| | | | - King Kit Li
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University , Kowloon, Hong Kong, China
| | - Ka Man Chun
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University , Kowloon, Hong Kong, China
| | - William Daniel Stamer
- Department of Ophthalmology and Department of Biomedical Engineering, Duke University , Durham, North Carolina 27708, United States
| | - Chi Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University , Kowloon, Hong Kong, China
| |
Collapse
|
29
|
A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions. Sci Rep 2017; 7:9718. [PMID: 28887440 PMCID: PMC5591248 DOI: 10.1038/s41598-017-10059-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/24/2017] [Indexed: 12/16/2022] Open
Abstract
Data-independent acquisition mass spectrometry promises higher performance in terms of quantification and reproducibility compared to data-dependent acquisition mass spectrometry methods. To enable high-accuracy quantification of Staphylococcus aureus proteins, we have developed a global ion library for data-independent acquisition approaches employing high-resolution time of flight or Orbitrap instruments for this human pathogen. We applied this ion library resource to investigate the time-resolved adaptation of S. aureus to the intracellular niche in human bronchial epithelial cells and in a murine pneumonia model. In epithelial cells, abundance changes for more than 400 S. aureus proteins were quantified, revealing, e.g., the precise temporal regulation of the SigB-dependent stress response and differential regulation of translation, fermentation, and amino acid biosynthesis. Using an in vivo murine pneumonia model, our data-independent acquisition quantification analysis revealed for the first time the in vivo proteome adaptation of S. aureus. From approximately 2.15 × 105 S. aureus cells, 578 proteins were identified. Increased abundance of proteins required for oxidative stress response, amino acid biosynthesis, and fermentation together with decreased abundance of ribosomal proteins and nucleotide reductase NrdEF was observed in post-infection samples compared to the pre-infection state.
Collapse
|
30
|
Teleman J, Hauri S, Malmström J. Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics. J Proteome Res 2017; 16:2384-2392. [PMID: 28516777 DOI: 10.1021/acs.jproteome.6b00928] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In data-independent acquisition mass spectrometry (DIA-MS), targeted extraction of peptide signals in silico using mass spectrometry assay libraries is a successful method for the identification and quantification of proteins. However, it remains unclear if high quality assay libraries with more accurate peptide ion coordinates can improve peptide target identification rates in DIA analysis. In this study, we systematically improved and evaluated the common algorithmic steps for assay library generation and demonstrate that increased assay quality results in substantially higher identification rates of peptide targets from mouse organ protein lysates measured by DIA-MS. The introduced changes are (1) a new spectrum interpretation algorithm, (2) reapplication of segmented retention time normalization, (3) a ppm fragment mass error matching threshold, (4) usage of internal peptide fragments, and (5) a multilevel false discovery rate calculation. Taken together, these changes yielded 14-36% more identified peptide targets at 1% assay false discovery rate and are implemented in three new open source tools, Fraggle, Tramler, and Franklin, available at https://github.com/fickludd/eviltools . The improved algorithms provide ways to better utilize discovery MS data, translating to substantially increased DIA performance and ultimately better foundations for drawing biological conclusions in DIA-based experiments.
Collapse
Affiliation(s)
- Johan Teleman
- Department of Clinical Sciences, Lund University , BMC D13, 221 84 Lund, Sweden.,Department of Immunotechnology, Lund University , Medicon Village (Building 406), 223 81 Lund, Sweden
| | - Simon Hauri
- Department of Clinical Sciences, Lund University , BMC D13, 221 84 Lund, Sweden
| | - Johan Malmström
- Department of Clinical Sciences, Lund University , BMC D13, 221 84 Lund, Sweden
| |
Collapse
|
31
|
Whyte JD. FastPrep ® Systems for Sample Preparation for Proteomic Characterization with Mass Spec. Biotechniques 2017. [DOI: 10.2144/000114550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Jeffrey D. Whyte
- Global Product Manager MP Biomedicals Inc., 3 Hutton Centre Drive, Santa Ana, CA, USA, 92707
| |
Collapse
|
32
|
Ingram T, Chakrabarti L. Proteomic profiling of mitochondria: what does it tell us about the ageing brain? Aging (Albany NY) 2016; 8:3161-3179. [PMID: 27992860 PMCID: PMC5270661 DOI: 10.18632/aging.101131] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/01/2016] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is evident in numerous neurodegenerative and age-related disorders. It has also been linked to cellular ageing, however our current understanding of the mitochondrial changes that occur are unclear. Functional studies have made some progress reporting reduced respiration, dynamic structural modifications and loss of membrane potential, though there are conflicts within these findings. Proteomic analyses, together with functional studies, are required in order to profile the mitochondrial changes that occur with age and can contribute to unravelling the complexity of the ageing phenotype. The emergence of improved protein separation techniques, combined with mass spectrometry analyses has allowed the identification of age and cell-type specific mitochondrial changes in energy metabolism, antioxidants, fusion and fission machinery, chaperones, membrane proteins and biosynthesis pathways. Here, we identify and review recent data from the analyses of mitochondria from rodent brains. It is expected that knowledge gained from understanding age-related mitochondrial changes of the brain should lead to improved biomarkers of normal ageing and also age-related disease progression.
