ltq mass spectrometer Search Results


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  • 99
    Thermo Fisher maldi ltq orbitrap mass spectrometer
    Workflow for MS imaging of Pseudonocardia on the ant propleural plate. a) Photograph and b) cartoon of Pseudonocardia on the ant exoskeleton. c) Grooves were cut into glass slides and double-sided tape was applied to the back of the slide. The ant thoraxes were removed and positioned into the groove of the slide with the propleural plate facing outward and even with the top of the slide. An additional thin strip of double-sided tape was applied below the propleural plate to stabilize and secure the thorax into place. d) Matrix was applied to the slide using an automatic sprayer. e) A laser was fired at the sample to ionize compounds of interest and introduce them into the mass spectrometer. f) An array of mass spectra was acquired using a <t>MALDI-LTQ</t> <t>Orbitrap</t> and g) compiled into MS images. Photo courtesy of Alex Wild.
    Maldi Ltq Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    maldi ltq orbitrap mass spectrometer - by Bioz Stars, 2020-04
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    99
    Thermo Fisher ltq mass spectrometer
    Mass spectrometry analysis of immunopurified protein interactors for QIL1, MIC27, MIC19, MIC25, MIC60, MTX2, DNAJC11 and GFP in 293T and/or HCT116 cells. Spectra search with Sequest, target-decoy peptide filtering, and linear discriminant analysis ( Huttlin et al., 2010 ) was performed on raw data obtained from technical duplicate runs on either an Thermo <t>LTQ</t> or a LTQ <t>Orbitrap</t> Elite mass spectrometer. Protein Assembler was used to convert spectral counts to APSMs. Peptide data (APSMs) were uploaded into the CompPASS algorithm housed within the CORE environment. Interaction confidence was ranked according to the NWD scores ( Sowa et al., 2009 ). The results obtained from the CompPASS analysis were filtered to determine proteins with a NWD score > 1 or high confidence interactors (HCIPs). HCIPs were then filtered for mitochondrial proteins based on the proteins present in Mitocarta ( Pagliarini et al., 2008 ). For the 293T data set, HCIPs with 2 or more ASPMs were included. DOI: http://dx.doi.org/10.7554/eLife.06265.005
    Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3515 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New Objective Inc ltq mass spectrometer
    Mass spectrometry analysis of immunopurified protein interactors for QIL1, MIC27, MIC19, MIC25, MIC60, MTX2, DNAJC11 and GFP in 293T and/or HCT116 cells. Spectra search with Sequest, target-decoy peptide filtering, and linear discriminant analysis ( Huttlin et al., 2010 ) was performed on raw data obtained from technical duplicate runs on either an Thermo <t>LTQ</t> or a LTQ <t>Orbitrap</t> Elite mass spectrometer. Protein Assembler was used to convert spectral counts to APSMs. Peptide data (APSMs) were uploaded into the CompPASS algorithm housed within the CORE environment. Interaction confidence was ranked according to the NWD scores ( Sowa et al., 2009 ). The results obtained from the CompPASS analysis were filtered to determine proteins with a NWD score > 1 or high confidence interactors (HCIPs). HCIPs were then filtered for mitochondrial proteins based on the proteins present in Mitocarta ( Pagliarini et al., 2008 ). For the 293T data set, HCIPs with 2 or more ASPMs were included. DOI: http://dx.doi.org/10.7554/eLife.06265.005
    Ltq Mass Spectrometer, supplied by New Objective Inc, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ltq mass spectrometer - by Bioz Stars, 2020-04
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    86
    Agilent technologies ltq mass spectrometer
    Mass spectrometry analysis of immunopurified protein interactors for QIL1, MIC27, MIC19, MIC25, MIC60, MTX2, DNAJC11 and GFP in 293T and/or HCT116 cells. Spectra search with Sequest, target-decoy peptide filtering, and linear discriminant analysis ( Huttlin et al., 2010 ) was performed on raw data obtained from technical duplicate runs on either an Thermo <t>LTQ</t> or a LTQ <t>Orbitrap</t> Elite mass spectrometer. Protein Assembler was used to convert spectral counts to APSMs. Peptide data (APSMs) were uploaded into the CompPASS algorithm housed within the CORE environment. Interaction confidence was ranked according to the NWD scores ( Sowa et al., 2009 ). The results obtained from the CompPASS analysis were filtered to determine proteins with a NWD score > 1 or high confidence interactors (HCIPs). HCIPs were then filtered for mitochondrial proteins based on the proteins present in Mitocarta ( Pagliarini et al., 2008 ). For the 293T data set, HCIPs with 2 or more ASPMs were included. DOI: http://dx.doi.org/10.7554/eLife.06265.005
    Ltq Mass Spectrometer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 86/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ltq mass spectrometer - by Bioz Stars, 2020-04
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    95
    Thermo Fisher velos ltq mass spectrometer
    Distinct peptide identification methods produce different QC metrics with similar variation. Five technical replicates of yeast lysate samples were analyzed on a Thermo Fisher <t>LTQ-Velos</t> mass spectrometer. Spectra were identified by a MyriMatch (MM) database
    Velos Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 171 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher ltq orbitrap mass spectrometer
    Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an <t>LTQ-Orbitrap</t> mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.
    Ltq Orbitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5869 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 5869 article reviews
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    ltq orbitrap mass spectrometer - by Bioz Stars, 2020-04
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    93
    Thermo Fisher finnigan ltq mass spectrometer
    Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an <t>LTQ-Orbitrap</t> mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.
    Finnigan Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 398 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    finnigan ltq mass spectrometer - by Bioz Stars, 2020-04
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    85
    Thermo Fisher ltq obitrap mass spectrometer
    Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an <t>LTQ-Orbitrap</t> mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.
    Ltq Obitrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher ltq orbitrapxl mass spectrometer
    LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a <t>LTQ</t> <t>OrbitrapXL</t> mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.
    Ltq Orbitrapxl Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 147 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher ltq orbitrapvelos mass spectrometer
    LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a <t>LTQ</t> <t>OrbitrapXL</t> mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.
    Ltq Orbitrapvelos Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 137 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher ltq obritrap mass spectrometer
    LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a <t>LTQ</t> <t>OrbitrapXL</t> mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.
    Ltq Obritrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher ltq fticr mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Ltq Fticr Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 151 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher proteomex ltq mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Proteomex Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher finniqan ltq mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Finniqan Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher ltq tandem mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Ltq Tandem Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 57 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher ltq iontrap mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Ltq Iontrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher ltq orbitrab mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Ltq Orbitrab Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher linear it ltq mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Linear It Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher ltq xltm mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Ltq Xltm Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher nesi ltq mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Nesi Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher standalone ltq mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Standalone Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher ltq deca mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
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    Thermo Fisher ltq ft ultra mass spectrometer
    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the <t>LTQ-FTICR</t> data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.
    Ltq Ft Ultra Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 521 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ltq orbitrap elite mass spectrometer
    Rationale and experimental design. A , Confirmation of Δ hik33 growth phenotype under photoautotrophic condition. The deletion of hik33 ), which also contains the photo of the cell culture. B , The WCLs of the WT and Δ hik33 strains of Synechocystis were separated into the membrane (Mem) and the soluble (Sol) fractions. Proteins extracted from either fraction and the WCL were subsequently separated by SDS-PAGE and visualized with Coomassie blue staining. C , Schematic representation of the workflow for the quantitative analysis of the Δ hik33 proteome. Total proteins were extracted from the WCLs of three biological replicates of the WT and Δ hik33 and digested with trypsin. The tryptic peptides were labeled with 6-plex TMT reagents in the order as indicated. The labeled peptides were mixed together with an equal molar ratio, and separated into 15 fractions with RP-HPLC. The peptides in each fraction were quantitatively analyzed by LC-MS/MS using a <t>LTQ-Orbitrap-Elite</t> mass spectrometer.
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    Thermo Fisher scientific ltq orbitrap mass spectrometer
    Rationale and experimental design. A , Confirmation of Δ hik33 growth phenotype under photoautotrophic condition. The deletion of hik33 ), which also contains the photo of the cell culture. B , The WCLs of the WT and Δ hik33 strains of Synechocystis were separated into the membrane (Mem) and the soluble (Sol) fractions. Proteins extracted from either fraction and the WCL were subsequently separated by SDS-PAGE and visualized with Coomassie blue staining. C , Schematic representation of the workflow for the quantitative analysis of the Δ hik33 proteome. Total proteins were extracted from the WCLs of three biological replicates of the WT and Δ hik33 and digested with trypsin. The tryptic peptides were labeled with 6-plex TMT reagents in the order as indicated. The labeled peptides were mixed together with an equal molar ratio, and separated into 15 fractions with RP-HPLC. The peptides in each fraction were quantitatively analyzed by LC-MS/MS using a <t>LTQ-Orbitrap-Elite</t> mass spectrometer.
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    Thermo Fisher ltq orbitrap discovery mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
    Ltq Orbitrap Discovery Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 390 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ltq orbitrap fusion mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
    Ltq Orbitrap Fusion Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 895 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher nanolc ltq orbitrap mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
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    Thermo Fisher ltq orbitrap discoverytm mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
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    Thermo Fisher ltq orbitrap velostm mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
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    Thermo Fisher ltq velos tandem mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
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    Thermo Fisher ltq obitrap etd mass spectrometer
    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in <t>Orbitrap.</t> B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the <t>LTQ</t> ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.
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    Image Search Results


