ltq xl ion trap mass spectrometer  (Thermo Fisher)


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    Name:
    LTQ XL Linear Ion Trap Mass Spectrometer
    Description:
    Obtain more structural information for proteomics and metabolism applications The Thermo Scientific LTQ XL ion trap mass spectrometer offers multiple dissociation techniques PQD ETD and CID for routine structural elucidation PQD is a proprietary technique that eliminates low mass cut off concerns The result is more extensive coverage for predicted and unpredicted metabolites and the ability to perform peptide quantification using isobaric labels
    Catalog Number:
    iqlaaegaavfaczmaik
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    Applications:
    Industrial & Applied Science|Industrial Mass Spectrometry
    Category:
    Instruments and Equipment
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    Structured Review

    Thermo Fisher ltq xl ion trap mass spectrometer
    Workflow of label free quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were separated by SDS-PAGE. After trypsin digestion, the resulting peptides were analysed by <t>nanoLC-MS/MS</t> on an <t>LTQ-XL</t> linear ion trap mass spectrometer. The raw files acquired from the mass spectrometer were converted into mzXML files and searched against the rice database using the GPM software. The outputs from the GPM search were further processed using the Scrappy software package to calculate normalized spectral abundance factors. The Gene ontology (GO) annotation of differentially expressed proteins was extracted from the UniProt database and matched to the list of reproducibly identified proteins using PloGo.
    Obtain more structural information for proteomics and metabolism applications The Thermo Scientific LTQ XL ion trap mass spectrometer offers multiple dissociation techniques PQD ETD and CID for routine structural elucidation PQD is a proprietary technique that eliminates low mass cut off concerns The result is more extensive coverage for predicted and unpredicted metabolites and the ability to perform peptide quantification using isobaric labels
    https://www.bioz.com/result/ltq xl ion trap mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 156 article reviews
    Price from $9.99 to $1999.99
    ltq xl ion trap mass spectrometer - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery"

    Article Title: Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery

    Journal: Data in Brief

    doi: 10.1016/j.dib.2018.12.041

    Workflow of label free quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were separated by SDS-PAGE. After trypsin digestion, the resulting peptides were analysed by nanoLC-MS/MS on an LTQ-XL linear ion trap mass spectrometer. The raw files acquired from the mass spectrometer were converted into mzXML files and searched against the rice database using the GPM software. The outputs from the GPM search were further processed using the Scrappy software package to calculate normalized spectral abundance factors. The Gene ontology (GO) annotation of differentially expressed proteins was extracted from the UniProt database and matched to the list of reproducibly identified proteins using PloGo.
    Figure Legend Snippet: Workflow of label free quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were separated by SDS-PAGE. After trypsin digestion, the resulting peptides were analysed by nanoLC-MS/MS on an LTQ-XL linear ion trap mass spectrometer. The raw files acquired from the mass spectrometer were converted into mzXML files and searched against the rice database using the GPM software. The outputs from the GPM search were further processed using the Scrappy software package to calculate normalized spectral abundance factors. The Gene ontology (GO) annotation of differentially expressed proteins was extracted from the UniProt database and matched to the list of reproducibly identified proteins using PloGo.

    Techniques Used: SDS Page, Mass Spectrometry, Software

    2) Product Images from "Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery"

    Article Title: Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery

    Journal: Data in Brief

    doi: 10.1016/j.dib.2018.12.041

    Workflow of label free quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were separated by SDS-PAGE. After trypsin digestion, the resulting peptides were analysed by nanoLC-MS/MS on an LTQ-XL linear ion trap mass spectrometer. The raw files acquired from the mass spectrometer were converted into mzXML files and searched against the rice database using the GPM software. The outputs from the GPM search were further processed using the Scrappy software package to calculate normalized spectral abundance factors. The Gene ontology (GO) annotation of differentially expressed proteins was extracted from the UniProt database and matched to the list of reproducibly identified proteins using PloGo.
    Figure Legend Snippet: Workflow of label free quantitative shotgun proteomic analysis. Proteins extracted from rice leaves were separated by SDS-PAGE. After trypsin digestion, the resulting peptides were analysed by nanoLC-MS/MS on an LTQ-XL linear ion trap mass spectrometer. The raw files acquired from the mass spectrometer were converted into mzXML files and searched against the rice database using the GPM software. The outputs from the GPM search were further processed using the Scrappy software package to calculate normalized spectral abundance factors. The Gene ontology (GO) annotation of differentially expressed proteins was extracted from the UniProt database and matched to the list of reproducibly identified proteins using PloGo.