Collapse
Affiliation(s)
- Thomas Ingram
- SVMS, Faculty of Medicine, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Lisa Chakrabarti
- SVMS, Faculty of Medicine, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| |
Collapse
|
33
|
Enk VM, Baumann C, Thoß M, Luzynski KC, Razzazi-Fazeli E, Penn DJ. Regulation of highly homologous major urinary proteins in house mice quantified with label-free proteomic methods. MOLECULAR BIOSYSTEMS 2016; 12:3005-16. [PMID: 27464909 PMCID: PMC5166567 DOI: 10.1039/c6mb00278a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023]
Abstract
Major urinary proteins (MUPs) are highly homologous proteoforms that function in binding, transporting and releasing pheromones in house mice. The main analytical challenge for studying variation in MUPs, even for state-of-the-art proteomics techniques, is their high degree of amino acid sequence homology. In this study we used unique peptides for proteoform-specific identification. We applied different search engines (ProteinPilot™vs. PEAKS®) and protein databases (MUP database vs. SwissProt + unreviewed MUPs), and found that proteoform identification is influenced by addressing background proteins (unregulated urinary proteins, non-MUPs) during the database search. High resolution Q-TOF mass spectrometry was used to identify and precisely quantify the regulation of MUP proteoforms in male mice that were reared in standard housing and then transferred to semi-natural enclosures (within-subject design). By using a designated MUP database we were able to distinguish 19 MUP proteoforms, with A2CEK6 (a Mup11 gene product) being the most abundant based on spectral intensities. We compared three different quantification strategies based on MS1- (from IDA and SWATH™ spectra) and MS2 (SWATH™) data, and the results of these methods were correlated. Furthermore, three data normalization methods were compared and we found that increased statistical significance of fold-changes can be achieved by normalization based on urinary protein concentrations. We show that male mice living in semi-natural enclosures significantly up-regulated some but not all MUPs (differential regulation), e.g., A2ANT6, a Mup6 gene product, was upregulated between 9-fold (MS1) and 13-fold (MS2) using the designated MUP database. Finally, we show that 85 ± 7% of total MS intensity can be attributed to MUP-derived peptides, which supports the assumption that MUPs are the primary proteins in mouse urine. Our results provide new tools for assessing qualitative and quantitative variation of MUPs and suggest that male mice regulate the expression of specific MUP proteoforms, depending upon social conditions.
Collapse
Affiliation(s)
- Viktoria M. Enk
- VetCore-Facility for Research , University of Veterinary Medicine Vienna , Veterinärplatz 1 , A-1210-Vienna , Austria
| | - Christian Baumann
- SCIEX Germany GmbH , Landwehrstraße 54 , D-64293 Darmstadt , Germany
| | - Michaela Thoß
- Department of Integrative Biology and Evolution , Konrad Lorenz Institute of Ethology , University of Veterinary Medicine Vienna , Savoyenstraße 1 , A-1160-Vienna , Austria .
| | - Kenneth C. Luzynski
- Department of Integrative Biology and Evolution , Konrad Lorenz Institute of Ethology , University of Veterinary Medicine Vienna , Savoyenstraße 1 , A-1160-Vienna , Austria .
