orbitrap fusion instrument Search Results


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  • 99
    Thermo Fisher orbitrap fusion tribrid instrument
    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The <t>Orbitrap</t> image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .
    Orbitrap Fusion Tribrid Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1147 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion tribrid instrument/product/Thermo Fisher
    Average 99 stars, based on 1147 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion tribrid instrument - by Bioz Stars, 2020-05
    99/100 stars
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    93
    Thermo Fisher orbitrap fusion instrument
    Tandem MS (EThcD) of an AGP middle-down glycopeptide on an <t>Orbitrap</t> Fusion instrument (precursor m/z : 1302.4178, [M+7H] 7+ ). ETD reaction time was 8.75 msec and HCD normalized collision energy was set at 20 for this scan. C* = Carbamidomethyl Cysteine.
    Orbitrap Fusion Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 108 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion instrument/product/Thermo Fisher
    Average 93 stars, based on 108 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion instrument - by Bioz Stars, 2020-05
    93/100 stars
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    84
    Thermo Fisher instrument orbitrap fusion lumos
    MS/MS spectra of sequences generated on <t>Orbitrap</t> Fusion <t>Lumos</t> under ETD mode.
    Instrument Orbitrap Fusion Lumos, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 84/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/instrument orbitrap fusion lumos/product/Thermo Fisher
    Average 84 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    instrument orbitrap fusion lumos - by Bioz Stars, 2020-05
    84/100 stars
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    99
    Thermo Fisher orbitrap fusion lumos instrument
    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the <t>orbitrap</t> (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion <t>Lumos</t> three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash
    Orbitrap Fusion Lumos Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 168 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion lumos instrument/product/Thermo Fisher
    Average 99 stars, based on 168 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lumos instrument - by Bioz Stars, 2020-05
    99/100 stars
      Buy from Supplier

    90
    Thermo Fisher etd enabled orbitrap fusion tribrid instrument
    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the <t>orbitrap</t> (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion <t>Lumos</t> three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash
    Etd Enabled Orbitrap Fusion Tribrid Instrument, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/etd enabled orbitrap fusion tribrid instrument/product/Thermo Fisher
    Average 90 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    etd enabled orbitrap fusion tribrid instrument - by Bioz Stars, 2020-05
    90/100 stars
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    91
    Thermo Fisher orbitrap fusion lc ms ms instrumentation platform
    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the <t>orbitrap</t> (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion <t>Lumos</t> three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash
    Orbitrap Fusion Lc Ms Ms Instrumentation Platform, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion lc ms ms instrumentation platform/product/Thermo Fisher
    Average 91 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lc ms ms instrumentation platform - by Bioz Stars, 2020-05
    91/100 stars
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    Image Search Results


    Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The Orbitrap image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .

    Journal: Scientific Reports

    Article Title: Proteome-wide acetylation dynamics in human cells

    doi: 10.1038/s41598-017-09918-3

    Figure Lengend Snippet: Metabolic Labeling and Workflow. ( A ) Glucose, acetate, fatty acids, and amino acids produce acetyl-CoA for use in acetylating cytoplasmic and nuclear proteins. The thicker arrows indicate that glucose contributes more to the production of acetyl-coA that subsequently acetylates proteins, compared to acetate. ( B ) The workflow consisted of growing HeLa cells in heavy-labeled media, collecting samples at eight time points, lysing the cells, digesting the proteins, enriching for acetylated peptides, and analyzing the peptides by mass spectrometry. The Orbitrap image is adapted from Thermo Fisher Scientific 56 . The cartoon cell matter and lab equipment were slightly modified from Servier Medical Art 57 .

    Article Snippet: Acetylated peptides were then enriched using anti-acetyl-lysine antibodies and run on nano liquid chromatography coupled online with tandem mass spectrometry (nanoLC-MS/MS) on an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific), which allows for detection of isotope incorporation into acetylated proteins.

