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  • 99
    Thermo Fisher proteome discoverer
    Successful capture of alpha-satellite-associated proteomes in live human cells by C-BERST. ( a ) Ratiometric C-BERST (using SILAC) was used to profile the alpha-satellite-associated <t>proteome.</t> A volcano plot of C-BERST-labeled, centromere-associated proteins in U2OS cells is shown. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgAlpha vs. sgNS cells. 1,134 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value
    Proteome Discoverer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5508 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore proteomics grade trypsin
    Successful capture of alpha-satellite-associated proteomes in live human cells by C-BERST. ( a ) Ratiometric C-BERST (using SILAC) was used to profile the alpha-satellite-associated <t>proteome.</t> A volcano plot of C-BERST-labeled, centromere-associated proteins in U2OS cells is shown. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgAlpha vs. sgNS cells. 1,134 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value
    Proteomics Grade Trypsin, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 615 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher 4700 proteomics analyzer
    Successful capture of alpha-satellite-associated proteomes in live human cells by C-BERST. ( a ) Ratiometric C-BERST (using SILAC) was used to profile the alpha-satellite-associated <t>proteome.</t> A volcano plot of C-BERST-labeled, centromere-associated proteins in U2OS cells is shown. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgAlpha vs. sgNS cells. 1,134 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value
    4700 Proteomics Analyzer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 1692 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher proteome discoverer software
    Successful capture of alpha-satellite-associated proteomes in live human cells by C-BERST. ( a ) Ratiometric C-BERST (using SILAC) was used to profile the alpha-satellite-associated <t>proteome.</t> A volcano plot of C-BERST-labeled, centromere-associated proteins in U2OS cells is shown. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgAlpha vs. sgNS cells. 1,134 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value
    Proteome Discoverer Software, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 906 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Epigenomics proteomics
    <t>Proteomics</t>
    Proteomics, supplied by Epigenomics, used in various techniques. Bioz Stars score: 92/100, based on 827 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher 4800 proteomics analyzer
    <t>Proteomics</t>
    4800 Proteomics Analyzer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 515 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Nonlinear Dynamics proteomics
    Biological functions of the differentially expressed proteins in the myocardium of obese rats identified by <t>proteomics</t> ( A ) Protein-protein interaction network. The interaction network analyses were built using the STRING online software with a medium confidence level (0.4). The circles represent proteins, while the straight lines represent the interactions between different proteins. The line thickness indicates the strength of evidence, with thicker connections indicating higher confidence in the protein-protein interaction. Green circles represent the proteins involved in metabolic processes; shaded area delimits the proteins involved in lipid metabolic processes. ( B ) Gene ontology (GO) enrichment analysis. The analysis was performed using the PANTHER tool ( http://www.pantherdb.org ), providing the significantly enriched GO terms Molecular Function, Biological Process, and Cellular Component. On the left panel, the horizontal axis indicates the significance (−log10 p -value) of the functional association, which is dependent on the number of proteins in the class. On the right panel, changes are displayed as the number of proteins with increased or decreased levels (horizontal axis). ( C ) Violin plot of the fold changes for up- and down-regulated proteins in the WD group compared to their controls. The fold changes of up- and down-regulated proteins were further separated into the metabolic processes associated with fatty acid, glucose, amino acid, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (Oxi. Phosp.). The circles inside the plots represent the changed proteins. The detailed description of protein names is shown in Supplementary Tables S3 and S4 .
    Proteomics, supplied by Nonlinear Dynamics, used in various techniques. Bioz Stars score: 92/100, based on 279 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Millipore proteomic analysis
    Complement system is a canonical pathway significantly altered in naive scrub typhus patients compared with normal subjects ( a ) and in patients treated with antibiotics compared with naive patients ( b ). Red indicates up-regulated proteins, and green indicates down-regulated proteins. The colour intensity corresponds to the degree of up- or down-regulation (fold change). White represents proteins known to be part of the pathway but not identified in the <t>proteomic</t> analysis
    Proteomic Analysis, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 186 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Integrated Proteomics Applications integrated proteomics pipeline ip2
