orbitrap fusion lumos instrument  (Thermo Fisher)


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    Name:
    Orbitrap Fusion Lumos Tribrid Mass Spectrometer
    Description:
    Excel at the most challenging of applications including low level PTM analysis multiplexed relative quantitation using isobaric tags intact protein characterization as well as MSn analysis of small molecules with the new Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer This system incorporates the brightest ion source a segmented quadrupole mass filter with improved selectivity and ion transmission Advanced Vacuum Technology for improved ion transmission to the Thermo Scientific Orbitrap mass analyzer and ETD HD a higher capacity ETD fragmentation Latest innovations include the Advanced Peak Determination APD algorithm for improved data dependent experiments and two new hardware options UVPD a new fragmentation technique achieved with a 213 nm UV laser and 1M which provides 1 000 000 FWHM ultra high resolution for improved structural elucidation and quantitation of isobaric compounds
    Catalog Number:
    iqlaaegaapfadbmbhq
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    Applications:
    Industrial & Applied Science|Industrial Mass Spectrometry
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    Structured Review

    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
    Excel at the most challenging of applications including low level PTM analysis multiplexed relative quantitation using isobaric tags intact protein characterization as well as MSn analysis of small molecules with the new Thermo Scientific Orbitrap Fusion Lumos Tribrid Mass Spectrometer This system incorporates the brightest ion source a segmented quadrupole mass filter with improved selectivity and ion transmission Advanced Vacuum Technology for improved ion transmission to the Thermo Scientific Orbitrap mass analyzer and ETD HD a higher capacity ETD fragmentation Latest innovations include the Advanced Peak Determination APD algorithm for improved data dependent experiments and two new hardware options UVPD a new fragmentation technique achieved with a 213 nm UV laser and 1M which provides 1 000 000 FWHM ultra high resolution for improved structural elucidation and quantitation of isobaric compounds
    https://www.bioz.com/result/orbitrap fusion lumos instrument/product/Thermo Fisher
    Average 99 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lumos instrument - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Benchmarking common quantification strategies for large-scale phosphoproteomics"

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

    Journal: Nature Communications

    doi: 10.1038/s41467-018-03309-6

    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
    Figure Legend 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

    Techniques Used: 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
    Figure Legend 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

    Techniques Used: 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
    Figure Legend 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

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

    2) Product Images from "Proteome-Wide Evaluation of Two Common Protein Quantification Methods"

    Article Title: Proteome-Wide Evaluation of Two Common Protein Quantification Methods

    Journal: Journal of proteome research

    doi: 10.1021/acs.jproteome.8b00016

    Experimental design for comparing the ability of a label-free (LFQ) and a tandem mass tag (TMT) dependent method to quantify changes among the less abundant proteins in a proteome. Yeast lysate was spiked into human lysate to 10% of total protein concentration (1× group), 5% (2× group), and 3.3% (3× group) for a total of 11 samples so that the ratio between the first group and second was a 2-fold change, and between the first and third group was a 3-fold change. Samples for TMT were labeled with unique isobaric tags per sample, mixed, and fractionated by basic pH reversed phase HPLC (RP-HPLC). Eleven samples from LFQ and 11 fractions of the TMT set were analyzed on the same Orbitrap Fusion Lumos mass spectrometer with online RP-nHPLC separation with 3 h gradients. Data from label-free samples were processed through MaxQuant using the Andromeda search engine (including match-between-runs and the MaxLFQ algorithm). Data from the TMT fractions were processed using the SEQUEST search engine to identify peptides, and reporter ion abundances were extracted directly from associated SPS-MS3 spectra.
    Figure Legend Snippet: Experimental design for comparing the ability of a label-free (LFQ) and a tandem mass tag (TMT) dependent method to quantify changes among the less abundant proteins in a proteome. Yeast lysate was spiked into human lysate to 10% of total protein concentration (1× group), 5% (2× group), and 3.3% (3× group) for a total of 11 samples so that the ratio between the first group and second was a 2-fold change, and between the first and third group was a 3-fold change. Samples for TMT were labeled with unique isobaric tags per sample, mixed, and fractionated by basic pH reversed phase HPLC (RP-HPLC). Eleven samples from LFQ and 11 fractions of the TMT set were analyzed on the same Orbitrap Fusion Lumos mass spectrometer with online RP-nHPLC separation with 3 h gradients. Data from label-free samples were processed through MaxQuant using the Andromeda search engine (including match-between-runs and the MaxLFQ algorithm). Data from the TMT fractions were processed using the SEQUEST search engine to identify peptides, and reporter ion abundances were extracted directly from associated SPS-MS3 spectra.

