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    Thermo Fisher mass spectrometry mass spectrometry
    <t>Mass-spectrometry</t> validation of a subset of LinkPhinder predicted phosphorylations. Raw intensity values (dots) of the detected phosphorylation sites in GFP-LATS1 associated proteins under the indicated conditions (n=6 replicates), and corresponding box plots indicating median (red line), upper and lower quartile (grey box), whiskers (most extreme values not defined as outliers), and outliers (plus marks) defined as values outside 1.5 times the interquartile range.
    Mass Spectrometry Mass Spectrometry, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 4737 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mass spectrometry mass spectrometry/product/Thermo Fisher
    Average 88 stars, based on 4737 article reviews
    Price from $9.99 to $1999.99
    mass spectrometry mass spectrometry - by Bioz Stars, 2020-09
    88/100 stars

    Images

    1) Product Images from "Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs"

    Article Title: Accurate Prediction of Kinase-Substrate Networks Using Knowledge Graphs

    Journal: bioRxiv

    doi: 10.1101/865055

    Mass-spectrometry validation of a subset of LinkPhinder predicted phosphorylations. Raw intensity values (dots) of the detected phosphorylation sites in GFP-LATS1 associated proteins under the indicated conditions (n=6 replicates), and corresponding box plots indicating median (red line), upper and lower quartile (grey box), whiskers (most extreme values not defined as outliers), and outliers (plus marks) defined as values outside 1.5 times the interquartile range.
    Figure Legend Snippet: Mass-spectrometry validation of a subset of LinkPhinder predicted phosphorylations. Raw intensity values (dots) of the detected phosphorylation sites in GFP-LATS1 associated proteins under the indicated conditions (n=6 replicates), and corresponding box plots indicating median (red line), upper and lower quartile (grey box), whiskers (most extreme values not defined as outliers), and outliers (plus marks) defined as values outside 1.5 times the interquartile range.

    Techniques Used: Mass Spectrometry

    2) Product Images from "microRNA regulatory circuits in a mouse model of inherited retinal degeneration"

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration

    Journal: Scientific Reports

    doi: 10.1038/srep31431

    LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a LTQ OrbitrapXL mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.
    Figure Legend Snippet: LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a LTQ OrbitrapXL mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Mouse Assay, High Performance Liquid Chromatography, Expressing

    3) Product Images from "Potential Peripartum Markers of Infectious-Inflammatory Complications in Spontaneous Preterm Birth"

    Article Title: Potential Peripartum Markers of Infectious-Inflammatory Complications in Spontaneous Preterm Birth

    Journal: BioMed Research International

    doi: 10.1155/2015/343501

    Global and targeted quantification techniques used for the exploratory and verification phase as demonstrated on lipocalin-1 peptide GLSTESILIPR. (a) MALDI-TOF/TOF MS/MS spectra of iTRAQ-labeled peptides were used for protein identification and (b) for global quantification based on the iTRAQ reporter ions 114–117. (c) For LC-SRM verification, a library of HCD MS/MS spectra of dimethylated peptides was compiled first. SRM transitions for each peptide were then selected based on the spectral information in the library (e.g., peptide GLSTESILIPR was quantified by fragments y 9 and y 10 ). (d) For accurate quantification, intensities of LC-SRM peaks obtained on QqQ instrument were normalized against a global internal standard (GIS) prepared by reaction of the same peptides with formaldehyde-d 2 .
    Figure Legend Snippet: Global and targeted quantification techniques used for the exploratory and verification phase as demonstrated on lipocalin-1 peptide GLSTESILIPR. (a) MALDI-TOF/TOF MS/MS spectra of iTRAQ-labeled peptides were used for protein identification and (b) for global quantification based on the iTRAQ reporter ions 114–117. (c) For LC-SRM verification, a library of HCD MS/MS spectra of dimethylated peptides was compiled first. SRM transitions for each peptide were then selected based on the spectral information in the library (e.g., peptide GLSTESILIPR was quantified by fragments y 9 and y 10 ). (d) For accurate quantification, intensities of LC-SRM peaks obtained on QqQ instrument were normalized against a global internal standard (GIS) prepared by reaction of the same peptides with formaldehyde-d 2 .

    Techniques Used: Mass Spectrometry, Labeling

    4) Product Images from "Potential Peripartum Markers of Infectious-Inflammatory Complications in Spontaneous Preterm Birth"

    Article Title: Potential Peripartum Markers of Infectious-Inflammatory Complications in Spontaneous Preterm Birth

    Journal: BioMed Research International

    doi: 10.1155/2015/343501

    Global and targeted quantification techniques used for the exploratory and verification phase as demonstrated on lipocalin-1 peptide GLSTESILIPR. (a) MALDI-TOF/TOF MS/MS spectra of iTRAQ-labeled peptides were used for protein identification and (b) for global quantification based on the iTRAQ reporter ions 114–117. (c) For LC-SRM verification, a library of HCD MS/MS spectra of dimethylated peptides was compiled first. SRM transitions for each peptide were then selected based on the spectral information in the library (e.g., peptide GLSTESILIPR was quantified by fragments y 9 and y 10 ). (d) For accurate quantification, intensities of LC-SRM peaks obtained on QqQ instrument were normalized against a global internal standard (GIS) prepared by reaction of the same peptides with formaldehyde-d 2 .
    Figure Legend Snippet: Global and targeted quantification techniques used for the exploratory and verification phase as demonstrated on lipocalin-1 peptide GLSTESILIPR. (a) MALDI-TOF/TOF MS/MS spectra of iTRAQ-labeled peptides were used for protein identification and (b) for global quantification based on the iTRAQ reporter ions 114–117. (c) For LC-SRM verification, a library of HCD MS/MS spectra of dimethylated peptides was compiled first. SRM transitions for each peptide were then selected based on the spectral information in the library (e.g., peptide GLSTESILIPR was quantified by fragments y 9 and y 10 ). (d) For accurate quantification, intensities of LC-SRM peaks obtained on QqQ instrument were normalized against a global internal standard (GIS) prepared by reaction of the same peptides with formaldehyde-d 2 .