    Techniques Used: SDS Page, Mass Spectrometry, Software

    Related Articles

    Activation Assay:

    Article Title: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools
    Article Snippet: .. In fact, multistage activation resulted in more information for the suite of phosphopeptides studied (Table ) (see an example of the spectrum of an identified phosphorylated peptide when using SIMAC coupled to MSA in the LTQ ion Trap mass spectrometer and Mascot, Figure ). ..

    Mass Spectrometry:

    Article Title: Vaccination Targeting a Surface Sialidase of P. acnes: Implication for New Treatment of Acne Vulgaris
    Article Snippet: .. A reversed-phase LC directly coupled to a LTQ ion trap mass spectrometer (Thermo Electron, Waltham, MA) was run using a linear gradient elution from buffer A (H2 O plus 0.1% formic acid) to 50% buffer A plus 50% buffer B (acetonitrile plus 0.1% formic acid) in 100 min. ..

    Article Title: Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex
    Article Snippet: .. Individual TiO2 -bound phosphopeptide fractions were analyzed by multi-dimensional LC-MS/MS on an LTQ linear ion trap mass spectrometer (Thermo Scientific), according to published protocols . ..

    Article Title: High Throughput Characterization of Combinatorial Histone Codes *
    Article Snippet: .. Several other buffer systems for the B mobile phase were tried during method development as noted under “Results.” The column eluent was introduced into an LTQ-ETD ion trap mass spectrometer (Thermo Scientific, Waltham, MA) or an LTQ-Orbitrap XL (Thermo Scientific) (data in only) by nanoelectrospray ionization. .. Every cycle a full mass spectrum was acquired from 300 to 2000 m/z followed by narrower mass range full mass spectrum to select a given charge state of the histone for data-dependent selection.

    Article Title: Systematic metabolic profiling and bioactivity assays for bioconversion of Aceraceae family
    Article Snippet: .. UHPLC-LTQ-XL-IT-MS/MS analysis The Thermo Fischer Scientific LTQ XL linear ion trap mass spectrometry system used in the present study consisted of an electrospray interface (Thermo Fischer Scientific, San José, CA, USA) coupled with a DIONEX UltiMate 3000 RS Pump, RS Autosampler, RS Column Compartment, and RS Diode Array Detector (Dionex Corporation, Sunnyvale, CA, USA). .. The samples were separated on a Thermo Scientific Syncronis C18 UHPLC column with 1.7 μm particle size.

    Article Title: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools
    Article Snippet: .. In fact, multistage activation resulted in more information for the suite of phosphopeptides studied (Table ) (see an example of the spectrum of an identified phosphorylated peptide when using SIMAC coupled to MSA in the LTQ ion Trap mass spectrometer and Mascot, Figure ). ..

    Article Title: Ultrahigh Pressure Processing Produces Alterations in the Metabolite Profiles of Panax ginseng
    Article Snippet: .. UHPLC-LTQ-IT-MS/MS Analysis The Thermo Fisher Scientific LTQ XL ion trap mass spectrometer consisted of an electrospray interface (Thermo Fisher Scientific, San Jose, CA, USA) coupled with a DIONEX UltiMate 3000 RS Pump, RS autosampler, RS column compartment, and RS diode array detector (Dionex Corporation, Sunnyvale, CA, USA). .. Each 10 μL sample was injected into and separated on a Thermo Scientific Syncronis C18 UHPLC column (100 mm × 2.1 mm i.d.

    Article Title: Increased expression of the high-mannose M6N2 and NeuAc3H3N3M3N2F tri-antennary N-glycans in cholangiocarcinoma
    Article Snippet: .. Briefly, permethylated glycans were dissolved in 1 mM NaOH in 50% methanol and infused directly into a linear ion trap mass spectrometer (LTQ Orbitrap Discovery; Thermo Fisher Scientific, Inc., Waltham, MA, USA) using a Thermo Fisher Scientific™ nanospray ion source (Thermo Fisher Scientific, Inc.). .. MS analysis was performed in a positive ion mode and MS/MS spectra (at 28% collision energy) were obtained using the total ion mapping function of the Xcalibur software (version 2; Thermo Fisher Scientific, Inc.).

