ltq linear ion trap Search Results


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  • 87
    Thermo Fisher ltq linear ion trap
    High throughput as a function of improved instrument performance. The <t>LTQ</t> <t>Velos</t> identified more unique peptides and proteins in a 60-minute analysis than did the LTQ XL in a 180-minute analysis of the same complex mixture (1 µg of C. elegans digest).
    Ltq Linear Ion Trap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 2303 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher finnigan ltq linear ion trap
    High throughput as a function of improved instrument performance. The <t>LTQ</t> <t>Velos</t> identified more unique peptides and proteins in a 60-minute analysis than did the LTQ XL in a 180-minute analysis of the same complex mixture (1 µg of C. elegans digest).
    Finnigan Ltq Linear Ion Trap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 54 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher ltq classic linear ion trap
    High throughput as a function of improved instrument performance. The <t>LTQ</t> <t>Velos</t> identified more unique peptides and proteins in a 60-minute analysis than did the LTQ XL in a 180-minute analysis of the same complex mixture (1 µg of C. elegans digest).
    Ltq Classic Linear Ion Trap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher ltq velos linear ion trap
    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to <t>LTQ-Velos</t> Linear ion trap with standard nano source), Facility
    Ltq Velos Linear Ion Trap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher linear ion trap ltq orbitrap
    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to <t>LTQ-Velos</t> Linear ion trap with standard nano source), Facility
    Linear Ion Trap Ltq Orbitrap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher ltq linear ion trap system
    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to <t>LTQ-Velos</t> Linear ion trap with standard nano source), Facility
    Ltq Linear Ion Trap System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Fisher Scientific ltq linear ion trap mass spectrometer
    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to <t>LTQ-Velos</t> Linear ion trap with standard nano source), Facility
    Ltq Linear Ion Trap Mass Spectrometer, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 93/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ltq linear ion trap mass spectrometer/product/Fisher Scientific
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    91
    Thermo Fisher thermo ltq velos linear ion trap mass spectrometer
    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to <t>LTQ-Velos</t> Linear ion trap with standard nano source), Facility
    Thermo Ltq Velos Linear Ion Trap Mass Spectrometer, 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
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    96
    Thermo Fisher ion trap
    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to <t>LTQ-Velos</t> Linear ion trap with standard nano source), Facility
    Ion Trap, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 388 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    High throughput as a function of improved instrument performance. The LTQ Velos identified more unique peptides and proteins in a 60-minute analysis than did the LTQ XL in a 180-minute analysis of the same complex mixture (1 µg of C. elegans digest).

    Journal: Analytical chemistry

    Article Title: A Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Improves the Analysis of Complex Protein Mixtures

    doi: 10.1021/ac901278y

    Figure Lengend Snippet: High throughput as a function of improved instrument performance. The LTQ Velos identified more unique peptides and proteins in a 60-minute analysis than did the LTQ XL in a 180-minute analysis of the same complex mixture (1 µg of C. elegans digest).

    Article Snippet: The samples were analyzed on Thermo Scientific LTQ XL linear ion trap and on LTQ Velos dual pressure cell linear ion trap mass spectrometers.

    Techniques: High Throughput Screening Assay

    The increased resolution afforded by the LTQ Velos allows isotopic resolution of small intact proteins. A: Resolution of the 15+ molecular ion of horse heart myoglobin using ultra-zoom scan. B: Theoretical isotopic distribution for this ion at 25, 000 FWHM. C: MS/MS of 15+ molecular ion recorded using zoom scan with fragments up to 8 kDa isotopically resolved. Inset: Larger fragments are resolved using ultra-zoom scan. The mass difference (in units of 1.00235 Da) between the most abundant isotopic peak and the monoisotopic peak is denoted in italics after each M r value. D: Fragmentation map of horse heart myoglobin (from the output of ProSightPC), showing 10 −8 expectation score for this match.

