ltq mass spectrometer Search Results


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  • 94
    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: 94/100, based on 4015 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    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: 92/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    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: 92/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher ltq obritrap 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 Obritrap Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    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: 95/100, based on 7392 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher proteomex 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.
    Proteomex Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    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: 89/100, based on 161 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    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: 90/100, based on 134 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher finnigan ltq 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.
    Finnigan Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 514 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Thermo Fisher mass spectrometer ltq velos
    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
    Mass Spectrometer Ltq Velos, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 42 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher ltq orbitrab 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
    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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    91
    Thermo Fisher finniqan 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
    Finniqan Ltq Mass Spectrometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    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: 88/100, based on 155 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    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: 88/100, based on 61 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    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: 88/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    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: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    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

    Schematic representation of the geometrical arrangement for electron and IR laser beams in the ICR cell of Thermo-Finnigan LTQ FT. Top: overlap between ion trajectories, electron beam and IR beam in the plane A-A' at the entrance to the ICR cell.

    Journal: Journal of the American Society for Mass Spectrometry

    Article Title: Activated Ion Electron Capture Dissociation (AI ECD) of Proteins: Synchronization of Infrared and Electron Irradiation with Ion Magnetron Motion

    doi: 10.1016/j.jasms.2008.12.015

    Figure Lengend Snippet: Schematic representation of the geometrical arrangement for electron and IR laser beams in the ICR cell of Thermo-Finnigan LTQ FT. Top: overlap between ion trajectories, electron beam and IR beam in the plane A-A' at the entrance to the ICR cell.

    Article Snippet: 85 ms for 1 V trapping voltage in the ICR cell of a Thermo Finnigan LTQ FT mass spectrometer.

    Techniques:

    QuaMeter generates metrics similar to MSQC with the exception of chromatographic metrics due to the use of distinct chromatogram extraction tools. Metrics were generated from BSA QC experiments collected on a Thermo Fisher LTQ-XL mass spectrometer. The

    Journal: Analytical chemistry

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

    doi: 10.1021/ac300629p

    Figure Lengend Snippet: QuaMeter generates metrics similar to MSQC with the exception of chromatographic metrics due to the use of distinct chromatogram extraction tools. Metrics were generated from BSA QC experiments collected on a Thermo Fisher LTQ-XL mass spectrometer. The

    Article Snippet: Data from bovine serum albumin (BSA) QC samples analyzed on a Thermo Fisher LTQ-XL mass spectrometer were employed to evaluate how code differences altered values reported by these two tools.

    Techniques: Generated, 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

    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

    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

    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