    Article Title: Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery
    Article Snippet: .. The resulting peptides were analysed by nanoflow LC-MS/MS (nanoLC-MS/MS) using a LTQ-XL ion-trap mass spectrometer (Thermo, CA, USA). ..

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    Thermo Fisher ltq etd
    Phosphosite identification by mass spectrometry. Two phoshosites were identified on human β-catenin using nano-LC coupled to a <t>LTQ/Orbitrap</t> tandem MS with either CID or <t>ETD</t> activation. GST-catenin was phosphorylated by JNK in vitro , and the reaction
    Ltq Etd, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 107 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ltq etd/product/Thermo Fisher
    Average 99 stars, based on 107 article reviews
    Price from $9.99 to $1999.99
    ltq etd - by Bioz Stars, 2020-07
    99/100 stars
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    99
    Thermo Fisher maldi linear ion trap orbitrap hybrid mass spectrometer
    Accumulation of lipid droplets and spatial distribution of different triacylglycerol (TAG) molecular species within transgenic leaf tissue. (a) 3D reconstructed z-stacks of confocal images from wild-type (left) and transgenic (right) leaf tissue. Neutral lipids including TAG, stained with BODIPY, appear as green droplets within the leaf mesophyll cells that contain visible chloroplasts (red autofluorescence). Note that non-TAG features also fluorescing green include the vascular bundle and leaf epidermis. (b) Bright-field microscopy images of wild-type (upper) and transgenic (lower) leaf cross-sections subsequently used for <t>MALDI-Orbitrap</t> imaging. Scale bars correspond to 1000 microns. (c) Ratio of TAG total ion counts (TIC; all TAG molecular species summed at each analysed position) to PC-TIC as detected by MALDI-Orbitrap imaging in wild-type (upper) and transgenic (lower) leaf cross-sections. (d) Spatial distribution of selected dominant TAG and PC species across a transgenic leaf cross-section as observed by MALDI-Orbitrap.
    Maldi Linear Ion Trap Orbitrap Hybrid Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/maldi linear ion trap orbitrap hybrid mass spectrometer/product/Thermo Fisher
    Average 99 stars, based on 65 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Phosphosite identification by mass spectrometry. Two phoshosites were identified on human β-catenin using nano-LC coupled to a LTQ/Orbitrap tandem MS with either CID or ETD activation. GST-catenin was phosphorylated by JNK in vitro , and the reaction

    Journal: The FASEB Journal

    Article Title: JNK phosphorylates ?-catenin and regulates adherens junctions

    doi: 10.1096/fj.08-117804

    Figure Lengend Snippet: Phosphosite identification by mass spectrometry. Two phoshosites were identified on human β-catenin using nano-LC coupled to a LTQ/Orbitrap tandem MS with either CID or ETD activation. GST-catenin was phosphorylated by JNK in vitro , and the reaction

    Article Snippet: A lab-made dynamic-flow nanospray ion source was employed to couple the nano-LC system to either a LTQ/ETD (Thermo LTQ XL linear ion trap coupled to an electron-transferring dissociation; Thermo, San Jose, CA, USA) for ETD analysis or a LTQ/Orbitrap (Thermo) for CID analysis.