    Journal: Analytical chemistry

    Article Title: A Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Improves the Analysis of Complex Protein Mixtures

    doi: 10.1021/ac901278y

    Figure Lengend Snippet: The increased resolution afforded by the LTQ Velos allows isotopic resolution of small intact proteins. A: Resolution of the 15+ molecular ion of horse heart myoglobin using ultra-zoom scan. B: Theoretical isotopic distribution for this ion at 25, 000 FWHM. C: MS/MS of 15+ molecular ion recorded using zoom scan with fragments up to 8 kDa isotopically resolved. Inset: Larger fragments are resolved using ultra-zoom scan. The mass difference (in units of 1.00235 Da) between the most abundant isotopic peak and the monoisotopic peak is denoted in italics after each M r value. D: Fragmentation map of horse heart myoglobin (from the output of ProSightPC), showing 10 −8 expectation score for this match.

    Article Snippet: The samples were analyzed on Thermo Scientific LTQ XL linear ion trap and on LTQ Velos dual pressure cell linear ion trap mass spectrometers.

    Techniques: Mass Spectrometry

    Schematic representation of the Thermo Scientific LTQ Velos mass spectrometer, containing a stacked-ring ion guide (S-lens) source and a dual-pressure ion trap with differential pressure regulation.

    Journal: Analytical chemistry

    Article Title: A Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Improves the Analysis of Complex Protein Mixtures

    doi: 10.1021/ac901278y

    Figure Lengend Snippet: Schematic representation of the Thermo Scientific LTQ Velos mass spectrometer, containing a stacked-ring ion guide (S-lens) source and a dual-pressure ion trap with differential pressure regulation.

    Article Snippet: The samples were analyzed on Thermo Scientific LTQ XL linear ion trap and on LTQ Velos dual pressure cell linear ion trap mass spectrometers.

    Techniques: Mass Spectrometry

    A: Full MS scan from LTQ Velos (top) and LTQ XL (bottom) indicating greater than 10X improvement in sensitivity for the new instrument. Average observed improvement in sensitivity is 5-fold. B: Normal scan resolution for LTQ XL (top) and LTQ Velos (bottom) in full MS achieved at scan rates of 16, 000 amu/s and 33, 000 amu/s respectively.

    Journal: Analytical chemistry

    Article Title: A Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Improves the Analysis of Complex Protein Mixtures

    doi: 10.1021/ac901278y

    Figure Lengend Snippet: A: Full MS scan from LTQ Velos (top) and LTQ XL (bottom) indicating greater than 10X improvement in sensitivity for the new instrument. Average observed improvement in sensitivity is 5-fold. B: Normal scan resolution for LTQ XL (top) and LTQ Velos (bottom) in full MS achieved at scan rates of 16, 000 amu/s and 33, 000 amu/s respectively.

    Article Snippet: The samples were analyzed on Thermo Scientific LTQ XL linear ion trap and on LTQ Velos dual pressure cell linear ion trap mass spectrometers.

    Techniques: Mass Spectrometry

    Instrument scan lengths as composites of several events in MS and MSn modes on LTQ XL and LTQ Velos, calculated from a single top-ten 60 min LC-MS/MS run using 1 µg of C. elegans digest. Out of seven events, five (six for MS scan) have constant duration and two (injection time and MS/MS mass analysis time) have variable durations. The error bars represent standard deviation and reflect injection time variability for MS and MS/MS events and mass analysis time variability for MS/MS events.

    Journal: Analytical chemistry

    Article Title: A Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Improves the Analysis of Complex Protein Mixtures

    doi: 10.1021/ac901278y

    Figure Lengend Snippet: Instrument scan lengths as composites of several events in MS and MSn modes on LTQ XL and LTQ Velos, calculated from a single top-ten 60 min LC-MS/MS run using 1 µg of C. elegans digest. Out of seven events, five (six for MS scan) have constant duration and two (injection time and MS/MS mass analysis time) have variable durations. The error bars represent standard deviation and reflect injection time variability for MS and MS/MS events and mass analysis time variability for MS/MS events.

    Article Snippet: The samples were analyzed on Thermo Scientific LTQ XL linear ion trap and on LTQ Velos dual pressure cell linear ion trap mass spectrometers.