    Workflow for MS imaging of Pseudonocardia on the ant propleural plate. a) Photograph and b) cartoon of Pseudonocardia on the ant exoskeleton. c) Grooves were cut into glass slides and double-sided tape was applied to the back of the slide. The ant thoraxes were removed and positioned into the groove of the slide with the propleural plate facing outward and even with the top of the slide. An additional thin strip of double-sided tape was applied below the propleural plate to stabilize and secure the thorax into place. d) Matrix was applied to the slide using an automatic sprayer. e) A laser was fired at the sample to ionize compounds of interest and introduce them into the mass spectrometer. f) An array of mass spectra was acquired using a MALDI-LTQ Orbitrap and g) compiled into MS images. Photo courtesy of Alex Wild.

    Journal: ACS chemical biology

    Article Title: Imaging with Mass Spectrometry of Bacteria on the Exoskeleton of Fungus-Growing Ants

    doi: 10.1021/acschembio.7b00038

    Figure Lengend Snippet: Workflow for MS imaging of Pseudonocardia on the ant propleural plate. a) Photograph and b) cartoon of Pseudonocardia on the ant exoskeleton. c) Grooves were cut into glass slides and double-sided tape was applied to the back of the slide. The ant thoraxes were removed and positioned into the groove of the slide with the propleural plate facing outward and even with the top of the slide. An additional thin strip of double-sided tape was applied below the propleural plate to stabilize and secure the thorax into place. d) Matrix was applied to the slide using an automatic sprayer. e) A laser was fired at the sample to ionize compounds of interest and introduce them into the mass spectrometer. f) An array of mass spectra was acquired using a MALDI-LTQ Orbitrap and g) compiled into MS images. Photo courtesy of Alex Wild.

    Article Snippet: A MALDI- LTQ Orbitrap mass spectrometer (Thermo Scientific) equipped with an N2 laser (spot diameter of 75 μ m) was used in positive ion mode for MSI.