    Complement system is a canonical pathway significantly altered in naive scrub typhus patients compared with normal subjects ( a ) and in patients treated with antibiotics compared with naive patients ( b ). Red indicates up-regulated proteins, and green indicates down-regulated proteins. The colour intensity corresponds to the degree of up- or down-regulation (fold change). White represents proteins known to be part of the pathway but not identified in the <t>proteomic</t> analysis
    Integrated Proteomics Pipeline Ip2, supplied by Integrated Proteomics Applications, used in various techniques. Bioz Stars score: 90/100, based on 332 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher proteome discoverer v1 4
    Sample processing workflow. a Proteins were extracted from five invasive breast cancer specimens using three different methods, generating a total of 15 protein samples. In Method 1, flash-frozen specimens were homogenized (FF/HOM) and protein isolated using the illustra triplePrep kit. In Methods 2A and 2B, sections from OCT-embedded specimens were laser microdissected to isolate tumor cells only (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS), respectively. In both Methods 2A and 2B, the laser microdissected material was then incubated at 37 °C for 10 min followed by protein isolation using the illustra triplePrep kit. Extracted proteins were trypsin digested and TMT-labeled. TMT-labeled peptides were analyzed using 2D-LC–MS/MS and proteins quantified using <t>Proteome</t> Discoverer <t>v1.4</t> followed by data analysis to identify differentially expressed proteins among the three different sample storage/processing methods. b Sample-to-TMT channel mapping. Samples were analyzed in 3 TMT sets with 7 channels in each set. In each TMT set, channel 126 contained the QCP (quality control pooled sample) while the remaining 6 channels contained the individual TMT-labeled samples. The last three TMT channels in set 3 contained technical replicates, one for each sample storage/preparation method
    Proteome Discoverer V1 4, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 311 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Nonlinear Dynamics proteomics software
    Overview of the complex multi-system pathophysiology of dystrophinopathy and proteomic workflow to analyse the mdx - 4cv liver. Duchenne muscular dystrophy is caused by primary abnormalities in dystrophin and triggers progressive skeletal muscle wasting, cardio-respiratory abnormalities and cognitive impairments. In addition, X-linked muscular dystrophy is also characterized by secondary effects on a variety of organ systems including the liver. Proteome-wide changes in liver tissue were determined by comparative <t>proteomics</t> using the dystrophic mdx - 4cv mouse model of Duchenne muscular dystrophy. Results obtained by mass spectrometry using an Orbitrap Fusion Tribrid apparatus were analysed by systems bioinformatics, and key findings were confirmed by verification studies employing immunoblotting and immunofluorescence microscopy
    Proteomics Software, supplied by Nonlinear Dynamics, used in various techniques. Bioz Stars score: 89/100, based on 208 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Agilent technologies spectrum mill ms proteomics workbench
    ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + <t>proteomics</t> distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).
    Spectrum Mill Ms Proteomics Workbench, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 424 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore proteoextract subcellular proteome extraction kit
    ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + <t>proteomics</t> distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).
    Proteoextract Subcellular Proteome Extraction Kit, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 219 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher proteome discoverer v2 1
    ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + <t>proteomics</t> distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).
    Proteome Discoverer V2 1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 86 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    98
    Thermo Fisher proteomics
    ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + <t>proteomics</t> distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).
    Proteomics, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 782 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/proteomics/product/Thermo Fisher
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    89
    Thermo Fisher 4700 proteomics analyzer maldi tof tof
    ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + <t>proteomics</t> distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).
    4700 Proteomics Analyzer Maldi Tof Tof, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 181 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    N/A
    Western blot classroom study kit includes antibodies color detection reagents 10x TG buffer 10x PBS 10 Tween nitrocellulose curriculum and more for 32 students education use only
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    500 ml ultrapure water for use with ReadyPrep fractionation and general purpose cleanup kits
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    Protein profiling classroom study kit includes buffers standards stains DTT test tubes holders disposable pipets tips trays curriculum and more for 32 students education use only
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    Image Search Results