    Techniques: Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy, Injection, Standard Deviation

    A: A typical base peak LC/MS trace from 1 µg C. elegans digest recorded on LTQ Velos. Inset shows that the sampling frequency (inversely proportional to the distance between the two adjacent full MS base peaks) is ~ 2.3 times higher for LTQ Velos (inset top) than for LTQ XL (inset bottom, equivalent run). B: Running averages (100 points) for MS peak depth sampling for LTQ Velos and LTQ XL. C: Number of MS/MS events vs. estimated local signal-to-noise ratios of precursor ions. LTQ Velos spent most of the 2x extra scans sampling lower abundance precursors than LTQ XL.

    Journal: Analytical chemistry

    Article Title: A Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Improves the Analysis of Complex Protein Mixtures

    doi: 10.1021/ac901278y

    Figure Lengend Snippet: A: A typical base peak LC/MS trace from 1 µg C. elegans digest recorded on LTQ Velos. Inset shows that the sampling frequency (inversely proportional to the distance between the two adjacent full MS base peaks) is ~ 2.3 times higher for LTQ Velos (inset top) than for LTQ XL (inset bottom, equivalent run). B: Running averages (100 points) for MS peak depth sampling for LTQ Velos and LTQ XL. C: Number of MS/MS events vs. estimated local signal-to-noise ratios of precursor ions. LTQ Velos spent most of the 2x extra scans sampling lower abundance precursors than LTQ XL.

    Article Snippet: The samples were analyzed on Thermo Scientific LTQ XL linear ion trap and on LTQ Velos dual pressure cell linear ion trap mass spectrometers.

    Techniques: Liquid Chromatography with Mass Spectroscopy, Sampling, Mass Spectrometry

    Quantification of calcium-dependent regulation of phosphorylation sites of Toxoplasma invasion motor complex components. A ) Work flow to identify individual phosphorylation sites and quantitatively assess their responsiveness to calcium signals using a SILAC-based proteomics approach. A 1∶1 mixture of Triton X-100 lysates from “Heavy” (H; Arg4/Lys8)-labeled ethanol-stimulated tachyzoites or

    Journal: PLoS Pathogens

    Article Title: Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    doi: 10.1371/journal.ppat.1002222

    Figure Lengend Snippet: Quantification of calcium-dependent regulation of phosphorylation sites of Toxoplasma invasion motor complex components. A ) Work flow to identify individual phosphorylation sites and quantitatively assess their responsiveness to calcium signals using a SILAC-based proteomics approach. A 1∶1 mixture of Triton X-100 lysates from “Heavy” (H; Arg4/Lys8)-labeled ethanol-stimulated tachyzoites or "Light" (L; Arg0/Lys0)-labeled non-stimulated parasites was generated, and a TiO 2 -enriched phosphopeptide sample of H/L-labeled Toxoplasma invasion motor complexes was prepared and analysed by LC-MS/MS on an LTQ-Orbitrap instrument. Mascot and MaxQuant search engines facilitated subsequent manual identification, phosphosite localization and quantification of proteins or peptides as detailed in materials and mathods. B ) Sypro Ruby-stained SDS-PAGE separation of the relative amounts of light (lane 1) or heavy (lane 2) Triton X-100 whole protein extracts are shown. Intact tachyzoite invasion motor complexes comprising the five major components MyoA, GAP50, GAP45 and MLC1 were precipitated from a 1∶1 H/L mixture by GAP45-specific immuno-affinity chromatography (lane 3).

    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 .

    Techniques: Flow Cytometry, Labeling, Generated, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Staining, SDS Page, Affinity Chromatography

    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

    Negative ion nanoelectrospray spectra of the V. fischeri lipid A mixture. A , sample run on an LTQ XL linear ion trap mass spectrometer with spray conditions producing multiply charged ions. This spectrum highlights the diphosphorylated lipid A species. B , sample run on an LCQ Deca quadrupole ion trap instrument, where singly charged, monophosphorylated lipid A species predominate. The ion clusters tentatively labeled as “ hexaacyl ” and “ heptaacyl ” were ultimately found to contain primarily pentaacyl and hexaacyl species, respectively (see “Results”).