    Techniques: Labeling, Mass Spectrometry, Modification

    Proteomic analysis of tryptic peptides from (a) expressed archetype and splice variants of human OGDH E1 and (b) OGDH E1 separated from rat brain and heart mitochondria. Results are shown as PSM for the indicated peptide or the mean of peptides a and b expressed as percentages of the total E1 protein PSM and are means ± S.E.M. for three or four observations. Values of total E1 protein PSM were archetype 3571 ± 552 ( n = 4), LS1 3719 ± 552 ( n = 3), Insert 3782 ± 1961 ( n = 3), LS1/Insert 3407 ± 156 ( n = 3), rat brain OGDH E1 620 ± 126 ( n = 4) and rat heart OGDH E1 1086 ± 126 ( n = 4). All observations were obtained using an Orbitrap Fusion Tribrid mass spectrometer. The number of PSM is a measure of the amount of a peptide.

    Journal: The Biochemical journal

    Article Title: Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression

    doi: 10.1042/BCJ20160135

    Figure Lengend Snippet: Proteomic analysis of tryptic peptides from (a) expressed archetype and splice variants of human OGDH E1 and (b) OGDH E1 separated from rat brain and heart mitochondria. Results are shown as PSM for the indicated peptide or the mean of peptides a and b expressed as percentages of the total E1 protein PSM and are means ± S.E.M. for three or four observations. Values of total E1 protein PSM were archetype 3571 ± 552 ( n = 4), LS1 3719 ± 552 ( n = 3), Insert 3782 ± 1961 ( n = 3), LS1/Insert 3407 ± 156 ( n = 3), rat brain OGDH E1 620 ± 126 ( n = 4) and rat heart OGDH E1 1086 ± 126 ( n = 4). All observations were obtained using an Orbitrap Fusion Tribrid mass spectrometer. The number of PSM is a measure of the amount of a peptide.

    Article Snippet: The number of peptide spectral matches (PSM) can be used as a measure of the amount of a particular peptide [ – ]. shows the values of PSM for the various relevant peptides with mass/charge ratios in the range 300–2000 which were detected in studies using the Orbitrap Fusion Tribrid mass spectrometer on samples of expressed human archetype and the three splice variants.

    Techniques: Mass Spectrometry

    Tandem MS (EThcD) of an AGP middle-down glycopeptide on an Orbitrap Fusion instrument (precursor m/z : 1302.4178, [M+7H] 7+ ). ETD reaction time was 8.75 msec and HCD normalized collision energy was set at 20 for this scan. C* = Carbamidomethyl Cysteine.

    Journal: Journal of the American Society for Mass Spectrometry

    Article Title: Comparison of collisional and electron-based dissociation modes for middle-down analysis of multiply glycosylated peptides

    doi: 10.1007/s13361-018-1909-y

    Figure Lengend Snippet: Tandem MS (EThcD) of an AGP middle-down glycopeptide on an Orbitrap Fusion instrument (precursor m/z : 1302.4178, [M+7H] 7+ ). ETD reaction time was 8.75 msec and HCD normalized collision energy was set at 20 for this scan. C* = Carbamidomethyl Cysteine.

    Article Snippet: HCD and EThcD (Higher-energy Collisional Dissociation and Electron Transfer Dissociation supplemental collisional activation) ( – ) experiments were performed on ZIC-HILIC-enriched and unfractionated bottom-up and middle-down glycopeptide samples by LC-MS using an EASY-nLC chromatograph with an EASY-Spray C18 LC column on a Thermo Orbitrap Fusion™ instrument.

    Techniques: Mass Spectrometry

    MS/MS spectra of sequences generated on Orbitrap Fusion Lumos under ETD mode.

    Journal: EuPA Open Proteomics

    Article Title: Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search

    doi: 10.1016/j.euprot.2019.07.010

    Figure Lengend Snippet: MS/MS spectra of sequences generated on Orbitrap Fusion Lumos under ETD mode.

    Article Snippet: At the same time, we decided to analyze the sample on a different instrument – Orbitrap Fusion Lumos (Thermo Fisher) – to take advantage of multiple fragmentation modes (CID, HCD, ETD and EThcD) since we had plenty of sample left.

    Techniques: Mass Spectrometry, Generated

    MS/MS spectra of sequences generated on Orbitrap Fusion Lumos under CID mode and on Q Exactive HF-X under HCD mode.

    Journal: EuPA Open Proteomics

    Article Title: Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search

    doi: 10.1016/j.euprot.2019.07.010

    Figure Lengend Snippet: MS/MS spectra of sequences generated on Orbitrap Fusion Lumos under CID mode and on Q Exactive HF-X under HCD mode.