    Successful capture of alpha-satellite-associated proteomes in live human cells by C-BERST. ( a ) Ratiometric C-BERST (using SILAC) was used to profile the alpha-satellite-associated proteome. A volcano plot of C-BERST-labeled, centromere-associated proteins in U2OS cells is shown. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgAlpha vs. sgNS cells. 1,134 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value

    Journal: Nature methods

    Article Title: C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2

    doi: 10.1038/s41592-018-0006-2

    Figure Lengend Snippet: Successful capture of alpha-satellite-associated proteomes in live human cells by C-BERST. ( a ) Ratiometric C-BERST (using SILAC) was used to profile the alpha-satellite-associated proteome. A volcano plot of C-BERST-labeled, centromere-associated proteins in U2OS cells is shown. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgAlpha vs. sgNS cells. 1,134 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value

    Article Snippet: Raw data files were processed with Proteome Discoverer (Thermo, version 2.1.1.21) and searched with Mascot (Matrix Science, version 2.6) against the SwissProt Homo sapiens database.

    Techniques: Labeling

    Using C-BERST to biotinylate telomere-associated proteins in living human cells. ( a ) Diagram of the C-BERST workflow. ( b ) Telomere-associated proteome identification by ratiometric C-BERST. A volcano plot is shown for C-BERST-labeled, telomere-associated proteins in U2OS cells. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgTelo vs. sgNS cells. 359 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value

    Journal: Nature methods

    Article Title: C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2

    doi: 10.1038/s41592-018-0006-2

    Figure Lengend Snippet: Using C-BERST to biotinylate telomere-associated proteins in living human cells. ( a ) Diagram of the C-BERST workflow. ( b ) Telomere-associated proteome identification by ratiometric C-BERST. A volcano plot is shown for C-BERST-labeled, telomere-associated proteins in U2OS cells. For each protein, the H/M SILAC ratio reflects the enrichment of identified proteins in sgTelo vs. sgNS cells. 359 proteins (indicated by blue and red dots) are statistically enriched [BH-adjusted p value

    Article Snippet: Raw data files were processed with Proteome Discoverer (Thermo, version 2.1.1.21) and searched with Mascot (Matrix Science, version 2.6) against the SwissProt Homo sapiens database.

    Techniques: Labeling

    Experimental workflow. Comparison between two sEV isolation procedures: precipitation (PPT) and Size Exclusion Chromatography (SEC) using 100 µl of mouse serum. SEC was then scaled down on vesicles isolated from 50 µl of serum. As a proof of concept, the ultrasensitive microproteomics workflow was then applied to a longitudinal study of a glioblastoma multiforme mouse model. Purified sEV’s were concentrated and lysed on protein concentrator spin filters; then extracted, quantified and digested with a modified SP3 protocol. Peptides were analyzed by nLC-MS/MS, and the data analyzed with Proteome Discoverer 2.1 and MaxQuant software. Statistical analysis was performed using Perseus and Matlab.

    Journal: Scientific Reports

    Article Title: Proteomics analysis of serum small extracellular vesicles for the longitudinal study of a glioblastoma multiforme mouse model

    doi: 10.1038/s41598-020-77535-8

    Figure Lengend Snippet: Experimental workflow. Comparison between two sEV isolation procedures: precipitation (PPT) and Size Exclusion Chromatography (SEC) using 100 µl of mouse serum. SEC was then scaled down on vesicles isolated from 50 µl of serum. As a proof of concept, the ultrasensitive microproteomics workflow was then applied to a longitudinal study of a glioblastoma multiforme mouse model. Purified sEV’s were concentrated and lysed on protein concentrator spin filters; then extracted, quantified and digested with a modified SP3 protocol. Peptides were analyzed by nLC-MS/MS, and the data analyzed with Proteome Discoverer 2.1 and MaxQuant software. Statistical analysis was performed using Perseus and Matlab.

    Article Snippet: Protein identification Raw data files were processed using Proteome Discoverer 2.1 (Thermo Scientific).