    Journal: The Journal of Biological Chemistry

    Article Title: The Lipid A from Vibrio fischeri Lipopolysaccharide

    doi: 10.1074/jbc.M111.239475

    Figure Lengend Snippet: Negative ion nanoelectrospray spectra of the V. fischeri lipid A mixture. A , sample run on an LTQ XL linear ion trap mass spectrometer with spray conditions producing multiply charged ions. This spectrum highlights the diphosphorylated lipid A species. B , sample run on an LCQ Deca quadrupole ion trap instrument, where singly charged, monophosphorylated lipid A species predominate. The ion clusters tentatively labeled as “ hexaacyl ” and “ heptaacyl ” were ultimately found to contain primarily pentaacyl and hexaacyl species, respectively (see “Results”).

    Article Snippet: The V. fischeri lipid A sample, dissolved in CHCl3 /CH3 OH (1:2, v/v) at a concentration of ∼0.1–0.5 μg/μl, was analyzed by static or dynamic nanoelectrospray using either a LCQDeca quadrupole ion trap or an LTQ XL linear ion trap mass spectrometer (both instruments from Thermo Scientific, San Jose, CA).

    Techniques: Mass Spectrometry, Labeling

    Comparison of samples making up each dataset. For each, on the left ( a , c , e , g ) is the principal component analysis, plotting PC1 (93–98% of variance, as indicated) against PC2 (1–5% of variance); on the right ( b , d , f , h ) are box plots showing relative molar abundance (im) values for all proteins in the indicated samples. ( a , b ) Chick LTQ. ( c , d ) Chick Velos. ( e , f ) Rat LTQ. ( g , h ) Mouse Velos.

    Journal: Scientific Data

    Article Title: Hair-bundle proteomes of avian and mammalian inner-ear utricles

    doi: 10.1038/sdata.2015.74

    Figure Lengend Snippet: Comparison of samples making up each dataset. For each, on the left ( a , c , e , g ) is the principal component analysis, plotting PC1 (93–98% of variance, as indicated) against PC2 (1–5% of variance); on the right ( b , d , f , h ) are box plots showing relative molar abundance (im) values for all proteins in the indicated samples. ( a , b ) Chick LTQ. ( c , d ) Chick Velos. ( e , f ) Rat LTQ. ( g , h ) Mouse Velos.

    Article Snippet: Peptides were separated with a Waters nanoAcquity LC system, and then delivered to an LTQ Velos linear ion trap mass spectrometer (Thermo Scientific) using electrospray ionization with a Microm Captivespray source fitted with a 20 μm taper spray tip and 1.0 kV source voltage.

    Techniques:

    MS spectra of permethylated N -linked glycans in the serum of patients with CCA compared with healthy controls, as detected using NSI-MS. Glycans released from the serum of patients with CCA and healthy controls were permethylated and analyzed. MS spectra present the predominance of the complex type and high-mannose type oligosaccharides in (A) healthy sera vs. (B) CCA sera. The glycan profiles (A vs. B) demonstrate similar glycan patterns, but they differ in their relative quantities. Glycans were detected as doubly [2+] and triply charged species [3+]. The graphical representation of monosaccharide residues are defined in the figure and are consistent with the suggested nomenclature of the Consortium for Functional Glycomics ( http://glycomics.scripps.edu/CFGnomenclature.pdf ). MS, mass spectrometry; CCA, cholangiocarcinoma; NSI-MS, nanospray ionization-linear ion trap mass spectrometry; m / z , mass/charge ratio; Glc, N-acetylglucosamine.

    Journal: Oncology Letters

    Article Title: Increased expression of the high-mannose M6N2 and NeuAc3H3N3M3N2F tri-antennary N-glycans in cholangiocarcinoma

    doi: 10.3892/ol.2017.7384

    Figure Lengend Snippet: MS spectra of permethylated N -linked glycans in the serum of patients with CCA compared with healthy controls, as detected using NSI-MS. Glycans released from the serum of patients with CCA and healthy controls were permethylated and analyzed. MS spectra present the predominance of the complex type and high-mannose type oligosaccharides in (A) healthy sera vs. (B) CCA sera. The glycan profiles (A vs. B) demonstrate similar glycan patterns, but they differ in their relative quantities. Glycans were detected as doubly [2+] and triply charged species [3+]. The graphical representation of monosaccharide residues are defined in the figure and are consistent with the suggested nomenclature of the Consortium for Functional Glycomics ( http://glycomics.scripps.edu/CFGnomenclature.pdf ). MS, mass spectrometry; CCA, cholangiocarcinoma; NSI-MS, nanospray ionization-linear ion trap mass spectrometry; m / z , mass/charge ratio; Glc, N-acetylglucosamine.

