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  • 99
    Thermo Fisher q exactive mass spectrometer
    Q Exactive Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 12630 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher ltq orbitrap xl mass spectrometer
    (A) Scheme of the methods used to analyze BMSCs Proteins identification was done on an <t>orbitrap</t> <t>LTQ</t> XL with a protein threshold of 99% (FDR 0.1%) and peptide threshold of 97% (FDR 0.1%) and contained at least 2 identified peptides as parameters ( Supplementary data 1 2 ). (B) Label free quantification of immune modulators, neurotrophic and growth factors and apoptotic molecules identified in conditioned media obtained from BMSCs, spinal cord lesion (SCI) or control (non injured) using Scaffold_4.0.6.1. Label-free quantification was done on top3 of the total ion current (TIC). (BMP 1: Bone morphogenic protein 1, Cdh13: T-Cadherin, CLEC11a: C-type lectin domain family 11 member A CTGF: connective tissue growth factor, Epha 3: Ephrin A isoform 3, Epdr1: Ependymin related protein 1, FAM3C: family with sequence similarity 3, member C Gal 1: galectin 1; GAP-43: Growth associated protein 43, Ltbp: Latent TGF-beta binding protein, IgFbp 7: Insulin growth factor binding protein 7, MIF: macrophage inhibiting factor, PDGF: Platelet derived growth factor, PGF: placenta growth factor, spondin 2, SPARC, TIMP-1: Tissue inhibitor metalloproteinase 1 2).
    Ltq Orbitrap Xl Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 10916 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher ltq orbitrap velos mass spectrometer
    Extracted ion electropherograms (EIEs) of all (A) fucosylated and (B) nonfucosylated P1 (TKPREEQFN 176 STFR, IgG2) peptides enriched from 34 fmol amounts of IgG digest by CZE-ESI-MS analysis. An <t>Orbitrap</t> <t>Velos</t> mass spectrometer with an 80 cm long, 20/150 μm i.d./o.d. bare capillary was used to generate this data.
    Ltq Orbitrap Velos Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 8508 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher mass spectrometer
    Extracted ion electropherograms (EIEs) of all (A) fucosylated and (B) nonfucosylated P1 (TKPREEQFN 176 STFR, IgG2) peptides enriched from 34 fmol amounts of IgG digest by CZE-ESI-MS analysis. An <t>Orbitrap</t> <t>Velos</t> mass spectrometer with an 80 cm long, 20/150 μm i.d./o.d. bare capillary was used to generate this data.
    Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 6316 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher orbitrap fusion tribrid mass spectrometer
    Extracted ion electropherograms (EIEs) of all (A) fucosylated and (B) nonfucosylated P1 (TKPREEQFN 176 STFR, IgG2) peptides enriched from 34 fmol amounts of IgG digest by CZE-ESI-MS analysis. An <t>Orbitrap</t> <t>Velos</t> mass spectrometer with an 80 cm long, 20/150 μm i.d./o.d. bare capillary was used to generate this data.
    Orbitrap Fusion Tribrid Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2842 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher orbitrap elite mass spectrometer
    TIC chromatograms of <t>UPLC-Orbitrap-HRMS</t> of A . elaphroxylon flower extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .
    Orbitrap Elite Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 3333 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher q exactive hf mass spectrometer
    TIC chromatograms of <t>UPLC-Orbitrap-HRMS</t> of A . elaphroxylon flower extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .
    Q Exactive Hf Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1946 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher q exactive orbitrap mass spectrometer
    TIC chromatograms of <t>UPLC-Orbitrap-HRMS</t> of A . elaphroxylon flower extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .
    Q Exactive Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2578 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher ltq mass spectrometer
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 3470 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ltq linear ion trap mass spectrometer
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Ltq Linear Ion Trap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3671 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher mass spectrometric analysis
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Mass Spectrometric Analysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2436 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies mass spectrometer
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Mass Spectrometer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 2742 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher orbitrap fusion lumos mass spectrometer
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Orbitrap Fusion Lumos Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1094 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher triple quadrupole mass spectrometer
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Triple Quadrupole Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1822 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    SCIEX tripletof 5600 mass spectrometer
    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of <t>BSA</t> standards on a <t>LTQ-XL</t> instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.
    Tripletof 5600 Mass Spectrometer, supplied by SCIEX, used in various techniques. Bioz Stars score: 99/100, based on 2027 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher ltq orbitrap elite mass spectrometer
    LC-MS/MS coverage of MNSOD. ( a ) Whole cell lysates from kidney tissues were separated by SDS-PAGE and stained by Coomassie Blue (arrow indicated MNSOD). The gel image is the representative of 4 pairs of tumor and adjacent tissues used for PTMs analysis. A: adjacent; T: tumor; ( b ) CID-based sequence coverage of MNSOD. After Coomassie Blue staining, the 22 kDa protein bands corresponding to MNSOD were cut from the gel and digested, and peptides were analyzed by LC-MS/MS on <t>LTQ-Orbitrap</t> mass spectrometer (MS). The underlined amino acids (bold letters) were identified by Proteome Discoverer 1.4 (MASCOT and SEQUEST), which covered 76.13% sequence of MNSOD. Signal: the signal peptide; α: the α-helices; β: the β-sheets, subscript numbers represent original numbers; solid arrows: metal (Mn 2+ ) binding sites.
    Ltq Orbitrap Elite Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1841 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Thermo Fisher isotope ratio mass spectrometer
    LC-MS/MS coverage of MNSOD. ( a ) Whole cell lysates from kidney tissues were separated by SDS-PAGE and stained by Coomassie Blue (arrow indicated MNSOD). The gel image is the representative of 4 pairs of tumor and adjacent tissues used for PTMs analysis. A: adjacent; T: tumor; ( b ) CID-based sequence coverage of MNSOD. After Coomassie Blue staining, the 22 kDa protein bands corresponding to MNSOD were cut from the gel and digested, and peptides were analyzed by LC-MS/MS on <t>LTQ-Orbitrap</t> mass spectrometer (MS). The underlined amino acids (bold letters) were identified by Proteome Discoverer 1.4 (MASCOT and SEQUEST), which covered 76.13% sequence of MNSOD. Signal: the signal peptide; α: the α-helices; β: the β-sheets, subscript numbers represent original numbers; solid arrows: metal (Mn 2+ ) binding sites.
    Isotope Ratio Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    (A) Scheme of the methods used to analyze BMSCs Proteins identification was done on an orbitrap LTQ XL with a protein threshold of 99% (FDR 0.1%) and peptide threshold of 97% (FDR 0.1%) and contained at least 2 identified peptides as parameters ( Supplementary data 1 2 ). (B) Label free quantification of immune modulators, neurotrophic and growth factors and apoptotic molecules identified in conditioned media obtained from BMSCs, spinal cord lesion (SCI) or control (non injured) using Scaffold_4.0.6.1. Label-free quantification was done on top3 of the total ion current (TIC). (BMP 1: Bone morphogenic protein 1, Cdh13: T-Cadherin, CLEC11a: C-type lectin domain family 11 member A CTGF: connective tissue growth factor, Epha 3: Ephrin A isoform 3, Epdr1: Ependymin related protein 1, FAM3C: family with sequence similarity 3, member C Gal 1: galectin 1; GAP-43: Growth associated protein 43, Ltbp: Latent TGF-beta binding protein, IgFbp 7: Insulin growth factor binding protein 7, MIF: macrophage inhibiting factor, PDGF: Platelet derived growth factor, PGF: placenta growth factor, spondin 2, SPARC, TIMP-1: Tissue inhibitor metalloproteinase 1 2).