    Techniques: Mass Spectrometry, Imaging, Stripping Membranes, Introduce

    Mass spectrometry analysis of immunopurified protein interactors for QIL1, MIC27, MIC19, MIC25, MIC60, MTX2, DNAJC11 and GFP in 293T and/or HCT116 cells. Spectra search with Sequest, target-decoy peptide filtering, and linear discriminant analysis ( Huttlin et al., 2010 ) was performed on raw data obtained from technical duplicate runs on either an Thermo LTQ or a LTQ Orbitrap Elite mass spectrometer. Protein Assembler was used to convert spectral counts to APSMs. Peptide data (APSMs) were uploaded into the CompPASS algorithm housed within the CORE environment. Interaction confidence was ranked according to the NWD scores ( Sowa et al., 2009 ). The results obtained from the CompPASS analysis were filtered to determine proteins with a NWD score > 1 or high confidence interactors (HCIPs). HCIPs were then filtered for mitochondrial proteins based on the proteins present in Mitocarta ( Pagliarini et al., 2008 ). For the 293T data set, HCIPs with 2 or more ASPMs were included. DOI: http://dx.doi.org/10.7554/eLife.06265.005

    Journal: eLife

    Article Title: QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology

    doi: 10.7554/eLife.06265

    Figure Lengend Snippet: Mass spectrometry analysis of immunopurified protein interactors for QIL1, MIC27, MIC19, MIC25, MIC60, MTX2, DNAJC11 and GFP in 293T and/or HCT116 cells. Spectra search with Sequest, target-decoy peptide filtering, and linear discriminant analysis ( Huttlin et al., 2010 ) was performed on raw data obtained from technical duplicate runs on either an Thermo LTQ or a LTQ Orbitrap Elite mass spectrometer. Protein Assembler was used to convert spectral counts to APSMs. Peptide data (APSMs) were uploaded into the CompPASS algorithm housed within the CORE environment. Interaction confidence was ranked according to the NWD scores ( Sowa et al., 2009 ). The results obtained from the CompPASS analysis were filtered to determine proteins with a NWD score > 1 or high confidence interactors (HCIPs). HCIPs were then filtered for mitochondrial proteins based on the proteins present in Mitocarta ( Pagliarini et al., 2008 ). For the 293T data set, HCIPs with 2 or more ASPMs were included. DOI: http://dx.doi.org/10.7554/eLife.06265.005

    Article Snippet: Samples were ran in technical duplicate on either an Thermo LTQ mass spectrometer or an LTQ-Orbitrap Elite, and spectra search with Sequest prior to target-decoy peptide filtering, and linear discriminant analysis ( ).

    Techniques: Mass Spectrometry

    Demonstrating the reproducibility of the quantitative mass spectrometric method. Biological triplicate analyses of HaCaT cells not exposed to arsenic (passage control) and HaCaT cellexposed to 0.5 ppm arsenic for 8 passages, (passage in this study means sub-culturing after confluence). Ctrl=Control (no arsenic exposure, passage control) while Ars=Arsenic exposure (0.5ppm of arsenic for up-to 8 passages). Proteins were extracted from both exposed and unexposed HaCaT cell samples. An aliquot of protein lysate from each of the 6 culture plates was collected and resolved by SDS-PAGE/Coomassie. Each of the 6 gel lanes was entirely sliced into 24 bands, subjected to trypsin digestion, and peptides were analyzed by LC-MS/MS with a Thermo LTQ-XL mass spectrometer equipped with an Eksigent nano2D-LC. Proteins were identified with Mascot (95% confidence threshold). Pearson correlation analyses were performed to test reproducibility.

    Journal: Journal of proteomics & bioinformatics

    Article Title: Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide

    doi: 10.4172/jpb.1000317

    Figure Lengend Snippet: Demonstrating the reproducibility of the quantitative mass spectrometric method. Biological triplicate analyses of HaCaT cells not exposed to arsenic (passage control) and HaCaT cellexposed to 0.5 ppm arsenic for 8 passages, (passage in this study means sub-culturing after confluence). Ctrl=Control (no arsenic exposure, passage control) while Ars=Arsenic exposure (0.5ppm of arsenic for up-to 8 passages). Proteins were extracted from both exposed and unexposed HaCaT cell samples. An aliquot of protein lysate from each of the 6 culture plates was collected and resolved by SDS-PAGE/Coomassie. Each of the 6 gel lanes was entirely sliced into 24 bands, subjected to trypsin digestion, and peptides were analyzed by LC-MS/MS with a Thermo LTQ-XL mass spectrometer equipped with an Eksigent nano2D-LC. Proteins were identified with Mascot (95% confidence threshold). Pearson correlation analyses were performed to test reproducibility.