    Article Snippet: At the same time, we decided to analyze the sample on a different instrument – Orbitrap Fusion Lumos (Thermo Fisher) – to take advantage of multiple fragmentation modes (CID, HCD, ETD and EThcD) since we had plenty of sample left.

    Techniques: Mass Spectrometry, Generated

    Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the orbitrap (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash

    Journal: Nature Communications

    Article Title: Benchmarking common quantification strategies for large-scale phosphoproteomics

    doi: 10.1038/s41467-018-03309-6

    Figure Lengend Snippet: Evaluation of phosphorylation-optimized MS 2 - and MS 3 -based TMT methods. a Colored peaks illustrate MS n peak selection. MS 2 analysis either took place in the orbitrap (OT) or ion trap (IT). Ion selection for MS 3 analysis was based on synchronous precursor selection (SPS) or neutral loss (NL)-triggered peak isolation. In the multiple charge state (MC) method, the MS 3 isolation width was decreased for higher charge states. IT, OT and OT MC used multi-stage activation (MSA) with neutral loss mass 97.9673 Da. b Heatmap of correlation slopes of the 5% highest and lowest log2 ratios for all replicates. U2OS cells were treated 2 h with 5 µ M doxorubicin (DOX) or DMSO (C). The resulting TMT sample was measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. c Bar plot showing the total number of quantified phosphopeptide DOX vs. C ratios per method for all replicates. d Violin plot showing log 10 signal-to-noise ratio distributions of the TMT reporter ions with the median marked as a dash

    Article Snippet: Nanoflow LC tandem MS All samples were analyzed on an Easy-nLC 1000 coupled to a Q-Exactive HF instrument (Thermo Fisher Scientific; TMT MS2 of Fig. ), an Orbitrap Fusion Lumos instrument (Thermo Fisher Scientific; Figs. , , TMT MS3 of 3, , Supplementary Fig. ), or a Q-Exactive HF-X instrument (Thermo Fisher Scientific; Fig. ), all equipped with a nanoelectrospray source.

    Techniques: Mass Spectrometry, Selection, Isolation, Activation Assay

    Evaluation of quantification methods with focus on accuracy and precision. a Yeast phosphopeptides were diluted in fixed ratios 1:4:10 and added to a background of 1:1:1 HeLa phosphopeptides. Same total protein starting amounts were used for each method and SILAC ratios were mixed before digestion. All samples were measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. For SILAC and TMT, MS samples were diluted to contain a total peptide amount equal to one LFQ injection based on protein starting amount. For TMT, all mixing replicates were measured within the same TMT10-plex run. b Box plot showing yeast 4:1 and 10:1 phosphopeptide ratios for the different quantification methods and all replicates. Boxes mark the first and third quartile, with the median highlighted as dash, and whiskers marking the minimum/maximum value within 1.5 interquartile range. Outliers are not shown. Both LFQ and SILAC were tested with and without the MaxQuant feature match-between-runs (MBR), and SILAC additionally with both MBR and requantify (REQ) activated. As SILAC-MBR only results were essentially identical to SILAC only, they are not shown here. c Mean squared errors were calculated as a sum of positive bias and variance for each method and all replicates. d Receiver operating characteristic (ROC) curves were calculated by using the d-score from SAM testing as an indicator for significant regulation at 4:1 and 10:1 dilution. SAM testing for significantly regulated phosphopeptides was performed at default settings (s0 estimation automatic). ROC plots are presented as zoomed-in excerpts from the total plots, shown on the lower right each

    Journal: Nature Communications

    Article Title: Benchmarking common quantification strategies for large-scale phosphoproteomics