    Journal: Scientific Reports

    Article Title: Modulation properties of factors released by bone marrow stromal cells on activated microglia: an in vitro study

    doi: 10.1038/srep07514

    Figure Lengend Snippet: (A) Scheme of the methods used to analyze BMSCs Proteins identification was done on an orbitrap LTQ XL with a protein threshold of 99% (FDR 0.1%) and peptide threshold of 97% (FDR 0.1%) and contained at least 2 identified peptides as parameters ( Supplementary data 1 2 ). (B) Label free quantification of immune modulators, neurotrophic and growth factors and apoptotic molecules identified in conditioned media obtained from BMSCs, spinal cord lesion (SCI) or control (non injured) using Scaffold_4.0.6.1. Label-free quantification was done on top3 of the total ion current (TIC). (BMP 1: Bone morphogenic protein 1, Cdh13: T-Cadherin, CLEC11a: C-type lectin domain family 11 member A CTGF: connective tissue growth factor, Epha 3: Ephrin A isoform 3, Epdr1: Ependymin related protein 1, FAM3C: family with sequence similarity 3, member C Gal 1: galectin 1; GAP-43: Growth associated protein 43, Ltbp: Latent TGF-beta binding protein, IgFbp 7: Insulin growth factor binding protein 7, MIF: macrophage inhibiting factor, PDGF: Platelet derived growth factor, PGF: placenta growth factor, spondin 2, SPARC, TIMP-1: Tissue inhibitor metalloproteinase 1 2).