    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.).

    Techniques: Mass Spectrometry, Functional Assay, Gas Chromatography

    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.

    Journal: Data in Brief

    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

    doi: 10.1016/j.dib.2018.12.041

    Figure Lengend 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.

    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).

    Techniques: SDS Page, Mass Spectrometry, Software

    (A) UV spectra of HNOH-PhIP (solid curve) and NO-PhIP (dash curve), (B) ESI/MS/MS product ion spectra of HONH-PhIP and NO-PhIP were acquired with a triple quadrupole mass spectrometer.

    Journal: Chemical research in toxicology

    Article Title: Mass Spectrometric Characterization of 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine N-Oxidized Metabolites Bound at Cys34 of Human Serum Albumin

    doi: 10.1021/tx2003504

    Figure Lengend Snippet: (A) UV spectra of HNOH-PhIP (solid curve) and NO-PhIP (dash curve), (B) ESI/MS/MS product ion spectra of HONH-PhIP and NO-PhIP were acquired with a triple quadrupole mass spectrometer.

    Article Snippet: MS spectra were acquired with a linear quadrupole ion trap mass spectrometer (LTQ, Thermo Fisher, San Jose, CA).

    Techniques: Mass Spectrometry

    The ETD MS 2 spectrum of the K14acK23acK27me3 species from f analyzed in a parallel experiment on an LTQ-Orbitrap equipped with ETD fragmentation. The inset accurate mass error analysis of the z25 ion (−1.4 ppm for me3 versus 11.8 ppm for

    Journal:

    Article Title: High Throughput Characterization of Combinatorial Histone Codes *

    doi: 10.1074/mcp.M900238-MCP200

    Figure Lengend Snippet: The ETD MS 2 spectrum of the K14acK23acK27me3 species from f analyzed in a parallel experiment on an LTQ-Orbitrap equipped with ETD fragmentation. The inset accurate mass error analysis of the z25 ion (−1.4 ppm for me3 versus 11.8 ppm for

    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.

    Techniques: Mass Spectrometry

    Proposed bioconversion pathways derived for the selected metabolites in UHPLC-LTQ-IT-MS/MS datasets relevant to the time-correlated production of (A) quercetin, and (B) gallic acid during the fermentative bioconversion process. The inset graphs indicate the metabolite peak area plotted along the y-axis, whereas the incubation period (0, 4, and 8 days) during fermentation is plotted along the x-axis. The seven Acer species are indicated with different color codes in the inset graph.

    Journal: PLoS ONE

    Article Title: Systematic metabolic profiling and bioactivity assays for bioconversion of Aceraceae family

    doi: 10.1371/journal.pone.0198739

    Figure Lengend Snippet: Proposed bioconversion pathways derived for the selected metabolites in UHPLC-LTQ-IT-MS/MS datasets relevant to the time-correlated production of (A) quercetin, and (B) gallic acid during the fermentative bioconversion process. The inset graphs indicate the metabolite peak area plotted along the y-axis, whereas the incubation period (0, 4, and 8 days) during fermentation is plotted along the x-axis. The seven Acer species are indicated with different color codes in the inset graph.

    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).

    Techniques: Derivative Assay, Mass Spectrometry, Incubation

    (A) Partial least-square discriminant analysis (PLS-DA) score plot based on UHPLC–LTQ-IT-MS/MS datasets, (B) average antioxidant activity (2,2-diphenyl-1-picrylhydrazyl: DPPH) for seven Acer species plant extracts (different letters are indicative of statistically significant differences for observed bioactivities according to Duncan’s multiple-range test at p

    Journal: PLoS ONE

    Article Title: Systematic metabolic profiling and bioactivity assays for bioconversion of Aceraceae family

    doi: 10.1371/journal.pone.0198739

    Figure Lengend Snippet: (A) Partial least-square discriminant analysis (PLS-DA) score plot based on UHPLC–LTQ-IT-MS/MS datasets, (B) average antioxidant activity (2,2-diphenyl-1-picrylhydrazyl: DPPH) for seven Acer species plant extracts (different letters are indicative of statistically significant differences for observed bioactivities according to Duncan’s multiple-range test at p

    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).