    doi: 10.1038/s41467-018-03309-6

    Figure Lengend Snippet: Evaluation of quantification methods with focus on accuracy and precision. a Yeast phosphopeptides were diluted in fixed ratios 1:4:10 and added to a background of 1:1:1 HeLa phosphopeptides. Same total protein starting amounts were used for each method and SILAC ratios were mixed before digestion. All samples were measured on an Orbitrap Fusion Lumos three times as technical replicates with each quantification method. For SILAC and TMT, MS samples were diluted to contain a total peptide amount equal to one LFQ injection based on protein starting amount. For TMT, all mixing replicates were measured within the same TMT10-plex run. b Box plot showing yeast 4:1 and 10:1 phosphopeptide ratios for the different quantification methods and all replicates. Boxes mark the first and third quartile, with the median highlighted as dash, and whiskers marking the minimum/maximum value within 1.5 interquartile range. Outliers are not shown. Both LFQ and SILAC were tested with and without the MaxQuant feature match-between-runs (MBR), and SILAC additionally with both MBR and requantify (REQ) activated. As SILAC-MBR only results were essentially identical to SILAC only, they are not shown here. c Mean squared errors were calculated as a sum of positive bias and variance for each method and all replicates. d Receiver operating characteristic (ROC) curves were calculated by using the d-score from SAM testing as an indicator for significant regulation at 4:1 and 10:1 dilution. SAM testing for significantly regulated phosphopeptides was performed at default settings (s0 estimation automatic). ROC plots are presented as zoomed-in excerpts from the total plots, shown on the lower right each

    Article Snippet: Nanoflow LC tandem MS All samples were analyzed on an Easy-nLC 1000 coupled to a Q-Exactive HF instrument (Thermo Fisher Scientific; TMT MS2 of Fig. ), an Orbitrap Fusion Lumos instrument (Thermo Fisher Scientific; Figs. , , TMT MS3 of 3, , Supplementary Fig. ), or a Q-Exactive HF-X instrument (Thermo Fisher Scientific; Fig. ), all equipped with a nanoelectrospray source.

    Techniques: Mass Spectrometry, Injection

    Evaluation of quantification methods in a biological setting. a Non- or SILAC-labeled U2OS cells were treated with 5 µ M doxorubicin (DOX), 2.5 µ M 4-nitroquinoline 1-oxide (4NQO) or DMSO (C) for 2 h before lysis. Three biological replicates were measured for all quantification methods. For MS measurement, each quantification method was given a total of 2 days instrument time (including LC overhead). SILAC samples were fractionated into ten fractions per sample on an Ultimate 3000 high-flow system, and TMT into 24 fractions total on an Ultimate 3000 micro-flow system. Samples were then measured using a 15- or 50-cm (only LFQ) column on a Q Exactive HF or Orbitrap Fusion Lumos (only TMT MS 3 OT MC). For SILAC and TMT, MS samples were injected without dilution, so that each labeling channel resembles one LFQ injection. b Bar plot showing total numbers of identified and quantified phosphopeptides for all replicates of each quantification method, respectively. Calculations of ratios were performed within biological replicates and filtered for measurement in a minimum of one, two or three replicates, and > 75% confident phosphorylation site localization. For further analysis, ratios quantified in all three replicates only and with a localization probability of at least 75% (black arrows) were used. c SAM-based identification of significantly regulated phosphorylation sites was performed with two sample paired t- test and standard settings (s0 estimation automatic, delta estimation based on FDR = 0.20). Significantly regulated phosphorylation sites (sig) are highlighted in red, non-significant sites in gray. Applied s0 and delta values, as well as the total number of tested phosphorylation sites ( n ) are shown. For LFQ and SILAC nearest neighbor imputation (IMP), phosphorylation sites quantified in at least one replicate and with a localization probability of at least 75% were used. d , e The bar plots show the number of significantly regulated phosphorylation sites for each quantification method d in total, and e as a fraction relative to the total number of tested sites. f , g The Venn diagrams show the overlap of SAM-regulated phosphorylation sites identified f in total, and g for commonly identified sites

    Journal: Nature Communications

    Article Title: Benchmarking common quantification strategies for large-scale phosphoproteomics