    Article Snippet: Therefore, to reliably identify proteins perturbed by arsenic trioxide in HaCaT keratinocyte model, we have used a combination of LC-MS/MS with a Thermo LTQ-XL mass spectrometer coupled to an Eksigent nanoLC-2D [ ].

    Techniques: SDS Page, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    Calibration curves (unweighted) of nicotine and cotinine in ALI and PBS from the pre-exposure HTBECs experiments using the Velox 360 and Thermo LTQ-FT. Bars represent standard deviation of triplicate measurements at each concentration. Limit of quantitation

    Journal: Analytical methods : advancing methods and applications

    Article Title: Paper Spray Mass Spectrometry for High-Throughput Quantification of Nicotine and Cotinine

    doi: 10.1039/C7AY02204B

    Figure Lengend Snippet: Calibration curves (unweighted) of nicotine and cotinine in ALI and PBS from the pre-exposure HTBECs experiments using the Velox 360 and Thermo LTQ-FT. Bars represent standard deviation of triplicate measurements at each concentration. Limit of quantitation

    Article Snippet: PS-MS/MS experiments were performed with a Prosolia Velox 360 coupled to a Thermo Scientific LTQ-FT mass spectrometer.

    Techniques: Standard Deviation, Concentration Assay, Quantitation Assay

    Distinct peptide identification methods produce different QC metrics with similar variation. Five technical replicates of yeast lysate samples were analyzed on a Thermo Fisher LTQ-Velos mass spectrometer. Spectra were identified by a MyriMatch (MM) database

    Journal: Analytical chemistry

    Article Title: QuaMeter: Multivendor Performance Metrics for LC-MS/MS Proteomics Instrumentation

    doi: 10.1021/ac300629p

    Figure Lengend Snippet: Distinct peptide identification methods produce different QC metrics with similar variation. Five technical replicates of yeast lysate samples were analyzed on a Thermo Fisher LTQ-Velos mass spectrometer. Spectra were identified by a MyriMatch (MM) database

    Article Snippet: To evaluate this, we employed a yeast lysate LC-MS/MS data set with five technical replicates acquired on a Thermo Fisher LTQ-Velos mass spectrometer.

    Techniques: Mass Spectrometry

    Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an LTQ-Orbitrap mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.