    Article Snippet: The chromatography system was coupled to a Thermo Scientific LTQ-Orbitrap XL mass spectrometer programmed to acquire in data-dependent mode.

    Techniques: Sequencing, Binding Assay, Derivative Assay

    Distributions of pp2 MCS score from the MCS-based score models for peptides with (a) all charges; (b) +1 charges; and (c) +2/+3 charges from LCQ mass spectrometer and peptides with (d) all charges; (e) +1 charges; and (f) +2/+3 charges from LTQ-Orbitrap

    Journal:

    Article Title: Monte Carlo Simulation-Based Algorithms for Analysis of Shotgun Proteomic Data

    doi: 10.1021/pr800002u

    Figure Lengend Snippet: Distributions of pp2 MCS score from the MCS-based score models for peptides with (a) all charges; (b) +1 charges; and (c) +2/+3 charges from LCQ mass spectrometer and peptides with (d) all charges; (e) +1 charges; and (f) +2/+3 charges from LTQ-Orbitrap

    Article Snippet: The digested peptides were identified by use of data-dependent LC–MS/MS on a LCQ Deca XP ion trap and a LTQ-Orbitrap mass spectrometer (ThermoFisher, San Jose, CA).

    Techniques: Mass Spectrometry

    ROC curves of pp2 MCS and pp tag from the MCS-based score models in MassMatrix along with other statistical scores from Mascot, OMSSA and X!Tandem for (a) the LCQ data set and (b) the LTQ-Orbitrap data set.

    Journal:

    Article Title: Monte Carlo Simulation-Based Algorithms for Analysis of Shotgun Proteomic Data

    doi: 10.1021/pr800002u

    Figure Lengend Snippet: ROC curves of pp2 MCS and pp tag from the MCS-based score models in MassMatrix along with other statistical scores from Mascot, OMSSA and X!Tandem for (a) the LCQ data set and (b) the LTQ-Orbitrap data set.

    Article Snippet: The digested peptides were identified by use of data-dependent LC–MS/MS on a LCQ Deca XP ion trap and a LTQ-Orbitrap mass spectrometer (ThermoFisher, San Jose, CA).

    Techniques:

    Search speed in terms of MS/MS spectra per second for MassMatrix, Mascot, OMSSA, and X!Tandem on a PC with an Intel quad core CPU (2.4 GHz) and Linux operating system. The two merged data sets from LCQ and LTQ-Orbitrap mass spectrometers were searched

    Journal:

    Article Title: Monte Carlo Simulation-Based Algorithms for Analysis of Shotgun Proteomic Data

    doi: 10.1021/pr800002u

    Figure Lengend Snippet: Search speed in terms of MS/MS spectra per second for MassMatrix, Mascot, OMSSA, and X!Tandem on a PC with an Intel quad core CPU (2.4 GHz) and Linux operating system. The two merged data sets from LCQ and LTQ-Orbitrap mass spectrometers were searched

    Article Snippet: The digested peptides were identified by use of data-dependent LC–MS/MS on a LCQ Deca XP ion trap and a LTQ-Orbitrap mass spectrometer (ThermoFisher, San Jose, CA).

    Techniques: Mass Spectrometry

    ROC curves of different score standards in MassMatrix for peptides with (a) all charges; (b) +1 charges; and (c) +2/+3 charges from LCQ mass spectrometer and peptides with (d) all charges; (e) +1 charges; and (f) +2/+3 charges from LTQ-Orbitrap mass spectrometer.

    Journal:

    Article Title: Monte Carlo Simulation-Based Algorithms for Analysis of Shotgun Proteomic Data

    doi: 10.1021/pr800002u

    Figure Lengend Snippet: ROC curves of different score standards in MassMatrix for peptides with (a) all charges; (b) +1 charges; and (c) +2/+3 charges from LCQ mass spectrometer and peptides with (d) all charges; (e) +1 charges; and (f) +2/+3 charges from LTQ-Orbitrap mass spectrometer.