| | - Ebrahim Razzazi-Fazeli
- VetCore-Facility for Research , University of Veterinary Medicine Vienna , Veterinärplatz 1 , A-1210-Vienna , Austria
| | - Dustin J. Penn
- Department of Integrative Biology and Evolution , Konrad Lorenz Institute of Ethology , University of Veterinary Medicine Vienna , Savoyenstraße 1 , A-1160-Vienna , Austria .
| |
Collapse
|
34
|
Bruderer R, Bernhardt OM, Gandhi T, Reiter L. High-precision iRT prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation. Proteomics 2016; 16:2246-56. [PMID: 27213465 PMCID: PMC5094550 DOI: 10.1002/pmic.201500488] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/18/2016] [Accepted: 05/19/2016] [Indexed: 01/30/2023]
Abstract
Targeted analysis of data‐independent acquisition (DIA) data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires a spectral library, which contains for all considered peptide precursor ions empirically determined fragment ion intensities and their predicted retention time (RT). RTs, however, are not comparable on an absolute scale, especially if heterogeneous measurements are combined. Here, we present a method for high‐precision prediction of RT, which significantly improves the quality of targeted DIA analysis compared to in silico RT prediction and the state of the art indexed retention time (iRT) normalization approach. We describe a high‐precision normalized RT algorithm, which is implemented in the Spectronaut software. We, furthermore, investigate the influence of nine different experimental factors, such as chromatographic mobile and stationary phase, on iRT precision. In summary, we show that using targeted analysis of DIA data with high‐precision iRT significantly increases sensitivity and data quality. The iRT values are generally transferable across a wide range of experimental conditions. Best results, however, are achieved if library generation and analytical measurements are performed on the same system.
Collapse
Affiliation(s)
| | | | - Tejas Gandhi
- Biognosys, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | - Lukas Reiter
- Biognosys, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| |
Collapse
|
35
|
Campbell K, Vowinckel J, Keller MA, Ralser M. Methionine Metabolism Alters Oxidative Stress Resistance via the Pentose Phosphate Pathway. Antioxid Redox Signal 2016; 24:543-7. [PMID: 26596469 PMCID: PMC4827311 DOI: 10.1089/ars.2015.6516] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/16/2015] [Accepted: 11/20/2015] [Indexed: 01/17/2023]
Abstract
Nutrient uptake and metabolism have a significant impact on the way cells respond to stress. The amino acid methionine is, in particular, a key player in the oxidative stress response, and acting as a reactive oxygen species scavenger, methionine is implicated in caloric restriction phenotypes and aging. We here provide evidence that some effects of methionine in stress situations are indirect and caused by altered activity of the nicotinamide adenine dinucleotide phosphate (NADPH) producing oxidative part of the pentose phosphate pathway (PPP). In Saccharomyces cerevisiae, both methionine prototrophic (MET15) and auxotrophic (met15Δ) cells supplemented with methionine showed an increase in PPP metabolite concentrations downstream of the NADPH producing enzyme, 6-phosphogluconate dehydrogenase. Proteomics revealed this enzyme to also increase in expression compared to methionine self-synthesizing cells. Oxidant tolerance was increased in cells preincubated with methionine; however, this effect was abolished when flux through the oxidative PPP was prevented by deletion of its rate limiting enzyme, ZWF1. Stress resistance phenotypes that follow methionine supplementation hence involve the oxidative PPP. Effects of methionine on oxidative metabolism, stress signaling, and aging have thus to be seen in the context of an altered activity of this NADP reducing pathway.