    Journal: Open Biology

    Article Title: PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65

    doi: 10.1098/rsob.120080

    Figure Lengend Snippet: Human Parkin Ser 65 is a substrate of human PINK1 upon CCCP stimulation. ( a ) Confirmation by mass spectrometry that Ser 65 of human Parkin is phosphorylated by CCCP-induced activation of human wild-type PINK1-FLAG. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG (D384A) were co-transfected with HA-Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. Whole-cell extracts were obtained following lysis with 1% Triton and approximately 30 mg of whole-cell extract were subjected to immunoprecipitation with anti-HA-agarose and run on 10% SDS-PAGE and stained with colloidal Coomassie blue. Coomassie-stained bands migrating with the expected molecular mass of HA-Parkin were excised from the gel, digested with trypsin, and subjected to high performance liquid chromatography with tandem mass spectrometry (LC-MS-MS) on an LTQ-Orbitrap mass spectrometer. Extracted ion chromatogram analysis of Ser 131 and Ser 65 phosphopeptide (3 + R.NDWTVQNCDLDQQ S IVHIVQRPWR.K+P). The total signal intensity of the phosphopeptide is plotted on the y -axis and retention time is plotted on the x -axis. The m / z value corresponding to the Ser 131 phosphopeptide was detected in all conditions whilst that of the Ser 65 phosphopeptide was only detected in samples from wild-type PINK1-FLAG-expressing cells following CCCP treatment. ( b ) Characterization of Parkin phospho-Ser 65 antibody. Flp-In T-Rex HEK293 cells expressing FLAG-empty, wild-type PINK1-FLAG, and kinase-inactive PINK1-FLAG were co-transfected with untagged wild-type (WT) or Ser 65 Ala (S65A) mutant Parkin, induced with doxycycline and stimulated with 10 μM of CCCP for 3 h. 0.25 mg of 1% Triton whole-cell lysate were subjected to immunoprecipitation with anti-Parkin antibody (S966C) covalently coupled to protein G Sepharose and then immunoblotted with anti-phospho-Ser 65 antibody in the presence of dephosphorylated peptide. Ten per cent of the immunoprecipitate (IP) was immunoblotted with total anti-Parkin antibody. Twenty five micrograms of whole cell lysate was immunoblotted with total PINK1 antibody.

    Article Snippet: Isolated phosphopeptides were analysed by LC-MS-MS on a proxeon Easy-nLC nano liquid chromatography system coupled to a Thermo LTQ-orbitrap mass spectrometer.

    Techniques: Mass Spectrometry, Activation Assay, Expressing, Transfection, Lysis, Immunoprecipitation, SDS Page, Staining, High Performance Liquid Chromatography, Liquid Chromatography with Mass Spectroscopy, Mutagenesis

    (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

    Flowchart of the label-free quantification approach. Protein digests of lysates of IECs were prepared from six mice per time point and analyzed in duplicate on the LTQ-Orbitrap, as described in the Experimental Procedures. Raw data sets were processed

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Time-resolved Quantitative Proteome Analysis of In Vivo

    doi: 10.1074/mcp.M110.005231

    Figure Lengend Snippet: Flowchart of the label-free quantification approach. Protein digests of lysates of IECs were prepared from six mice per time point and analyzed in duplicate on the LTQ-Orbitrap, as described in the Experimental Procedures. Raw data sets were processed

    Article Snippet: Protein digests were analyzed in duplicate using a LC-ESI-MS/MS system consisting of a Rheos Allegro pump (Thermo Fisher Scientific, Waltham, MA), a PAL HTC autosampler (CTC Analytics, Zwingen, Switzerland), and an LTQ-XL Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA) equipped with a nano-ESI source from the same supplier.

    Techniques: Mouse Assay

    Merged network map showing endothelin-1-induced changes in the fetal cardiomyocyte proteome Primary fetal cardiomyocytes were treated with control or endothelin-1 (10 nM) for 24 hours. Protein expression analysis was performed in fetal cardiomyocytes by TMT-LC-MS/MS analysis with a LTQ-Orbitrap-Velos instrument. IPA pathway analysis revealed five separate sub-networks for endothelin-1-modulated proteins. Panel A depicts a merged network of all detected proteins with their subcellular distribution. Panel B is the key.

    Journal: Current topics in medicinal chemistry

    Article Title: Proteomic Analysis of Endothelin-1 Targets in the Regulation of Cardiomyocyte Proliferation

    doi: 10.2174/1568026617666161116142417

    Figure Lengend Snippet: Merged network map showing endothelin-1-induced changes in the fetal cardiomyocyte proteome Primary fetal cardiomyocytes were treated with control or endothelin-1 (10 nM) for 24 hours. Protein expression analysis was performed in fetal cardiomyocytes by TMT-LC-MS/MS analysis with a LTQ-Orbitrap-Velos instrument. IPA pathway analysis revealed five separate sub-networks for endothelin-1-modulated proteins. Panel A depicts a merged network of all detected proteins with their subcellular distribution. Panel B is the key.