    Techniques Used: Protein Concentration, Labeling, High Performance Liquid Chromatography, Mass Spectrometry

    Related Articles

    High Performance Liquid Chromatography:

    Article Title: Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication
    Article Snippet: .. Liquid chromatography mass spectrometry All mass spectrometry data was acquired in centroid mode on an Orbitrap Fusion Lumos mass spectrometer hyphenated to an easy-nLC 1200 nano HPLC system using a nanoFlex ion source (ThermoFisher Scientific) applying a spray voltage of 2.6 kV with the transfer tube heated to 300°C and a funnel RF of 30%. .. Internal mass calibration was enabled (lock mass 445.12003 m/z).

    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
    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). .. The peptides were subjected to a dual column setup: an Acclaim PepMap RSLC C18 trap column, 75 μm × 20 mm (Thermo Fisher Scientific, Cat# 164261); and an EASY-Spray LC Column, 75 μm × 250 mm (Thermo Fisher Scientific, Cat# ES802).

    Article Title: Early urine proteome changes in the Walker-256 tail-vein injection rat model
    Article Snippet: .. PRM samples were analyzed by the EASY-nLC 1200 HPLC system (Thermo Fisher Scientific, Waltham, MA) coupled to the Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific, Waltham, MA). ..

    other:

    Article Title: Quantitative Method for Assessing the Role of Lysine Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis
    Article Snippet: For DDA-MS methods used for the Orbitrap Fusion Lumos, see Supplementary Methods.

    Liquid Chromatography:

    Article Title: Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication
    Article Snippet: .. Liquid chromatography mass spectrometry All mass spectrometry data was acquired in centroid mode on an Orbitrap Fusion Lumos mass spectrometer hyphenated to an easy-nLC 1200 nano HPLC system using a nanoFlex ion source (ThermoFisher Scientific) applying a spray voltage of 2.6 kV with the transfer tube heated to 300°C and a funnel RF of 30%. .. Internal mass calibration was enabled (lock mass 445.12003 m/z).

    Mass Spectrometry:

    Article Title: Early urine proteome changes in the Walker-256 tail-vein injection rat model
    Article Snippet: .. Peptides were analyzed with an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific, Waltham, MA). .. MS data were acquired in high-sensitivity mode using the following parameters: data-dependent MS/MS scans per full scan with top-speed mode (3 s), MS scans at a resolution of 120,000 and MS/MS scans at a resolution of 30,000 in the Orbitrap, 30% HCD collision energy, charge-state screening (+2 to +7), dynamic exclusion (exclusion duration 30 s), and a maximum injection time of 45 ms .

    Article Title: Quantitative Method for Assessing the Role of Lysine Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis
    Article Snippet: .. Orbitrap Fusion Lumos MS AcquisitionFor DIA-MS analysis, a Orbitrap LUMOS Fusion mass spectrometer (Thermo Scientific) was equipped with an EasySpray ion source and connected to Ultimate 3000 nano LC system (Thermo Scientific). .. Peptides were loaded onto a PepMap RSLC C18 column (2 μm, 100 Å, 150 μm i.d. x 15 cm, Thermo) using a flow rate of 1.4 μL/min for 7 min at 1% B (mobile phase A was 0.1% formic acid in water and mobile phase B was 0.1 % formic acid in acetonitrile) after which point they were separated with a linear gradient of 5-20%B for 45 minutes, 20-35%B for 15 min, 35-85%B for 3 min, holding at 85%B for 5 minutes and re-equilibrating at 1%B for 5 minutes.

    Article Title: Increased N,N-Dimethyl Leucine Isobaric Tag Multiplexing by a Combined Precursor Isotopic Labeling and Isobaric Tagging Approach
    Article Snippet: .. Samples were analyzed by nanoLC-MS/MS using a Dionex UltiMate 3000 UPLC system coupled to a Thermo Scientific Orbitrap Fusion Lumos mass spectrometer. .. Labeled peptide samples were dried in vacuo and dissolved in 3% ACN, 0.1% formic acid in water.

    Article Title: Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication
    Article Snippet: .. Liquid chromatography mass spectrometry All mass spectrometry data was acquired in centroid mode on an Orbitrap Fusion Lumos mass spectrometer hyphenated to an easy-nLC 1200 nano HPLC system using a nanoFlex ion source (ThermoFisher Scientific) applying a spray voltage of 2.6 kV with the transfer tube heated to 300°C and a funnel RF of 30%. .. Internal mass calibration was enabled (lock mass 445.12003 m/z).