    Techniques: Mass Spectrometry, Antioxidant Activity Assay

    (A) Principal component analysis score plot derived from UHPLC-LTQ-IT-MS/MS datasets displaying a variance between unfermented (0 day) and fermented (8 days) samples, and (B) antioxidant activity assays, where each of the five columns indicates average 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) activity for 0-, 2-, 4-, 6-, and 8-day fermented Acer extracts. TR: Acer triflorum ; PM: Acer pictum subsp. mono ; BU: Acer buergerianum ; KO: Acer komarovii ; TA: Acer tataricum ; PS: Acer pseudosieboldianum ; PI: Acer pictum ; PA: Acer palmatum ; C: control (only broth).

    Journal: PLoS ONE

    Article Title: Systematic metabolic profiling and bioactivity assays for bioconversion of Aceraceae family

    doi: 10.1371/journal.pone.0198739

    Figure Lengend Snippet: (A) Principal component analysis score plot derived from UHPLC-LTQ-IT-MS/MS datasets displaying a variance between unfermented (0 day) and fermented (8 days) samples, and (B) antioxidant activity assays, where each of the five columns indicates average 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) activity for 0-, 2-, 4-, 6-, and 8-day fermented Acer extracts. TR: Acer triflorum ; PM: Acer pictum subsp. mono ; BU: Acer buergerianum ; KO: Acer komarovii ; TA: Acer tataricum ; PS: Acer pseudosieboldianum ; PI: Acer pictum ; PA: Acer palmatum ; C: control (only broth).

    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).

    Techniques: Derivative Assay, Mass Spectrometry, Antioxidant Activity Assay, Activity Assay

    (A) Partial least-square discriminant analysis score plot based on UHPLC–LTQ-IT-MS/MS datasets, and (B) average antioxidant activity (2,2-diphenyl-1-picrylhydrazyl: DPPH), for the metabolite extracts derived from plant species belonging to the families Aceraceae, Rosaceae, and Asteraceae. The different letters are indicative of statistically significant differences for observed bioactivities according to Duncan’s multiple-range test at p

    Journal: PLoS ONE

    Article Title: Systematic metabolic profiling and bioactivity assays for bioconversion of Aceraceae family

    doi: 10.1371/journal.pone.0198739

    Figure Lengend Snippet: (A) Partial least-square discriminant analysis score plot based on UHPLC–LTQ-IT-MS/MS datasets, and (B) average antioxidant activity (2,2-diphenyl-1-picrylhydrazyl: DPPH), for the metabolite extracts derived from plant species belonging to the families Aceraceae, Rosaceae, and Asteraceae. The different letters are indicative of statistically significant differences for observed bioactivities according to Duncan’s multiple-range test at p

    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).

    Techniques: Mass Spectrometry, Antioxidant Activity Assay, Derivative Assay

    Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to LTQ-Velos Linear ion trap with standard nano source), Facility

    Journal: Journal of Chromatographic Science

    Article Title: Performance Comparisons of Nano-LC Systems, Electrospray Sources and LC–MS-MS Platforms

    doi: 10.1093/chromsci/bms255

    Figure Lengend Snippet: Comparison of the sensitivity of facilities and different mass spectrometer platforms. Using standardized data analysis, Mascot scores of data from Facility A (Agilent 1200 HPLC coupled to LTQ-Velos Linear ion trap with standard nano source), Facility

    Article Snippet: Finally, three mass spectrometers were evaluated: Bruker Daltonics HCT-Ultra PTM Discovery ion trap, Thermo Scientific LTQ-Velos Linear ion trap and Thermo Scientific LTQ-Orbitrap XL-ETD.

    Techniques: Mass Spectrometry, High Performance Liquid Chromatography