    doi: 10.1038/s41467-018-03309-6

    Figure Lengend Snippet: Evaluation of quantification methods in a biological setting. a Non- or SILAC-labeled U2OS cells were treated with 5 µ M doxorubicin (DOX), 2.5 µ M 4-nitroquinoline 1-oxide (4NQO) or DMSO (C) for 2 h before lysis. Three biological replicates were measured for all quantification methods. For MS measurement, each quantification method was given a total of 2 days instrument time (including LC overhead). SILAC samples were fractionated into ten fractions per sample on an Ultimate 3000 high-flow system, and TMT into 24 fractions total on an Ultimate 3000 micro-flow system. Samples were then measured using a 15- or 50-cm (only LFQ) column on a Q Exactive HF or Orbitrap Fusion Lumos (only TMT MS 3 OT MC). For SILAC and TMT, MS samples were injected without dilution, so that each labeling channel resembles one LFQ injection. b Bar plot showing total numbers of identified and quantified phosphopeptides for all replicates of each quantification method, respectively. Calculations of ratios were performed within biological replicates and filtered for measurement in a minimum of one, two or three replicates, and > 75% confident phosphorylation site localization. For further analysis, ratios quantified in all three replicates only and with a localization probability of at least 75% (black arrows) were used. c SAM-based identification of significantly regulated phosphorylation sites was performed with two sample paired t- test and standard settings (s0 estimation automatic, delta estimation based on FDR = 0.20). Significantly regulated phosphorylation sites (sig) are highlighted in red, non-significant sites in gray. Applied s0 and delta values, as well as the total number of tested phosphorylation sites ( n ) are shown. For LFQ and SILAC nearest neighbor imputation (IMP), phosphorylation sites quantified in at least one replicate and with a localization probability of at least 75% were used. d , e The bar plots show the number of significantly regulated phosphorylation sites for each quantification method d in total, and e as a fraction relative to the total number of tested sites. f , g The Venn diagrams show the overlap of SAM-regulated phosphorylation sites identified f in total, and g for commonly identified sites

    Article Snippet: Nanoflow LC tandem MS All samples were analyzed on an Easy-nLC 1000 coupled to a Q-Exactive HF instrument (Thermo Fisher Scientific; TMT MS2 of Fig. ), an Orbitrap Fusion Lumos instrument (Thermo Fisher Scientific; Figs. , , TMT MS3 of 3, , Supplementary Fig. ), or a Q-Exactive HF-X instrument (Thermo Fisher Scientific; Fig. ), all equipped with a nanoelectrospray source.

    Techniques: Labeling, Lysis, Mass Spectrometry, Flow Cytometry, Injection

    Gas phase segmentation (GPS) improves ADPr peptide detection. (A) A screenshot of the ADP-ribose product ion triggered EThcD and HCD data acquisition method on the Orbitrap Fusion Lumos. (B) Area under the curve (AUC) of the four ADPr fragment ions (136.06, 250.09, 348.07, and 428.04 m / z ) dissociated from an ARTD8/PARP14-MARylated STAT1 peptide using HCD. (C) Pilot Af1521 enrichment study to determine the optimal collision energy for ADP-ribose product ion screening and ADPr peptide identification. Only high confidence (HCD and EThcD combined peptides) were used in this plot (more details in Figure 3 ). (D) A schematic showing the principle of GPS using multiple injections. (E) The extracted ion chromatograms of the ADPr fragment peak (348.07 m / z ) in each full scan and GPS injection. (F,G) Precursor ion m / z and retention time of triggered EThcD spectra in full scan and combined GPS scans.

    Journal: Journal of Proteome Research

    Article Title: A Study into the ADP-Ribosylome of IFN-γ-Stimulated THP-1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-Ribosylation

    doi: 10.1021/acs.jproteome.8b00895

    Figure Lengend Snippet: Gas phase segmentation (GPS) improves ADPr peptide detection. (A) A screenshot of the ADP-ribose product ion triggered EThcD and HCD data acquisition method on the Orbitrap Fusion Lumos. (B) Area under the curve (AUC) of the four ADPr fragment ions (136.06, 250.09, 348.07, and 428.04 m / z ) dissociated from an ARTD8/PARP14-MARylated STAT1 peptide using HCD. (C) Pilot Af1521 enrichment study to determine the optimal collision energy for ADP-ribose product ion screening and ADPr peptide identification. Only high confidence (HCD and EThcD combined peptides) were used in this plot (more details in Figure 3 ). (D) A schematic showing the principle of GPS using multiple injections. (E) The extracted ion chromatograms of the ADPr fragment peak (348.07 m / z ) in each full scan and GPS injection. (F,G) Precursor ion m / z and retention time of triggered EThcD spectra in full scan and combined GPS scans.

    Article Snippet: LC–MS/MS Analysis All peptide samples were analyzed on an Orbitrap Fusion Lumos mass spectrometer fronted with an EASY-Spray Source, coupled to an Easy-nLC1000 HPLC pump (Thermo Fisher Scientific).

    Techniques: Injection