    Article Snippet: The digested peptides were identified by use of data-dependent LC–MS/MS on a LCQ Deca XP ion trap and a LTQ-Orbitrap mass spectrometer (ThermoFisher, San Jose, CA).

    Techniques: Mass Spectrometry

    Distributions of pp tag score from the MCS-based score models for peptides with (a) all charges; (b) +1 charges; and (c) +2/+3 charges from LCQ mass spectrometer and peptides with (d) all charges; (e) +1 charges; and (f) +2/+3 charges from LTQ-Orbitrap

    Journal:

    Article Title: Monte Carlo Simulation-Based Algorithms for Analysis of Shotgun Proteomic Data

    doi: 10.1021/pr800002u

    Figure Lengend Snippet: Distributions of pp tag score from the MCS-based score models for peptides with (a) all charges; (b) +1 charges; and (c) +2/+3 charges from LCQ mass spectrometer and peptides with (d) all charges; (e) +1 charges; and (f) +2/+3 charges from LTQ-Orbitrap

    Article Snippet: The digested peptides were identified by use of data-dependent LC–MS/MS on a LCQ Deca XP ion trap and a LTQ-Orbitrap mass spectrometer (ThermoFisher, San Jose, CA).

    Techniques: Mass Spectrometry

    Extracted ion electropherograms (EIEs) of all (A) fucosylated and (B) nonfucosylated P1 (TKPREEQFN 176 STFR, IgG2) peptides enriched from 34 fmol amounts of IgG digest by CZE-ESI-MS analysis. An Orbitrap Velos mass spectrometer with an 80 cm long, 20/150 μm i.d./o.d. bare capillary was used to generate this data.

    Journal: Talanta

    Article Title: Sensitive and Fast Characterization of Site-specific Protein Glycosylation with Capillary Electrophoresis Coupled to Mass Spectrometry

    doi: 10.1016/j.talanta.2017.10.015

    Figure Lengend Snippet: Extracted ion electropherograms (EIEs) of all (A) fucosylated and (B) nonfucosylated P1 (TKPREEQFN 176 STFR, IgG2) peptides enriched from 34 fmol amounts of IgG digest by CZE-ESI-MS analysis. An Orbitrap Velos mass spectrometer with an 80 cm long, 20/150 μm i.d./o.d. bare capillary was used to generate this data.

    Article Snippet: An LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) was operated in positive ion mode.

    Techniques: Mass Spectrometry

    Reproducibility of CZE-ESI-MS analysis of IgG digest after enrichment on a HILIC column. A – butterfly plot of duplicate runs. B - relative abundance of the glycoforms contributing to the N 176 glycosylation site of IgG2 and the corresponding RSD value in triplicate runs on the same CZE-ESI-MS setup using an LTQ Orbitrap Velos mass spectrometer.

    Journal: Talanta

    Article Title: Sensitive and Fast Characterization of Site-specific Protein Glycosylation with Capillary Electrophoresis Coupled to Mass Spectrometry

    doi: 10.1016/j.talanta.2017.10.015

    Figure Lengend Snippet: Reproducibility of CZE-ESI-MS analysis of IgG digest after enrichment on a HILIC column. A – butterfly plot of duplicate runs. B - relative abundance of the glycoforms contributing to the N 176 glycosylation site of IgG2 and the corresponding RSD value in triplicate runs on the same CZE-ESI-MS setup using an LTQ Orbitrap Velos mass spectrometer.

    Article Snippet: An LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) was operated in positive ion mode.

    Techniques: Mass Spectrometry, Hydrophilic Interaction Liquid Chromatography

    S/N ratio of IgG2 glycopeptides in CZE-ESI-MS versus nanoLC-ESI-MS analysis. The same LTQ Orbitrap Velos mass spectrometer was employed in both setups. Assigned glycoforms are presented with TKPREEQFN 176 STFR backbone. Equal injection amounts of analyte were used for CZE and nanoLC analysis. Errorbars are standard deviations (n=3).

    Journal: Talanta

    Article Title: Sensitive and Fast Characterization of Site-specific Protein Glycosylation with Capillary Electrophoresis Coupled to Mass Spectrometry

    doi: 10.1016/j.talanta.2017.10.015

    Figure Lengend Snippet: S/N ratio of IgG2 glycopeptides in CZE-ESI-MS versus nanoLC-ESI-MS analysis. The same LTQ Orbitrap Velos mass spectrometer was employed in both setups. Assigned glycoforms are presented with TKPREEQFN 176 STFR backbone. Equal injection amounts of analyte were used for CZE and nanoLC analysis. Errorbars are standard deviations (n=3).