    Article Title: Targeted MultiNotch MS3 Approach for Relative Quantification of N-Glycans Using Multiplexed Carbonyl-Reactive Isobaric Tags
    Article Snippet: .. An Orbitrap Fusion Lumos Tribrid quadrupole-ion trap-Orbitrap mass spectrometer with NanoSpray Flex ion source (Thermo Scientific, Bremen, Germany) was used for data acquisition. ..

    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
    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). .. The peptides were subjected to a dual column setup: an Acclaim PepMap RSLC C18 trap column, 75 μm × 20 mm (Thermo Fisher Scientific, Cat# 164261); and an EASY-Spray LC Column, 75 μm × 250 mm (Thermo Fisher Scientific, Cat# ES802).

    Article Title: Early urine proteome changes in the Walker-256 tail-vein injection rat model
    Article Snippet: .. PRM samples were analyzed by the EASY-nLC 1200 HPLC system (Thermo Fisher Scientific, Waltham, MA) coupled to the Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific, Waltham, MA). ..

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  • 99
    Thermo Fisher orbitrap fusion lumos mass spectrometer
    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 <t>Orbitrap</t> Fusion <t>Lumos.</t> (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.
    Orbitrap Fusion Lumos Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 374 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/orbitrap fusion lumos mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 374 article reviews
    Price from $9.99 to $1999.99
    orbitrap fusion lumos mass spectrometer - by Bioz Stars, 2020-09
    99/100 stars
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    Image Search Results


    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

    Synthesized Methylated Peptides: Presence of synthesized methylated and unmodified peptides acquired on the Thermo Orbitrap Fusion Lumos with 4, 6, and 12 Dalton precursor mass windows were visualized in Skyline (A) Quantified transitions of DYSSGFGGKYGVQADR (B) Quantified transitions of DYSSGFGG K [ Me1 ]YGVQADR (C) Graphical representation of unmodified and monomethyl +2 and +3 precursors which can be differentiated from their unmodified forms using 4, 6, and 12 Dalton precursor mass windows. Black represents peptides eluting in different precursor mass windows while grey represents peptides co-eluting in the same precursor mass window.

    Journal: bioRxiv

    Article Title: Quantitative Method for Assessing the Role of Lysine Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis

    doi: 10.1101/2020.01.17.910943

    Figure Lengend Snippet: Synthesized Methylated Peptides: Presence of synthesized methylated and unmodified peptides acquired on the Thermo Orbitrap Fusion Lumos with 4, 6, and 12 Dalton precursor mass windows were visualized in Skyline (A) Quantified transitions of DYSSGFGGKYGVQADR (B) Quantified transitions of DYSSGFGG K [ Me1 ]YGVQADR (C) Graphical representation of unmodified and monomethyl +2 and +3 precursors which can be differentiated from their unmodified forms using 4, 6, and 12 Dalton precursor mass windows. Black represents peptides eluting in different precursor mass windows while grey represents peptides co-eluting in the same precursor mass window.

    Article Snippet: For DDA-MS methods used for the Orbitrap Fusion Lumos, see Supplementary Methods.

    Techniques: Synthesized, Methylation

    SIL Peptide Dilution Series: 71 SIL peptides were spiked into complex liver lysate in varying concentrations and acquired on the Thermo Orbitrap Fusion Lumos in DIA with 4da precursor mass windows (A) Distribution of points across the chromatographic peak of all endogenous peptides with a 60 minute LC gradient and (B) a 120 minute LC gradient. (C) Box plots showing the accuracy of quantitation using of a dilution series of SIL peptides in complex liver lysate acquired with different DIA acquisition methods and gradients for MS2 quantitation and (D) MS1 quantitation. (E) Heatmap corresponding to intensity of SIL peptides in dilution series with a 60 minute gradient. (F) Heatmap corresponding to intensity of SIL peptides in dilution series with a 120 minute gradient. For A/B: All data are mean ± s.e.m. of three technical replicates. For CZD: For all data, center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots; crosses represent sample means, n = 91 SIL precursors. For E/F: Color represents intensity of peptide, black represents missing data. Data is three replicates per concentration of SIL peptides.