    Techniques: Mass Spectrometry, Activation Assay, In Vitro

    The efficiency and reproducibility of the phosphopeptide purification and identification when using ~3 μg of protein kinases per each resin and/or phosphoenrichment method (SIMAC, TiO 2 and IMAC) coupled to R3/C18 and MSA-LTQ ion Trap mass spectrometer is illustrated . [A] Four triplicate experiments were carried out in order to identify the phosphopeptides. The phospho-site identifications were carried out from pooled and non-pooled assays (inter- and intra-assays) confirming a high reproducibility. The 6 phosphorylated peptides identified were isolated and validated in the four triplicate analyses, not only by Mascot (at least 4 continuously -y and -b ions matched)but also by manual inspection of all the spectra. SIMAC allowed the purification of 3 phosphorylated proteins: HuR RNA binding, p38 MAP Kinase and Trapped Ubiquitin-Like Protein Activation Complex, and 6 phosphorylated peptides related to those previously mentioned proteins. TiO 2 and IMAC allowed the isolation of 2 phoshorylated proteins: HuR RNA binding and p38 MAP Kinase, and 1 phosphopeptide related to the protein kinase HuR RNA binding. [B] SIMAC coupled to MSA allowed the identification of one more phosphopeptide compared to SIMAC coupled to DDNLMS3. Nevertheless, both strategies (SIMAC coupled to MSA and SIMAC coupled to DDNLMS3) allowed the identification of the same number of phosphorylated proteins (3). [C] and [D] Three phosphorylated proteins and six phosphopeptides were identified when using SIMAC coupled to MSA. From those three phosphoproteins identified, six phosphopeptides were identified: (a) TiO 2 coupled to MSA allowed the identification of two equal/same phosphorylated proteins and four equal/same phosphopeptides as SIMAC and (b) IMAC allowed the identification of one equal/same protein and two equal/same phosphopeptides. Thus, SIMAC is more efficient than the other tested resins for this study, while TiO 2 and IMAC corroborate the reproducibility of the phosphorylated proteins and phosphopeptides identified.

    Journal: Journal of Clinical Bioinformatics

    Article Title: Discovering and validating unknown phospho-sites from p38 and HuR protein kinases in vitro by Phosphoproteomic and Bioinformatic tools

    doi: 10.1186/2043-9113-1-16

    Figure Lengend Snippet: The efficiency and reproducibility of the phosphopeptide purification and identification when using ~3 μg of protein kinases per each resin and/or phosphoenrichment method (SIMAC, TiO 2 and IMAC) coupled to R3/C18 and MSA-LTQ ion Trap mass spectrometer is illustrated . [A] Four triplicate experiments were carried out in order to identify the phosphopeptides. The phospho-site identifications were carried out from pooled and non-pooled assays (inter- and intra-assays) confirming a high reproducibility. The 6 phosphorylated peptides identified were isolated and validated in the four triplicate analyses, not only by Mascot (at least 4 continuously -y and -b ions matched)but also by manual inspection of all the spectra. SIMAC allowed the purification of 3 phosphorylated proteins: HuR RNA binding, p38 MAP Kinase and Trapped Ubiquitin-Like Protein Activation Complex, and 6 phosphorylated peptides related to those previously mentioned proteins. TiO 2 and IMAC allowed the isolation of 2 phoshorylated proteins: HuR RNA binding and p38 MAP Kinase, and 1 phosphopeptide related to the protein kinase HuR RNA binding. [B] SIMAC coupled to MSA allowed the identification of one more phosphopeptide compared to SIMAC coupled to DDNLMS3. Nevertheless, both strategies (SIMAC coupled to MSA and SIMAC coupled to DDNLMS3) allowed the identification of the same number of phosphorylated proteins (3). [C] and [D] Three phosphorylated proteins and six phosphopeptides were identified when using SIMAC coupled to MSA. From those three phosphoproteins identified, six phosphopeptides were identified: (a) TiO 2 coupled to MSA allowed the identification of two equal/same phosphorylated proteins and four equal/same phosphopeptides as SIMAC and (b) IMAC allowed the identification of one equal/same protein and two equal/same phosphopeptides. Thus, SIMAC is more efficient than the other tested resins for this study, while TiO 2 and IMAC corroborate the reproducibility of the phosphorylated proteins and phosphopeptides identified.

    Article Snippet: In fact, multistage activation resulted in more information for the suite of phosphopeptides studied (Table ) (see an example of the spectrum of an identified phosphorylated peptide when using SIMAC coupled to MSA in the LTQ ion Trap mass spectrometer and Mascot, Figure ).