Collapse
Affiliation(s)
- Kate Campbell
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Markus A. Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- The Francis Crick Institute Mill Hill Laboratory, London, United Kingdom
| |
Collapse
|
36
|
Mittal P, Klingler-Hoffmann M, Arentz G, Zhang C, Kaur G, Oehler MK, Hoffmann P. Proteomics of endometrial cancer diagnosis, treatment, and prognosis. Proteomics Clin Appl 2015; 10:217-29. [DOI: 10.1002/prca.201500055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/13/2015] [Accepted: 11/02/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Parul Mittal
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Manuela Klingler-Hoffmann
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Georgia Arentz
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Chao Zhang
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine; Universiti Sains Malaysia; Minden Pulau Pinang Malaysia
| | - Martin K. Oehler
- Department of Gynaecological Oncology; Royal Adelaide Hospital; North Terrace Adelaide Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
| |
Collapse
|
37
|
Proteomics discovery of radioresistant cancer biomarkers for radiotherapy. Cancer Lett 2015; 369:289-97. [DOI: 10.1016/j.canlet.2015.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/08/2015] [Accepted: 09/23/2015] [Indexed: 12/28/2022]
|
38
|
Scheerlinck E, Dhaenens M, Van Soom A, Peelman L, De Sutter P, Van Steendam K, Deforce D. Minimizing technical variation during sample preparation prior to label-free quantitative mass spectrometry. Anal Biochem 2015; 490:14-9. [PMID: 26302362 DOI: 10.1016/j.ab.2015.08.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/01/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022]
Abstract
Sample preparation is the crucial starting point to obtain high-quality mass spectrometry data and can be divided into two main steps in a bottom-up proteomics approach: cell/tissue lysis with or without detergents and a(n) (in-solution) digest comprising denaturation, reduction, alkylation, and digesting of the proteins. Here, some important considerations, among others, are that the reagents used for sample preparation can inhibit the digestion enzyme (e.g., 0.1% sodium dodecyl sulfate [SDS] and 0.5 M guanidine HCl), give rise to ion suppression (e.g., polyethylene glycol [PEG]), be incompatible with liquid chromatography-tandem mass spectrometry (LC-MS/MS) (e.g., SDS), and can induce additional modifications (e.g., urea). Taken together, all of these irreproducible effects are gradually becoming a problem when label-free quantitation of the samples is envisioned such as during the increasingly popular high-definition mass spectrometry (HDMS(E)) and sequential window acquisition of all theoretical fragment ion spectra (SWATH) data-independent acquisition strategies. Here, we describe the detailed validation of a reproducible method with sufficient protein yield for sample preparation without any known LC-MS/MS interfering substances by using 1% sodium deoxycholate (SDC) during both cell lysis and in-solution digest.
Collapse
Affiliation(s)
- E Scheerlinck
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - M Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - A Van Soom
- Department of Reproduction, Obstetrics, and Herd Health, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - L Peelman
- Department of Nutrition, Genetics, and Ethology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - P De Sutter
- Department of Reproductive Medicine, Ghent University Hospital, B-9000 Ghent, Belgium
| | - K Van Steendam
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - D Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, B-9000 Ghent, Belgium.
| |
Collapse
|
39
|
Zhang X. Less is More: Membrane Protein Digestion Beyond Urea-Trypsin Solution for Next-level Proteomics. Mol Cell Proteomics 2015; 14:2441-53. [PMID: 26081834 DOI: 10.1074/mcp.r114.042572] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Indexed: 12/13/2022] Open
Abstract
The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea-trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting-not destroying-structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics.
Collapse
Affiliation(s)
- Xi Zhang
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts; §Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
40
|
Schnell G, Boeuf A, Westermann B, Jaulhac B, Lipsker D, Carapito C, Boulanger N, Ehret-Sabatier L. Discovery and targeted proteomics on cutaneous biopsies infected by borrelia to investigate lyme disease. Mol Cell Proteomics 2015; 14:1254-64. [PMID: 25713121 DOI: 10.1074/mcp.m114.046540] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Indexed: 12/11/2022] Open
Abstract
Lyme disease is the most important vector-borne disease in the Northern hemisphere and represents a major public health challenge with insufficient means of reliable diagnosis. Skin is rarely investigated in proteomics but constitutes in the case of Lyme disease the key interface where the pathogens can enter, persist, and multiply. Therefore, we investigated proteomics on skin samples to detect Borrelia proteins directly in cutaneous biopsies in a robust and specific way. We first set up a discovery gel prefractionation-LC-MS/MS approach on a murine model infected by Borrelia burgdorferi sensu stricto that allowed the identification of 25 Borrelia proteins among more than 1300 mouse proteins. Then we developed a targeted gel prefractionation-LC-selected reaction monitoring (SRM) assay to detect 9/33 Borrelia proteins/peptides in mouse skin tissue samples using heavy labeled synthetic peptides. We successfully transferred this assay from the mouse model to human skin biopsies (naturally infected by Borrelia), and we were able to detect two Borrelia proteins: OspC and flagellin. Considering the extreme variability of OspC, we developed an extended SRM assay to target a large set of variants. This assay afforded the detection of nine peptides belonging to either OspC or flagellin in human skin biopsies. We further shortened the sample preparation and showed that Borrelia is detectable in mouse and human skin biopsies by directly using a liquid digestion followed by LC-SRM analysis without any prefractionation. This study thus shows that a targeted SRM approach is a promising tool for the early direct diagnosis of Lyme disease with high sensitivity (<10 fmol of OspC/mg of human skin biopsy).