    Journal: bioRxiv

    Article Title: Quantitative Method for Assessing the Role of Lysine Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis

    doi: 10.1101/2020.01.17.910943

    Figure Lengend Snippet: SIL Peptide Dilution Series: 71 SIL peptides were spiked into complex liver lysate in varying concentrations and acquired on the Thermo Orbitrap Fusion Lumos in DIA with 4da precursor mass windows (A) Distribution of points across the chromatographic peak of all endogenous peptides with a 60 minute LC gradient and (B) a 120 minute LC gradient. (C) Box plots showing the accuracy of quantitation using of a dilution series of SIL peptides in complex liver lysate acquired with different DIA acquisition methods and gradients for MS2 quantitation and (D) MS1 quantitation. (E) Heatmap corresponding to intensity of SIL peptides in dilution series with a 60 minute gradient. (F) Heatmap corresponding to intensity of SIL peptides in dilution series with a 120 minute gradient. For A/B: All data are mean ± s.e.m. of three technical replicates. For CZD: For all data, center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots; crosses represent sample means, n = 91 SIL precursors. For E/F: Color represents intensity of peptide, black represents missing data. Data is three replicates per concentration of SIL peptides.

    Article Snippet: For DDA-MS methods used for the Orbitrap Fusion Lumos, see Supplementary Methods.

    Techniques: Quantitation Assay, Software, Concentration Assay

    Schematic Overview of Experimental Design: (A) An equimolar pool of 400 synthesized peptides containing K[Unmodified]. K[Monomethyl]. K[Dimethyl], and K[Trimethyl] residues were acquired in DIA on the Sciex TripleTOF 6600 with 4 Dalton and 100 Variable Window (VW) precursor mass windows. (B) Same peptide pool was acquired in DIA on the Thermo Orbitrap Fusion Lumos with 4, 6, and 12 Dalton precursor mass windows. (C) Strategy to differentiate an unmodified peptide from it’s methylated form based off of precursor mass window difference. An unmodified precursor will be fragmented in a different mass window than its methylated form making it differentiable by precursor mass window.

    Journal: bioRxiv

    Article Title: Quantitative Method for Assessing the Role of Lysine Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis

    doi: 10.1101/2020.01.17.910943

    Figure Lengend Snippet: Schematic Overview of Experimental Design: (A) An equimolar pool of 400 synthesized peptides containing K[Unmodified]. K[Monomethyl]. K[Dimethyl], and K[Trimethyl] residues were acquired in DIA on the Sciex TripleTOF 6600 with 4 Dalton and 100 Variable Window (VW) precursor mass windows. (B) Same peptide pool was acquired in DIA on the Thermo Orbitrap Fusion Lumos with 4, 6, and 12 Dalton precursor mass windows. (C) Strategy to differentiate an unmodified peptide from it’s methylated form based off of precursor mass window difference. An unmodified precursor will be fragmented in a different mass window than its methylated form making it differentiable by precursor mass window.

    Article Snippet: For DDA-MS methods used for the Orbitrap Fusion Lumos, see Supplementary Methods.

    Techniques: Synthesized, Methylation

    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

    DiLeu cPILOT experimental workflow. Protein digest samples undergo stable isotope dimethyl labeling of peptide N-termini with either light [–(CH 3 ) 2 ] or heavy [–( 13 C 2 H 3 ) 2 ] dimethyl groups at low pH followed by labeling of lysine residues with 12-plex DiLeu isobaric tags at high pH. Pooled samples are analyzed by LC-MS/MS on the Orbitrap Fusion Lumos using CID MS 2 acquisition of peak pairs for peptide sequence identification and HCD SPS-MS 3 acquisition for accurate 24-plex quantification via DiLeu reporter ions.

    Journal: Analytical chemistry

    Article Title: Increased N,N-Dimethyl Leucine Isobaric Tag Multiplexing by a Combined Precursor Isotopic Labeling and Isobaric Tagging Approach

    doi: 10.1021/acs.analchem.8b01301

    Figure Lengend Snippet: DiLeu cPILOT experimental workflow. Protein digest samples undergo stable isotope dimethyl labeling of peptide N-termini with either light [–(CH 3 ) 2 ] or heavy [–( 13 C 2 H 3 ) 2 ] dimethyl groups at low pH followed by labeling of lysine residues with 12-plex DiLeu isobaric tags at high pH. Pooled samples are analyzed by LC-MS/MS on the Orbitrap Fusion Lumos using CID MS 2 acquisition of peak pairs for peptide sequence identification and HCD SPS-MS 3 acquisition for accurate 24-plex quantification via DiLeu reporter ions.

    Article Snippet: Samples were analyzed by nanoLC-MS/MS using a Dionex UltiMate 3000 UPLC system coupled to a Thermo Scientific Orbitrap Fusion Lumos mass spectrometer.

    Techniques: Labeling, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Sequencing