    Techniques: Purification, Mass Spectrometry, Isolation, RNA Binding Assay, Activation Assay

    Accumulation of lipid droplets and spatial distribution of different triacylglycerol (TAG) molecular species within transgenic leaf tissue. (a) 3D reconstructed z-stacks of confocal images from wild-type (left) and transgenic (right) leaf tissue. Neutral lipids including TAG, stained with BODIPY, appear as green droplets within the leaf mesophyll cells that contain visible chloroplasts (red autofluorescence). Note that non-TAG features also fluorescing green include the vascular bundle and leaf epidermis. (b) Bright-field microscopy images of wild-type (upper) and transgenic (lower) leaf cross-sections subsequently used for MALDI-Orbitrap imaging. Scale bars correspond to 1000 microns. (c) Ratio of TAG total ion counts (TIC; all TAG molecular species summed at each analysed position) to PC-TIC as detected by MALDI-Orbitrap imaging in wild-type (upper) and transgenic (lower) leaf cross-sections. (d) Spatial distribution of selected dominant TAG and PC species across a transgenic leaf cross-section as observed by MALDI-Orbitrap.

    Journal: Plant Biotechnology Journal

    Article Title: Metabolic engineering of biomass for high energy density: oilseed-like triacylglycerol yields from plant leaves

    doi: 10.1111/pbi.12131

    Figure Lengend Snippet: Accumulation of lipid droplets and spatial distribution of different triacylglycerol (TAG) molecular species within transgenic leaf tissue. (a) 3D reconstructed z-stacks of confocal images from wild-type (left) and transgenic (right) leaf tissue. Neutral lipids including TAG, stained with BODIPY, appear as green droplets within the leaf mesophyll cells that contain visible chloroplasts (red autofluorescence). Note that non-TAG features also fluorescing green include the vascular bundle and leaf epidermis. (b) Bright-field microscopy images of wild-type (upper) and transgenic (lower) leaf cross-sections subsequently used for MALDI-Orbitrap imaging. Scale bars correspond to 1000 microns. (c) Ratio of TAG total ion counts (TIC; all TAG molecular species summed at each analysed position) to PC-TIC as detected by MALDI-Orbitrap imaging in wild-type (upper) and transgenic (lower) leaf cross-sections. (d) Spatial distribution of selected dominant TAG and PC species across a transgenic leaf cross-section as observed by MALDI-Orbitrap.

    Article Snippet: Sections were scanned at 25 micron step-size in a MALDI linear ion-trap-Orbitrap hybrid mass spectrometer (MALDI LTQ Orbitrap-XL; Thermo Fisher Scientific, Bremen, Germany).

    Techniques: Transgenic Assay, Staining, Microscopy, Imaging

    Influence of the potential applied to the ESI source on retention of UDP-sugars. Chromatogram obtained with a newly installed or regenerated PGC column ( a ); chromatogram obtained after 20-min utilization of the column connected to the ESI source of an Orbitrap mass spectrometer ( b ). Conditions: column regeneration was performed with 80 % acetonitrile in water containing 0.10 % trifluoroacetic acid for 20 min, the sample measurements were done with the gradient program described in the materials and methods section for HPLC-MS; detection, UV, 262 nm; sample. UDP-Gal (100 μmol L −1 ) and UDP-Glc (100 μmol L −1 )

    Journal: Analytical and Bioanalytical Chemistry

    Article Title: Quantitative HPLC-MS analysis of nucleotide sugars in plant cells following off-line SPE sample preparation

    doi: 10.1007/s00216-014-7746-3

    Figure Lengend Snippet: Influence of the potential applied to the ESI source on retention of UDP-sugars. Chromatogram obtained with a newly installed or regenerated PGC column ( a ); chromatogram obtained after 20-min utilization of the column connected to the ESI source of an Orbitrap mass spectrometer ( b ). Conditions: column regeneration was performed with 80 % acetonitrile in water containing 0.10 % trifluoroacetic acid for 20 min, the sample measurements were done with the gradient program described in the materials and methods section for HPLC-MS; detection, UV, 262 nm; sample. UDP-Gal (100 μmol L −1 ) and UDP-Glc (100 μmol L −1 )

    Article Snippet: Fragmentation experiments were performed on a linear ion trap–Orbitrap mass spectrometer (Model LTQ Orbitrap XL, Thermo Fisher Scientific).

    Techniques: Pyrolysis Gas Chromatography, Mass Spectrometry, High Performance Liquid Chromatography, Gas Chromatography