    Article Snippet: Quantitation of SCX fractionated TMT-labeled peptides was performed on the Thermo LTQ-Orbitrap Pro mass spectrometer.

    Techniques: Expressing, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Indirect Immunoperoxidase Assay

    LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a LTQ OrbitrapXL mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.

    Journal: Scientific Reports

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration

    doi: 10.1038/srep31431

    Figure Lengend Snippet: LC-MS/MS retinal proteome analysis in R347 versus wt mice. Whole retina protein (n = 4) and retinal membrane protein (n = 4) extracts were prepared from one month-old R347 and wt mice. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system coupled to a LTQ OrbitrapXL mass spectrometer. ( a ) Representative LC-MS/MS profile detected in the retinal samples. ( b ) Distribution of the 1895 identified protein IDs, which were mapped to 1446 gene IDs. 1337 gene IDs were present in the GO database (GO); GO: M refers to entries with membrane in their GO search terms. ( c ) Volcano plot representation of the identified protein IDs in R347 versus wt retinas. X-axis indicates difference in expression level on a log2 scale, whereas the y-axis represents corresponding p-values (Student’s t-Test) on a negative log scale. Red lines indicate 0.5-fold and 2-fold differences in protein expression and significance level of p = 0.05, respectively. Scaling was limited to -6 and 6 on the horizontal axis and 4 on the vertical axis. Entries outside the limiting values were set to the corresponding limiting values.

    Article Snippet: LC-MS/MS analysis was carried out on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA, USA) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) .

    Techniques: Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry, Mouse Assay, High Performance Liquid Chromatography, Expressing

    Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the LTQ-FTICR data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.

    Journal: Proteomics

    Article Title: A Hierarchical MS2/MS3 Database Search Algorithm for Automated Analysis of Phosphopeptide Tandem Mass Spectra

    doi: 10.1002/pmic.200800282

    Figure Lengend Snippet: Score distributions of TPs and FPs in the hierarchical MS 2 /MS 3 searches and the searches of MS 2 data only: (a) all the peptide matches returned for the LCQ data set, (b) all the peptide matches returned for the LTQ-FTICR data set, (c) phospopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set. The score distributions for TPs were split into two groups as labeled “1” and “2”.

    Article Snippet: For high mass accuracy data collected on the LTQ-FTICR mass spectrometer, isotope distributions for the precursor ions of the MS2 spectra were deconvoluted to obtain the charges and monoisotopic m/z values of the precursor ions by use of ReAdW.

    Techniques: Mass Spectrometry, Labeling

    ROC analysis of search results from the hierarchical MS 2 /MS 3 searches in MassMatrix and two stage MS 2 /MS 3 searches in MassMatrix, Mascot and X!Tandem for a tryptic of αCasein: (a) all the peptide matches for the LCQ data set, (b) all the peptide matches for the LTQ-FTICR data set, (c) phosphopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set.

    Journal: Proteomics

    Article Title: A Hierarchical MS2/MS3 Database Search Algorithm for Automated Analysis of Phosphopeptide Tandem Mass Spectra

    doi: 10.1002/pmic.200800282

    Figure Lengend Snippet: ROC analysis of search results from the hierarchical MS 2 /MS 3 searches in MassMatrix and two stage MS 2 /MS 3 searches in MassMatrix, Mascot and X!Tandem for a tryptic of αCasein: (a) all the peptide matches for the LCQ data set, (b) all the peptide matches for the LTQ-FTICR data set, (c) phosphopeptide matches for the LCQ data set, and (d) phosphopeptide matches for the LTQ-FTICR data set.

    Article Snippet: For high mass accuracy data collected on the LTQ-FTICR mass spectrometer, isotope distributions for the precursor ions of the MS2 spectra were deconvoluted to obtain the charges and monoisotopic m/z values of the precursor ions by use of ReAdW.