    Techniques: Isolation, Size-exclusion Chromatography, Purification, Modification, Tandem Mass Spectroscopy, Software

    Proteomics

    Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

    Article Title: Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

    doi: 10.1159/000358693

    Figure Lengend Snippet: Proteomics

    Article Snippet: Keywords: Genomics, Proteomics, RNA-Seq, ChIP-Seq, Epigenomics, Systems Biology, Network Biology, Interactomes, Transcriptomes, Diseasosomes

    Techniques:

    Targeted and global metabolomics approach for metabolite identification and quantification. Data analysis workflows for global metabolomics are comparable to genomics and proteomics since many of the techniques generate raw data that are of similar format

    Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

    Article Title: Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

    doi: 10.1159/000358693

    Figure Lengend Snippet: Targeted and global metabolomics approach for metabolite identification and quantification. Data analysis workflows for global metabolomics are comparable to genomics and proteomics since many of the techniques generate raw data that are of similar format

    Article Snippet: Keywords: Genomics, Proteomics, RNA-Seq, ChIP-Seq, Epigenomics, Systems Biology, Network Biology, Interactomes, Transcriptomes, Diseasosomes

    Techniques:

    Systomics: Integrative approach for pulmonary medicine. The confluence of genomics, proteomics, metabolomics and epigenomics drives systems driven approach for studying pulmonary disorders. Integration of work flows and data obtained from these will contribute

    Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

    Article Title: Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

    doi: 10.1159/000358693

    Figure Lengend Snippet: Systomics: Integrative approach for pulmonary medicine. The confluence of genomics, proteomics, metabolomics and epigenomics drives systems driven approach for studying pulmonary disorders. Integration of work flows and data obtained from these will contribute

    Article Snippet: Keywords: Genomics, Proteomics, RNA-Seq, ChIP-Seq, Epigenomics, Systems Biology, Network Biology, Interactomes, Transcriptomes, Diseasosomes

    Techniques:

    Work flow for processing and analyzing epigenomics data. Epigenomics shares a number of technologies and applications with genomics and proteomics, which allows users to overlap work flows for data generation and analysis. While initial steps of data

    Journal: Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology

    Article Title: Integrating Omics Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

    doi: 10.1159/000358693

    Figure Lengend Snippet: Work flow for processing and analyzing epigenomics data. Epigenomics shares a number of technologies and applications with genomics and proteomics, which allows users to overlap work flows for data generation and analysis. While initial steps of data

    Article Snippet: Keywords: Genomics, Proteomics, RNA-Seq, ChIP-Seq, Epigenomics, Systems Biology, Network Biology, Interactomes, Transcriptomes, Diseasosomes

    Techniques: Flow Cytometry

    Biological functions of the differentially expressed proteins in the myocardium of obese rats identified by proteomics ( A ) Protein-protein interaction network. The interaction network analyses were built using the STRING online software with a medium confidence level (0.4). The circles represent proteins, while the straight lines represent the interactions between different proteins. The line thickness indicates the strength of evidence, with thicker connections indicating higher confidence in the protein-protein interaction. Green circles represent the proteins involved in metabolic processes; shaded area delimits the proteins involved in lipid metabolic processes. ( B ) Gene ontology (GO) enrichment analysis. The analysis was performed using the PANTHER tool ( http://www.pantherdb.org ), providing the significantly enriched GO terms Molecular Function, Biological Process, and Cellular Component. On the left panel, the horizontal axis indicates the significance (−log10 p -value) of the functional association, which is dependent on the number of proteins in the class. On the right panel, changes are displayed as the number of proteins with increased or decreased levels (horizontal axis). ( C ) Violin plot of the fold changes for up- and down-regulated proteins in the WD group compared to their controls. The fold changes of up- and down-regulated proteins were further separated into the metabolic processes associated with fatty acid, glucose, amino acid, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (Oxi. Phosp.). The circles inside the plots represent the changed proteins. The detailed description of protein names is shown in Supplementary Tables S3 and S4 .

    Journal: Scientific Reports

    Article Title: Landscape of heart proteome changes in a diet-induced obesity model

    doi: 10.1038/s41598-019-54522-2

    Figure Lengend Snippet: Biological functions of the differentially expressed proteins in the myocardium of obese rats identified by proteomics ( A ) Protein-protein interaction network. The interaction network analyses were built using the STRING online software with a medium confidence level (0.4). The circles represent proteins, while the straight lines represent the interactions between different proteins. The line thickness indicates the strength of evidence, with thicker connections indicating higher confidence in the protein-protein interaction. Green circles represent the proteins involved in metabolic processes; shaded area delimits the proteins involved in lipid metabolic processes. ( B ) Gene ontology (GO) enrichment analysis. The analysis was performed using the PANTHER tool ( http://www.pantherdb.org ), providing the significantly enriched GO terms Molecular Function, Biological Process, and Cellular Component. On the left panel, the horizontal axis indicates the significance (−log10 p -value) of the functional association, which is dependent on the number of proteins in the class. On the right panel, changes are displayed as the number of proteins with increased or decreased levels (horizontal axis). ( C ) Violin plot of the fold changes for up- and down-regulated proteins in the WD group compared to their controls. The fold changes of up- and down-regulated proteins were further separated into the metabolic processes associated with fatty acid, glucose, amino acid, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (Oxi. Phosp.). The circles inside the plots represent the changed proteins. The detailed description of protein names is shown in Supplementary Tables S3 and S4 .