    Article Snippet: An LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) was operated in positive ion mode.

    Techniques: Mass Spectrometry, Injection

    CZE-ESI-MS analysis of glycopeptides generated from IgG tryptic digest. Glycosylated peptides were enriched with a HILIC column, separated in an 80 cm long, 20/150 μm i.d./o.d. uncoated capillary, and detected with an LTQ Orbitrap Velos mass spectrometer. For this separation, 30 kV was applied at the injection end of capillary and 1.8 kV was applied at the sheath buffer reservoir. A - Base peak electropherograms. B - Summed MS spectra of terminally agalactosylated peptides (a) migrating at 13.53–13.68 min, monogalactosylated peptides (b) migrating at 13.68–13.83 min, digalactosylated peptides (c) migrating at 13.83–13.98 min, and monosialylated peptides (d) migrating at 15.33–15.54 min. Symbols: N-Acetylglucosamine, Mannose, Galactose, Sialic acid, Fucose

    Journal: Talanta

    Article Title: Sensitive and Fast Characterization of Site-specific Protein Glycosylation with Capillary Electrophoresis Coupled to Mass Spectrometry

    doi: 10.1016/j.talanta.2017.10.015

    Figure Lengend Snippet: CZE-ESI-MS analysis of glycopeptides generated from IgG tryptic digest. Glycosylated peptides were enriched with a HILIC column, separated in an 80 cm long, 20/150 μm i.d./o.d. uncoated capillary, and detected with an LTQ Orbitrap Velos mass spectrometer. For this separation, 30 kV was applied at the injection end of capillary and 1.8 kV was applied at the sheath buffer reservoir. A - Base peak electropherograms. B - Summed MS spectra of terminally agalactosylated peptides (a) migrating at 13.53–13.68 min, monogalactosylated peptides (b) migrating at 13.68–13.83 min, digalactosylated peptides (c) migrating at 13.83–13.98 min, and monosialylated peptides (d) migrating at 15.33–15.54 min. Symbols: N-Acetylglucosamine, Mannose, Galactose, Sialic acid, Fucose

    Article Snippet: An LTQ Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) was operated in positive ion mode.

    Techniques: Mass Spectrometry, Generated, Hydrophilic Interaction Liquid Chromatography, Injection

    TIC chromatograms of UPLC-Orbitrap-HRMS of A . elaphroxylon flower extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .

    Journal: PLoS ONE

    Article Title: Metabolic profile and hepatoprotective effect of Aeschynomene elaphroxylon (Guill. Perr.)

    doi: 10.1371/journal.pone.0210576

    Figure Lengend Snippet: TIC chromatograms of UPLC-Orbitrap-HRMS of A . elaphroxylon flower extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .

    Article Snippet: UPLC-Orbitrap- HRMS analysis Both negative and positive high resolution ESI modes and collision induced dissociation (CID) MSn spectra were obtained from an Orbitrap Elite mass spectrometer (Thermo Fischer Scientific, Darmstadt, Germany) equipped with a heated electronspray ion source adjusted at 3 kV and 4 kV in negative and positive modes, respectively, capillary voltage of 300°C, source heater temperature of 250°C, FTMS resolution of 30.000.

    Techniques:

    TIC chromatograms of UPLC-Orbitrap-HRMS of A . elaphroxylon bark extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .

    Journal: PLoS ONE

    Article Title: Metabolic profile and hepatoprotective effect of Aeschynomene elaphroxylon (Guill. Perr.)

    doi: 10.1371/journal.pone.0210576

    Figure Lengend Snippet: TIC chromatograms of UPLC-Orbitrap-HRMS of A . elaphroxylon bark extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .

    Article Snippet: UPLC-Orbitrap- HRMS analysis Both negative and positive high resolution ESI modes and collision induced dissociation (CID) MSn spectra were obtained from an Orbitrap Elite mass spectrometer (Thermo Fischer Scientific, Darmstadt, Germany) equipped with a heated electronspray ion source adjusted at 3 kV and 4 kV in negative and positive modes, respectively, capillary voltage of 300°C, source heater temperature of 250°C, FTMS resolution of 30.000.