    Techniques Used: Mass Spectrometry, Labeling

    Sample processing for the exploratory iTRAQ analysis. Representative MIAC and HCA-positive and negative samples were created and processed as two duplicates. Samples were depleted from 14 high-abundance proteins and digested. Resulting peptides were iTRAQ labeled, combined, and processed according to the CysTRAQ protocol. Cysteinyl and noncysteinyl iTRAQ peptides were further fractionated using high pH reversed-phase chromatography. Eventually, each fraction was analyzed using LC-MALDI-MS/MS.
    Figure Legend Snippet: Sample processing for the exploratory iTRAQ analysis. Representative MIAC and HCA-positive and negative samples were created and processed as two duplicates. Samples were depleted from 14 high-abundance proteins and digested. Resulting peptides were iTRAQ labeled, combined, and processed according to the CysTRAQ protocol. Cysteinyl and noncysteinyl iTRAQ peptides were further fractionated using high pH reversed-phase chromatography. Eventually, each fraction was analyzed using LC-MALDI-MS/MS.

    Techniques Used: High Content Screening, Labeling, Reversed-phase Chromatography, Mass Spectrometry

    5) Product Images from "Structural and functional protein network analyses predict novel signaling functions for rhodopsin"

    Article Title: Structural and functional protein network analyses predict novel signaling functions for rhodopsin

    Journal: Molecular Systems Biology

    doi: 10.1038/msb.2011.83

    Graphical representation of experiments performed in this work and its comparison with interactions described in the literature. Protein complexes that were obtained using Rac1, RhoA, or Rac1 as the bait protein are displayed within orange, blue, and yellow circles, respectively. The Rac1 and RhoA complexes were identified by western blot, and the Rac1 complex by Orbitrap. The overlap of the three circles indicates the proteins that were identified in the same complex in one of the three experiments. Connecting lines between proteins indicate either binary or co-IP interactions from the literature, or from BN-PAGE or co-sedimentation interactions as determined in this work. Proteins are colored according to their function.
    Figure Legend Snippet: Graphical representation of experiments performed in this work and its comparison with interactions described in the literature. Protein complexes that were obtained using Rac1, RhoA, or Rac1 as the bait protein are displayed within orange, blue, and yellow circles, respectively. The Rac1 and RhoA complexes were identified by western blot, and the Rac1 complex by Orbitrap. The overlap of the three circles indicates the proteins that were identified in the same complex in one of the three experiments. Connecting lines between proteins indicate either binary or co-IP interactions from the literature, or from BN-PAGE or co-sedimentation interactions as determined in this work. Proteins are colored according to their function.

    Techniques Used: Western Blot, Co-Immunoprecipitation Assay, Polyacrylamide Gel Electrophoresis, Sedimentation

    6) Product Images from "The nuclear transport receptor TNPO1 binds macrophage immunometabolism regulator MACIR via a PY-NLS motif"

    Article Title: The nuclear transport receptor TNPO1 binds macrophage immunometabolism regulator MACIR via a PY-NLS motif

    Journal: bioRxiv

    doi: 10.1101/841999

    Proteomic analysis of MACIR binding interactions. (A) EF2 agarose pull down and elution of (i) EF1-tagged MACIR with RIPA buffer (ii) EF1-tagged MACIR with MSB (iii) EF1-tagged empty vector control with MSB (1:Input, 2:Unbound, 3-7:washes, 8-10:Eluates), probed with anti-EF1 polyclonal antibody. (B) Venn diagram of significant interactors identified with mass spectrometry in RIPA and MSB samples. (C) Top 20 MACIR interactors ranked by LFQ intensity ratio with proteins identified in MSB alone identified in yellow and in both buffers in blue.
    Figure Legend Snippet: Proteomic analysis of MACIR binding interactions. (A) EF2 agarose pull down and elution of (i) EF1-tagged MACIR with RIPA buffer (ii) EF1-tagged MACIR with MSB (iii) EF1-tagged empty vector control with MSB (1:Input, 2:Unbound, 3-7:washes, 8-10:Eluates), probed with anti-EF1 polyclonal antibody. (B) Venn diagram of significant interactors identified with mass spectrometry in RIPA and MSB samples. (C) Top 20 MACIR interactors ranked by LFQ intensity ratio with proteins identified in MSB alone identified in yellow and in both buffers in blue.

    Techniques Used: Binding Assay, Plasmid Preparation, Mass Spectrometry

    7) Product Images from "microRNA regulatory circuits in a mouse model of inherited retinal degeneration"

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration

    Journal: Scientific Reports

    doi: 10.1038/srep31431

    LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a LTQ OrbitrapXL mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.
    Figure Legend Snippet: LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a LTQ OrbitrapXL mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Mouse Assay, High Performance Liquid Chromatography, Expressing

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