    Article Snippet: The MS raw data files were loaded into Progenesis QI for Proteomics v.4.0 (Nonlinear Dynamics, Waters, Newcastle upon Tyne, UK) to perform the quantitative analysis.

    Techniques: Software, Functional Assay

    Proteomics data based on 2-DE of heart tissue from control ( C ) and Western diet (WD) groups. ( A ) Correlation analysis between 2-DE gels triplicates of control ( C ) and Western diet (WD) groups performed by Image Master 2D Platinum software. ( B ) Representative 2-DE gel image. The position of molecular weight (MW) markers are indicated to the right and the p I (isoelectric point) at the bottom of the gel. The sequence of numbers (1–47) refers to identification spots of the significantly up- (red circle) and down-regulated (blue circle) proteins in the WD group compared to the C group identified by LC-MS/MS. The detailed list of proteins for highlighted spots are shown in Supplementary Table S3 .

    Journal: Scientific Reports

    Article Title: Landscape of heart proteome changes in a diet-induced obesity model

    doi: 10.1038/s41598-019-54522-2

    Figure Lengend Snippet: Proteomics data based on 2-DE of heart tissue from control ( C ) and Western diet (WD) groups. ( A ) Correlation analysis between 2-DE gels triplicates of control ( C ) and Western diet (WD) groups performed by Image Master 2D Platinum software. ( B ) Representative 2-DE gel image. The position of molecular weight (MW) markers are indicated to the right and the p I (isoelectric point) at the bottom of the gel. The sequence of numbers (1–47) refers to identification spots of the significantly up- (red circle) and down-regulated (blue circle) proteins in the WD group compared to the C group identified by LC-MS/MS. The detailed list of proteins for highlighted spots are shown in Supplementary Table S3 .

    Article Snippet: The MS raw data files were loaded into Progenesis QI for Proteomics v.4.0 (Nonlinear Dynamics, Waters, Newcastle upon Tyne, UK) to perform the quantitative analysis.

    Techniques: Western Blot, Software, Molecular Weight, Sequencing, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    Label-free proteomics data clustering of heart tissue from control ( C ) and Western diet (WD) groups. ( A ) Univariate, significance ( p -value) vs. fold change analyses highlighting several significant deregulated proteins of interest. ( B ) Unsupervised multivariate principal component analysis (PCA). ( C ) Hierarchical clustering analyses (Heatmap) using unsupervised Euclidean distance of all differentially expressed proteins between the groups. The detailed description of protein names is shown in Supplementary Table S4 .

    Journal: Scientific Reports

    Article Title: Landscape of heart proteome changes in a diet-induced obesity model

    doi: 10.1038/s41598-019-54522-2

    Figure Lengend Snippet: Label-free proteomics data clustering of heart tissue from control ( C ) and Western diet (WD) groups. ( A ) Univariate, significance ( p -value) vs. fold change analyses highlighting several significant deregulated proteins of interest. ( B ) Unsupervised multivariate principal component analysis (PCA). ( C ) Hierarchical clustering analyses (Heatmap) using unsupervised Euclidean distance of all differentially expressed proteins between the groups. The detailed description of protein names is shown in Supplementary Table S4 .

    Article Snippet: The MS raw data files were loaded into Progenesis QI for Proteomics v.4.0 (Nonlinear Dynamics, Waters, Newcastle upon Tyne, UK) to perform the quantitative analysis.