    Techniques: Mass Spectrometry

    Rationale and experimental design. A , Confirmation of Δ hik33 growth phenotype under photoautotrophic condition. The deletion of hik33 ), which also contains the photo of the cell culture. B , The WCLs of the WT and Δ hik33 strains of Synechocystis were separated into the membrane (Mem) and the soluble (Sol) fractions. Proteins extracted from either fraction and the WCL were subsequently separated by SDS-PAGE and visualized with Coomassie blue staining. C , Schematic representation of the workflow for the quantitative analysis of the Δ hik33 proteome. Total proteins were extracted from the WCLs of three biological replicates of the WT and Δ hik33 and digested with trypsin. The tryptic peptides were labeled with 6-plex TMT reagents in the order as indicated. The labeled peptides were mixed together with an equal molar ratio, and separated into 15 fractions with RP-HPLC. The peptides in each fraction were quantitatively analyzed by LC-MS/MS using a LTQ-Orbitrap-Elite mass spectrometer.

    Journal: Molecular & Cellular Proteomics : MCP

    Article Title: Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium *

    doi: 10.1074/mcp.M116.068080

    Figure Lengend Snippet: Rationale and experimental design. A , Confirmation of Δ hik33 growth phenotype under photoautotrophic condition. The deletion of hik33 ), which also contains the photo of the cell culture. B , The WCLs of the WT and Δ hik33 strains of Synechocystis were separated into the membrane (Mem) and the soluble (Sol) fractions. Proteins extracted from either fraction and the WCL were subsequently separated by SDS-PAGE and visualized with Coomassie blue staining. C , Schematic representation of the workflow for the quantitative analysis of the Δ hik33 proteome. Total proteins were extracted from the WCLs of three biological replicates of the WT and Δ hik33 and digested with trypsin. The tryptic peptides were labeled with 6-plex TMT reagents in the order as indicated. The labeled peptides were mixed together with an equal molar ratio, and separated into 15 fractions with RP-HPLC. The peptides in each fraction were quantitatively analyzed by LC-MS/MS using a LTQ-Orbitrap-Elite mass spectrometer.

    Article Snippet: For MS analysis, the peptides were resuspended in 0.1% formic acid (FA) and analyzed by a LTQ Orbitrap Elite mass spectrometer (Thermo Scientific) coupled online to an Easy-nLC 1000 in the data-dependent mode.

    Techniques: Cell Culture, SDS Page, Staining, Labeling, High Performance Liquid Chromatography, Liquid Chromatography with Mass Spectroscopy, Mass Spectrometry

    Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in Orbitrap. B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the LTQ ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.

    Journal: PLoS ONE

    Article Title: Analysis of the Proteolytic Processing of ABCA3: Identification of Cleavage Site and Involved Proteases

    doi: 10.1371/journal.pone.0152594

    Figure Lengend Snippet: Partial sequence (162–174) is present in unprocessed ABCA3 and missing in processed protein form. A : Intensity profiles of an m/z range corresponding to the monoisotopic peak of the doubly-charged ion at m/z 819.885 ( m/z window ±5 ppm) for 190 kDa and 170 kDa gel bands acquired in Orbitrap. B : Identification of the ABCA3 tryptic peptide comprising amino acid residues 162–174 of the precursor protein and containing methionine sulfoxide at position 164. MS/MS spectra after CID fragmentation measured in the LTQ ion trap are shown. Major b and y ions are labelled on the spectra and all fragment ions obtained are marked on the identified sequence. The ion at m/z 811 corresponds to the loss of water from the parent ion.

    Article Snippet: Mass spectrometric analysis was performed on an LTQ-Orbitrap Discovery mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) operated in a data dependent mode in which each full MS scan (m/z 200–1,450) acquired in Orbitrap with resolution of R = 30,000 (m/z 400) was followed by five MS/MS scans where the five most abundant molecular ions were dynamically selected and fragmented by collision-induced dissociation (CID) using a normalized collision energy of 35% in the LTQ ion trap.

    Techniques: Sequencing, Mass Spectrometry