Collapse
Affiliation(s)
- Gilles Schnell
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS-Université de Strasbourg, 67087 Strasbourg, France
| | - Amandine Boeuf
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS-Université de Strasbourg, 67087 Strasbourg, France
| | - Benoît Westermann
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS-Université de Strasbourg, 67087 Strasbourg, France
| | - Benoît Jaulhac
- ‖EA7290, Virulence bactérienne précoce, groupe Borréliose de Lyme, Facultés de Médecine et de Pharmacie, Université de Strasbourg, 67091 Strasbourg, France, and
| | - Dan Lipsker
- **Faculté de Médecine, Université de Strasbourg et Clinique Dermatologique, Hôpitaux Universitaires, 67091 Strasbourg, France
| | - Christine Carapito
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS-Université de Strasbourg, 67087 Strasbourg, France
| | - Nathalie Boulanger
- ‖EA7290, Virulence bactérienne précoce, groupe Borréliose de Lyme, Facultés de Médecine et de Pharmacie, Université de Strasbourg, 67091 Strasbourg, France, and
| | - Laurence Ehret-Sabatier
- From the ‡Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS-Université de Strasbourg, 67087 Strasbourg, France,
| |
Collapse
|
41
|
Arentz G, Weiland F, Oehler MK, Hoffmann P. State of the art of 2D DIGE. Proteomics Clin Appl 2015; 9:277-88. [DOI: 10.1002/prca.201400119] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/13/2014] [Accepted: 11/10/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Georgia Arentz
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Florian Weiland
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Martin K. Oehler
- School of Paediatrics and Reproductive Health; Research Centre for Reproductive Health; Robinson Institute; University of Adelaide; SA Australia
- Department of Gynaecological Oncology; Royal Adelaide Hospital; Adelaide SA Australia
| | - Peter Hoffmann
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| |
Collapse
|
42
|
Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M. Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biol 2015; 16:19. [PMID: 25631560 PMCID: PMC4373106 DOI: 10.1186/s13059-014-0578-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS We present the high quality assembly and annotation of a female 1.2-Gbp canary genome. Whole genome alignments between the canary and 13 genomes throughout the bird taxa show a much-conserved synteny, whereas at the single-base resolution there are considerable species differences. These differences impact small sequence motifs like transcription factor binding sites such as estrogen response elements and androgen response elements. To relate these species-specific response elements to the hormone-sensitivity of the canary singing behavior, we identify seasonal testosterone-sensitive transcriptomes of major song-related brain regions, HVC and RA, and find the seasonal gene networks related to neuronal differentiation only in the HVC. Testosterone-sensitive up-regulated gene networks of HVC of singing males concerned neuronal differentiation. Among the testosterone-regulated genes of canary HVC, 20% lack estrogen response elements and 4 to 8% lack androgen response elements in orthologous promoters in the zebra finch. CONCLUSIONS The canary genome sequence and complementary expression analysis reveal intra-regional evolutionary changes in a multi-regional neural circuit controlling seasonal singing behavior and identify gene evolution related to the hormone-sensitivity of this seasonal singing behavior. Such genes that are testosterone- and estrogen-sensitive specifically in the canary and that are involved in rewiring of neurons might be crucial for seasonal re-differentiation of HVC underlying seasonal song patterning.
Collapse
Affiliation(s)
- Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Heiner Kuhl
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Martin Werber
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Martin Kerick
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Edivaldo Hc de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém, 66075-110, Brazil.
| | - Christina Reusch
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Stefan Leitner
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, NW7 1AA, UK.
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| |
Collapse
|