    Techniques: Western Blot

    Complement system is a canonical pathway significantly altered in naive scrub typhus patients compared with normal subjects ( a ) and in patients treated with antibiotics compared with naive patients ( b ). Red indicates up-regulated proteins, and green indicates down-regulated proteins. The colour intensity corresponds to the degree of up- or down-regulation (fold change). White represents proteins known to be part of the pathway but not identified in the proteomic analysis

    Journal: Clinical Proteomics

    Article Title: Clinical proteomic analysis of scrub typhus infection

    doi: 10.1186/s12014-018-9181-5

    Figure Lengend Snippet: Complement system is a canonical pathway significantly altered in naive scrub typhus patients compared with normal subjects ( a ) and in patients treated with antibiotics compared with naive patients ( b ). Red indicates up-regulated proteins, and green indicates down-regulated proteins. The colour intensity corresponds to the degree of up- or down-regulation (fold change). White represents proteins known to be part of the pathway but not identified in the proteomic analysis

    Article Snippet: Preparation of clinical serum samples for proteomic analysis For proteomic analysis, albumin and IgG were removed from clinical serum samples using ProteoPrep Immunoaffinity Albumin and IgG Depletion Kit (Sigma-Aldrich, St. Louis, MO, USA).

    Techniques:

    Sample processing workflow. a Proteins were extracted from five invasive breast cancer specimens using three different methods, generating a total of 15 protein samples. In Method 1, flash-frozen specimens were homogenized (FF/HOM) and protein isolated using the illustra triplePrep kit. In Methods 2A and 2B, sections from OCT-embedded specimens were laser microdissected to isolate tumor cells only (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS), respectively. In both Methods 2A and 2B, the laser microdissected material was then incubated at 37 °C for 10 min followed by protein isolation using the illustra triplePrep kit. Extracted proteins were trypsin digested and TMT-labeled. TMT-labeled peptides were analyzed using 2D-LC–MS/MS and proteins quantified using Proteome Discoverer v1.4 followed by data analysis to identify differentially expressed proteins among the three different sample storage/processing methods. b Sample-to-TMT channel mapping. Samples were analyzed in 3 TMT sets with 7 channels in each set. In each TMT set, channel 126 contained the QCP (quality control pooled sample) while the remaining 6 channels contained the individual TMT-labeled samples. The last three TMT channels in set 3 contained technical replicates, one for each sample storage/preparation method

    Journal: Clinical Proteomics

    Article Title: Comparative analysis of differentially abundant proteins quantified by LC–MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples

    doi: 10.1186/s12014-020-09300-y

    Figure Lengend Snippet: Sample processing workflow. a Proteins were extracted from five invasive breast cancer specimens using three different methods, generating a total of 15 protein samples. In Method 1, flash-frozen specimens were homogenized (FF/HOM) and protein isolated using the illustra triplePrep kit. In Methods 2A and 2B, sections from OCT-embedded specimens were laser microdissected to isolate tumor cells only (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS), respectively. In both Methods 2A and 2B, the laser microdissected material was then incubated at 37 °C for 10 min followed by protein isolation using the illustra triplePrep kit. Extracted proteins were trypsin digested and TMT-labeled. TMT-labeled peptides were analyzed using 2D-LC–MS/MS and proteins quantified using Proteome Discoverer v1.4 followed by data analysis to identify differentially expressed proteins among the three different sample storage/processing methods. b Sample-to-TMT channel mapping. Samples were analyzed in 3 TMT sets with 7 channels in each set. In each TMT set, channel 126 contained the QCP (quality control pooled sample) while the remaining 6 channels contained the individual TMT-labeled samples. The last three TMT channels in set 3 contained technical replicates, one for each sample storage/preparation method

    Article Snippet: Protein quantificationRaw LC–MS/MS data were processed using Proteome Discoverer v1.4 (Thermo Scientific) and searched against the RefSeq protein database using the database search algorithm SEQUEST to identify and quantify proteins.