    Techniques:

    TIC chromatograms of UPLC-Orbitrap-HRMS of A . elaphroxylon leaf extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .

    Journal: PLoS ONE

    Article Title: Metabolic profile and hepatoprotective effect of Aeschynomene elaphroxylon (Guill. Perr.)

    doi: 10.1371/journal.pone.0210576

    Figure Lengend Snippet: TIC chromatograms of UPLC-Orbitrap-HRMS of A . elaphroxylon leaf extract in both negative (A) and positive (B) ion modes. Numbers refer to identified compounds listed in Table 1 .

    Article Snippet: UPLC-Orbitrap- HRMS analysis Both negative and positive high resolution ESI modes and collision induced dissociation (CID) MSn spectra were obtained from an Orbitrap Elite mass spectrometer (Thermo Fischer Scientific, Darmstadt, Germany) equipped with a heated electronspray ion source adjusted at 3 kV and 4 kV in negative and positive modes, respectively, capillary voltage of 300°C, source heater temperature of 250°C, FTMS resolution of 30.000.

    Techniques:

    Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of BSA standards on a LTQ-XL instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.

    Journal: Journal of Proteome Research

    Article Title: Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

    doi: 10.1021/pr200874e

    Figure Lengend Snippet: Quality Assessment (QA) Method for Shotgun Proteomics Data Sets We performed 902 LC-MS/MS analyses of BSA standards on a LTQ-XL instrument spanning 18 months. Experts reviewed the raw files and assigned a quality label (low or high) to each file. Pepitome identified peptides from the samples and IDPicker filtered the identifications at 2% FDR (a) Peptide and spectral identification rates from quality assessed raw files. (b) We developed an artificial neural network (ANN) for recapitulating the expert QA of a raw file from a collection of quality metrics. This figure shows the training and testing receiver operating curves when the ANN is employing different categorical collections of quality metrics as inputs.

    Article Snippet: The 1X BSA peptide mixtures were analyzed on a Thermo Fisher LTQ mass spectrometer (manufacturer serial no. LTQ20585; alias: Amigo-2) equipped with an Eksigent nanoLC and autosampler (Dublin, CA).

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    LC-MS/MS coverage of MNSOD. ( a ) Whole cell lysates from kidney tissues were separated by SDS-PAGE and stained by Coomassie Blue (arrow indicated MNSOD). The gel image is the representative of 4 pairs of tumor and adjacent tissues used for PTMs analysis. A: adjacent; T: tumor; ( b ) CID-based sequence coverage of MNSOD. After Coomassie Blue staining, the 22 kDa protein bands corresponding to MNSOD were cut from the gel and digested, and peptides were analyzed by LC-MS/MS on LTQ-Orbitrap mass spectrometer (MS). The underlined amino acids (bold letters) were identified by Proteome Discoverer 1.4 (MASCOT and SEQUEST), which covered 76.13% sequence of MNSOD. Signal: the signal peptide; α: the α-helices; β: the β-sheets, subscript numbers represent original numbers; solid arrows: metal (Mn 2+ ) binding sites.

    Journal: International Journal of Molecular Sciences

    Article Title: LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer

    doi: 10.3390/ijms18020319

    Figure Lengend Snippet: LC-MS/MS coverage of MNSOD. ( a ) Whole cell lysates from kidney tissues were separated by SDS-PAGE and stained by Coomassie Blue (arrow indicated MNSOD). The gel image is the representative of 4 pairs of tumor and adjacent tissues used for PTMs analysis. A: adjacent; T: tumor; ( b ) CID-based sequence coverage of MNSOD. After Coomassie Blue staining, the 22 kDa protein bands corresponding to MNSOD were cut from the gel and digested, and peptides were analyzed by LC-MS/MS on LTQ-Orbitrap mass spectrometer (MS). The underlined amino acids (bold letters) were identified by Proteome Discoverer 1.4 (MASCOT and SEQUEST), which covered 76.13% sequence of MNSOD. Signal: the signal peptide; α: the α-helices; β: the β-sheets, subscript numbers represent original numbers; solid arrows: metal (Mn 2+ ) binding sites.

    Article Snippet: The MS and MS/MS spectra were acquired by a LTQ-Orbitrap Elite mass spectrometer (Thermo Scientific) in a data-dependent mode, in which MS/MS fragmentation of the 20 most intense peaks were acquired for every full MS scan.

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, SDS Page, Staining, Sequencing, Binding Assay