    Techniques: Isolation, Laser Capture Microdissection, Incubation, Labeling, Liquid Chromatography with Mass Spectroscopy

    Overview of the complex multi-system pathophysiology of dystrophinopathy and proteomic workflow to analyse the mdx - 4cv liver. Duchenne muscular dystrophy is caused by primary abnormalities in dystrophin and triggers progressive skeletal muscle wasting, cardio-respiratory abnormalities and cognitive impairments. In addition, X-linked muscular dystrophy is also characterized by secondary effects on a variety of organ systems including the liver. Proteome-wide changes in liver tissue were determined by comparative proteomics using the dystrophic mdx - 4cv mouse model of Duchenne muscular dystrophy. Results obtained by mass spectrometry using an Orbitrap Fusion Tribrid apparatus were analysed by systems bioinformatics, and key findings were confirmed by verification studies employing immunoblotting and immunofluorescence microscopy

    Journal: Clinical Proteomics

    Article Title: Proteomic profiling of liver tissue from the mdx-4cv mouse model of Duchenne muscular dystrophy

    doi: 10.1186/s12014-018-9212-2

    Figure Lengend Snippet: Overview of the complex multi-system pathophysiology of dystrophinopathy and proteomic workflow to analyse the mdx - 4cv liver. Duchenne muscular dystrophy is caused by primary abnormalities in dystrophin and triggers progressive skeletal muscle wasting, cardio-respiratory abnormalities and cognitive impairments. In addition, X-linked muscular dystrophy is also characterized by secondary effects on a variety of organ systems including the liver. Proteome-wide changes in liver tissue were determined by comparative proteomics using the dystrophic mdx - 4cv mouse model of Duchenne muscular dystrophy. Results obtained by mass spectrometry using an Orbitrap Fusion Tribrid apparatus were analysed by systems bioinformatics, and key findings were confirmed by verification studies employing immunoblotting and immunofluorescence microscopy

    Article Snippet: Protein profiling by label-free LC–MS/MS Progenesis QI for Proteomics software (version 3.1; Non-Linear Dynamics, a Waters company, Newcastle upon Tyne, UK) was used for the quantitative analysis of liver homogenates from wild type versus mdx -4cv mice.

    Techniques: Mass Spectrometry, Immunofluorescence, Microscopy

    Heat map of differentially expressed proteins in the mdx - 4cv liver. Shown is the clustering of significantly increased versus decreased proteins in liver tissue from the dystrophic mdx - 4cv mouse model of Duchenne muscular dystrophy, as compared to control tissues. For the identification of proteome-wide changes in the liver, protein extracts from whole tissue preparations of 6-month-old mdx - 4cv mice (n = 4; MDX-4CV 1–4) versus age-matched wild type mice (n = 4; WT 1–4) were analysed by mass spectrometry-based proteomics

    Journal: Clinical Proteomics

    Article Title: Proteomic profiling of liver tissue from the mdx-4cv mouse model of Duchenne muscular dystrophy

    doi: 10.1186/s12014-018-9212-2

    Figure Lengend Snippet: Heat map of differentially expressed proteins in the mdx - 4cv liver. Shown is the clustering of significantly increased versus decreased proteins in liver tissue from the dystrophic mdx - 4cv mouse model of Duchenne muscular dystrophy, as compared to control tissues. For the identification of proteome-wide changes in the liver, protein extracts from whole tissue preparations of 6-month-old mdx - 4cv mice (n = 4; MDX-4CV 1–4) versus age-matched wild type mice (n = 4; WT 1–4) were analysed by mass spectrometry-based proteomics

    Article Snippet: Protein profiling by label-free LC–MS/MS Progenesis QI for Proteomics software (version 3.1; Non-Linear Dynamics, a Waters company, Newcastle upon Tyne, UK) was used for the quantitative analysis of liver homogenates from wild type versus mdx -4cv mice.

    Techniques: Mouse Assay, Mass Spectrometry

    ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + proteomics distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).

    Journal: Scientific Reports

    Article Title: Combining micro-RNA and protein sequencing to detect robust biomarkers for Graves’ disease and orbitopathy

    doi: 10.1038/s41598-018-26700-1

    Figure Lengend Snippet: ( a ) Canonical correspondence analysis (CCA) plot of ‘omics-based Euclidean distances between samples and their quantitative clinical features (TSH, TRAB and FT4 levels). ( b ) Multidimensional scaling plot of miRNA + proteomics distances with superimposed hyperthyroidism status (euthyroid vs. hyperthyroid).

    Article Snippet: MS/MS spectra of peptides were used for protein inference via database searching in Spectrum Mill MS Proteomics Workbench (Rev B.04; Agilent Technologies).

    Techniques: