nanoelectrospray ion source  (Thermo Fisher)


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    Structured Review

    Thermo Fisher nanoelectrospray ion source
    Nanoelectrospray Ion Source, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 309 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nanoelectrospray ion source/product/Thermo Fisher
    Average 99 stars, based on 309 article reviews
    Price from $9.99 to $1999.99
    nanoelectrospray ion source - by Bioz Stars, 2020-02
    99/100 stars

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    Related Articles

    Mass Spectrometry:

    Article Title: Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling
    Article Snippet: .. Mass spectrometry (MS) and data analysis Acidified peptide mixtures were analyzed by nanoflow reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) on a nanoAcquity system (Waters) coupled to a Q-Exactive mass spectrometer equipped with a nanoelectrospray ion source for automated MS/MS. (Thermo Fisher Scientific). .. Peptide mixtures were loaded on a 20 mm trap column with 180 mm inner diameter (nanoAcquity UPLC 2 G-V/MTrap 5 mm Symmetry C18 ) at 1% buffer B, and separated by reverse-phase chromatography using a 150 mm column with 75 mm inner diameter (nanoAcquity UPLC 1.7 mm BEH130 C18 ) on a 60 min linear gradient set at a constant flow rate of 300 nL/min from 100% buffer A (0.1% formic acid, Milli-Q water) to 30% B (0.1% formic acid, acetonitrile).

    Article Title: BubR1 Promotes Bub3-Dependent APC/C Inhibition during Spindle Assembly Checkpoint Signaling
    Article Snippet: .. Samples were then separated on a Thermo Fisher Scientific™ EASY-nLC 1000 HPLC system using a two hour gradient from 5%–60% with 0.1% formic acid and directly sprayed via a nanoelectrospray ion source (Proxeon Biosystems, now Thermo Fisher Scientific) in a quadrupole Orbitrap mass spectrometer (Q Exactive™, Thermo Fisher Scientific). .. The Q Exactive™ was operated in a data dependent mode acquiring one survey scan and subsequently ten MS/MS scans [ ].

    Article Title: Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
    Article Snippet: .. Lyophilized peptide samples were re-suspended in an aqueous solution containing 0.1% v/v formic acid (FA) and 5% v/v acetonitrile (ACN) and analyzed using nano-Reverse Phase LC coupled to a Q ExactiveTM Hybrid Quadrupole - Orbitrap mass spectrometer through a nanoelectrospray ion source (Thermo Scientific, Germany). .. Peptides were initially separated using a Dionex UltiMate 3000 UHPLC system on an EasySpray C18 column (Thermo Scientific, Germany, OD 360 μm, ID 50 μm, 15 cm length, C18 resin, 2 μm bead size) at a flow rate of 300 nL min−1 .

    Article Title: Cell-based HTS identifies a chemical chaperone for preventing ER protein aggregation and proteotoxicity
    Article Snippet: .. LC-MS/MS analysis of the resultant peptides was carried out on a Dionex UltiMate 3000 UHPLC system connected to an Orbitrap Fusion mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). ..

    Article Title: Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
    Article Snippet: Paragraph title: Mass-spectrometry analysis ... An LTQ Orbitrap Velos system was equipped with an Agilent HPLC System 1100 Series (Agilent Technologies, Santa Clara, CA, USA) and a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA).

    Article Title: Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
    Article Snippet: .. The samples were then transferred on a Thermo Surveyor MS pump connected to a LTQ linear ion trap mass spectrometer (Thermo Electron, San Jose, CA, USA) equipped with a nanoelectrospray ion source (Thermo Electron). .. Xcalibure 2.0 software was used for mass spectra acquisition.

    Article Title: Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns *
    Article Snippet: MS was controlled by Xcalibur software (Thermo Fisher Scientific). .. The nanoelectrospray ion source (Thermo Fisher Scientific) was used with a spray voltage of 1.9 kV.

    Article Title: Quantitative proteomic analysis of pancreatic cyst fluid proteins associated with malignancy in intraductal papillary mucinous neoplasms
    Article Snippet: .. The peptide samples were analyzed using an LC–MS/MS configuration, comprising an Easy-nLC 1000 (Thermo Fisher Scientific, Waltham, MA, USA) that was coupled to a Q Exactive mass spectrometer with a nanoelectrospray ion source (Thermo Fisher Scientific, Waltham, MA, USA), per our established protocol [ , , ]. ..

    Article Title: Oncogenic epithelial cell-derived exosomes containing Rac1 and PAK2 induce angiogenesis in recipient endothelial cells
    Article Snippet: .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific). .. Peptides were loaded (Acclaim PepMap100 C18 5 mm 100Å, Thermo Fisher Scientific) and separated (PepMapRSLC C18, 50 cm, 75 μm inner diameter, 2mm 100Å, Thermo Fisher Scientific).

    Article Title: Over-expression, purification, and confirmation of Bacillus anthracis transcriptional regulator NprR
    Article Snippet: .. Trypsin digestion was performed to cleave the proteins into peptides, and the peptide mixture was subjected to LC-MS/MS analysis using a Linear Trap Quadrupole (LTQ) ion-trap mass spectrometer equipped with a nanoelectrospray ion source (Thermo Electron), high-performance liquid chromatography pump, and an auto-sampler (LC Packings). .. A full-scan MS (m/z 320 1800) experiment was performed, followed by MS/MS experiments on abundant ions detected in the full-MS scan.

    Article Title: Absolute quantification of microbial proteomes at different states by directed mass spectrometry
    Article Snippet: .. The hybrid LTQ-FT-ICR mass spectrometer was interfaced to a nanoelectrospray ion source (both Thermo Electron, Bremen, Germany) coupled online to a Tempo 1D-plus nanoLC (Applied Biosystems/MDS Sciex, Foster City, CA). .. In all, 1 μg of total peptide mass was separated on a RPLC column (75 μm × 15 cm) packed in-house with C18 resin (Magic C18 AQ 3 μm; Michrom BioResources, Auburn, CA) using a linear gradient from 96% solvent A (98% water, 2% acetonitrile, 0.15% formic acid) and 4% solvent B (98% acetonitrile, 2% water, 0.15% formic acid) to 30% solvent B over 120 min at a flow rate of 0.3 μl/min.

    Article Title: Perturbations to the Ubiquitin Conjugate Proteome in Yeast ?ubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition *
    Article Snippet: .. Mass spectrometry experiments were performed on an EASY-nLC (Thermo Scientific) connected to a hybrid LTQ-Orbitrap Classic with a nanoelectrospray ion source (Thermo Scientific) using a setup and settings ( ) very similar to those previously described ( ). .. Binding and separation of the peptides took place on a 15 cm silica analytical column (75 μm ID) packed in-house with reversed phase ReproSil-Pur C18AQ 3 μm resin (Dr Maisch GmbH, Ammerbuch-Entringen, Germany).

    Article Title: Quantitative proteomic analysis of pancreatic cyst fluid proteins associated with malignancy in intraductal papillary mucinous neoplasms
    Article Snippet: .. LC–MS/MS analysis The peptide samples were analyzed using an LC–MS/MS configuration, comprising an Easy-nLC 1000 (Thermo Fisher Scientific, Waltham, MA, USA) that was coupled to a Q Exactive mass spectrometer with a nanoelectrospray ion source (Thermo Fisher Scientific, Waltham, MA, USA), per our established protocol [ , , ]. ..

    Article Title: Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation
    Article Snippet: .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific). .. For cellular and EXOs samples, ~ 3 μg peptides were loaded (Acclaim PepMap100 C18 5μm 100Å, Thermo Fisher Scientific) and separated (Vydac MS C18-RP column, 25 cm, 75 μm inner diameter, 3 μm 300Å, Grace, Hesperia, CA) with a 120-min linear gradient from 0-100% phase B (0.1% FA in 80% ACN) at a flow rate of 250 nL/min.

    Article Title: Systematic Analysis of Cell-Type Differences in the Epithelial Secretome Reveals Insights into the Pathogenesis of RSV-Induced Lower Respiratory Tract Infections
    Article Snippet: .. A nanoflow UHPLC instrument (Easy nLC, Thermo Fisher Scientific) was coupled on-line to a Q Exactive mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific). .. Peptides were loaded onto a C18 reversed-phase column (25 cm long, 75 μm inner diameter) and separated with a linear gradient of 5–35% buffer B (100% acetonitrile in 0.1% formic acid) at a flow rate of 300 nL/min over 240 min. MS data were acquired using a data-dependent Top15 method dynamically choosing the most abundant precursor ions from the survey scan (400–1400 m/z) using HCD fragmentation.

    Modification:

    Article Title: Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
    Article Snippet: Proteins were digested with 105 mM sequencing grade modified porcine trypsin (Promega, Madison, WI, USA) at 58°C for 1 h. Digestion products were first extracted with a solution of 1% formic acid and 2% acetonitrile, then with a solution of 1% formic acid and 50% acetonitrile. .. The samples were then transferred on a Thermo Surveyor MS pump connected to a LTQ linear ion trap mass spectrometer (Thermo Electron, San Jose, CA, USA) equipped with a nanoelectrospray ion source (Thermo Electron).

    Derivative Assay:

    Article Title: Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
    Article Snippet: A volume corresponding to the secreted polypeptides derived from 3 × 106 cells (usually a volume equivalent to 20–40 μL of the initial cell culture) was used for in-solution tryptic digestion. .. Lyophilized peptide samples were re-suspended in an aqueous solution containing 0.1% v/v formic acid (FA) and 5% v/v acetonitrile (ACN) and analyzed using nano-Reverse Phase LC coupled to a Q ExactiveTM Hybrid Quadrupole - Orbitrap mass spectrometer through a nanoelectrospray ion source (Thermo Scientific, Germany).

    High Performance Liquid Chromatography:

    Article Title: BubR1 Promotes Bub3-Dependent APC/C Inhibition during Spindle Assembly Checkpoint Signaling
    Article Snippet: .. Samples were then separated on a Thermo Fisher Scientific™ EASY-nLC 1000 HPLC system using a two hour gradient from 5%–60% with 0.1% formic acid and directly sprayed via a nanoelectrospray ion source (Proxeon Biosystems, now Thermo Fisher Scientific) in a quadrupole Orbitrap mass spectrometer (Q Exactive™, Thermo Fisher Scientific). .. The Q Exactive™ was operated in a data dependent mode acquiring one survey scan and subsequently ten MS/MS scans [ ].

    Article Title: Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
    Article Snippet: .. An LTQ Orbitrap Velos system was equipped with an Agilent HPLC System 1100 Series (Agilent Technologies, Santa Clara, CA, USA) and a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA). .. The peptide separation was carried out on an RP-HPLC column Zorbax 300SB-C18 (Agilent Technologies, Santa Clara, CA 95051, USA) (3.5 μm × 75 μm × 150 mm) using a linear gradient from 95% solvent A (100% water, 0.1% formic acid) and 5% solvent B (20% water, 80% acetonitrile, 0.1% formic acid) to 40% solvent A and 60% solvent B over 85 minutes at a flow rate of 300 nL/min.

    Article Title: Over-expression, purification, and confirmation of Bacillus anthracis transcriptional regulator NprR
    Article Snippet: .. Trypsin digestion was performed to cleave the proteins into peptides, and the peptide mixture was subjected to LC-MS/MS analysis using a Linear Trap Quadrupole (LTQ) ion-trap mass spectrometer equipped with a nanoelectrospray ion source (Thermo Electron), high-performance liquid chromatography pump, and an auto-sampler (LC Packings). .. A full-scan MS (m/z 320 1800) experiment was performed, followed by MS/MS experiments on abundant ions detected in the full-MS scan.

    Flow Cytometry:

    Article Title: Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling
    Article Snippet: Mass spectrometry (MS) and data analysis Acidified peptide mixtures were analyzed by nanoflow reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) on a nanoAcquity system (Waters) coupled to a Q-Exactive mass spectrometer equipped with a nanoelectrospray ion source for automated MS/MS. (Thermo Fisher Scientific). .. Peptide mixtures were loaded on a 20 mm trap column with 180 mm inner diameter (nanoAcquity UPLC 2 G-V/MTrap 5 mm Symmetry C18 ) at 1% buffer B, and separated by reverse-phase chromatography using a 150 mm column with 75 mm inner diameter (nanoAcquity UPLC 1.7 mm BEH130 C18 ) on a 60 min linear gradient set at a constant flow rate of 300 nL/min from 100% buffer A (0.1% formic acid, Milli-Q water) to 30% B (0.1% formic acid, acetonitrile).

    Article Title: Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
    Article Snippet: Lyophilized peptide samples were re-suspended in an aqueous solution containing 0.1% v/v formic acid (FA) and 5% v/v acetonitrile (ACN) and analyzed using nano-Reverse Phase LC coupled to a Q ExactiveTM Hybrid Quadrupole - Orbitrap mass spectrometer through a nanoelectrospray ion source (Thermo Scientific, Germany). .. Peptides were initially separated using a Dionex UltiMate 3000 UHPLC system on an EasySpray C18 column (Thermo Scientific, Germany, OD 360 μm, ID 50 μm, 15 cm length, C18 resin, 2 μm bead size) at a flow rate of 300 nL min−1 .

    Article Title: Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
    Article Snippet: An LTQ Orbitrap Velos system was equipped with an Agilent HPLC System 1100 Series (Agilent Technologies, Santa Clara, CA, USA) and a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA). .. The peptide separation was carried out on an RP-HPLC column Zorbax 300SB-C18 (Agilent Technologies, Santa Clara, CA 95051, USA) (3.5 μm × 75 μm × 150 mm) using a linear gradient from 95% solvent A (100% water, 0.1% formic acid) and 5% solvent B (20% water, 80% acetonitrile, 0.1% formic acid) to 40% solvent A and 60% solvent B over 85 minutes at a flow rate of 300 nL/min.

    Article Title: Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns *
    Article Snippet: Proteins were eluted directly into an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) with a 70-min linear gradient of 50–90% buffer B at flow rate of 300 nL/min. .. The nanoelectrospray ion source (Thermo Fisher Scientific) was used with a spray voltage of 1.9 kV.

    Article Title: Absolute quantification of microbial proteomes at different states by directed mass spectrometry
    Article Snippet: The hybrid LTQ-FT-ICR mass spectrometer was interfaced to a nanoelectrospray ion source (both Thermo Electron, Bremen, Germany) coupled online to a Tempo 1D-plus nanoLC (Applied Biosystems/MDS Sciex, Foster City, CA). .. In all, 1 μg of total peptide mass was separated on a RPLC column (75 μm × 15 cm) packed in-house with C18 resin (Magic C18 AQ 3 μm; Michrom BioResources, Auburn, CA) using a linear gradient from 96% solvent A (98% water, 2% acetonitrile, 0.15% formic acid) and 4% solvent B (98% acetonitrile, 2% water, 0.15% formic acid) to 30% solvent B over 120 min at a flow rate of 0.3 μl/min.

    Article Title: Perturbations to the Ubiquitin Conjugate Proteome in Yeast ?ubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition *
    Article Snippet: Mass spectrometry experiments were performed on an EASY-nLC (Thermo Scientific) connected to a hybrid LTQ-Orbitrap Classic with a nanoelectrospray ion source (Thermo Scientific) using a setup and settings ( ) very similar to those previously described ( ). .. Samples were run for 240 min on a 5% to 25% acetonitrile gradient in 0.2% formic acid at a flow rate of 350 nL per minute.

    Article Title: Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation
    Article Snippet: A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific). .. For cellular and EXOs samples, ~ 3 μg peptides were loaded (Acclaim PepMap100 C18 5μm 100Å, Thermo Fisher Scientific) and separated (Vydac MS C18-RP column, 25 cm, 75 μm inner diameter, 3 μm 300Å, Grace, Hesperia, CA) with a 120-min linear gradient from 0-100% phase B (0.1% FA in 80% ACN) at a flow rate of 250 nL/min.

    Article Title: Systematic Analysis of Cell-Type Differences in the Epithelial Secretome Reveals Insights into the Pathogenesis of RSV-Induced Lower Respiratory Tract Infections
    Article Snippet: A nanoflow UHPLC instrument (Easy nLC, Thermo Fisher Scientific) was coupled on-line to a Q Exactive mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific). .. Peptides were loaded onto a C18 reversed-phase column (25 cm long, 75 μm inner diameter) and separated with a linear gradient of 5–35% buffer B (100% acetonitrile in 0.1% formic acid) at a flow rate of 300 nL/min over 240 min. MS data were acquired using a data-dependent Top15 method dynamically choosing the most abundant precursor ions from the survey scan (400–1400 m/z) using HCD fragmentation.

    Chromatography:

    Article Title: Perturbations to the Ubiquitin Conjugate Proteome in Yeast ?ubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition *
    Article Snippet: Paragraph title: Fractionation and Liquid Chromatography-tandem MS (LC-MS/MS) ... Mass spectrometry experiments were performed on an EASY-nLC (Thermo Scientific) connected to a hybrid LTQ-Orbitrap Classic with a nanoelectrospray ion source (Thermo Scientific) using a setup and settings ( ) very similar to those previously described ( ).

    Immunoprecipitation:

    Article Title: BubR1 Promotes Bub3-Dependent APC/C Inhibition during Spindle Assembly Checkpoint Signaling
    Article Snippet: During the following anti-GFP IP (described in immunoprecipitation and immunoblotting) the washing steps were performed in a mild wash buffer (75 mM HEPES, pH 7.5, 1.5 mM EGTA, 1.5 mM MgCl2 , 10% glycerol) to preserve potentially weak interactions. .. Samples were then separated on a Thermo Fisher Scientific™ EASY-nLC 1000 HPLC system using a two hour gradient from 5%–60% with 0.1% formic acid and directly sprayed via a nanoelectrospray ion source (Proxeon Biosystems, now Thermo Fisher Scientific) in a quadrupole Orbitrap mass spectrometer (Q Exactive™, Thermo Fisher Scientific).

    Cell Culture:

    Article Title: Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
    Article Snippet: A volume corresponding to the secreted polypeptides derived from 3 × 106 cells (usually a volume equivalent to 20–40 μL of the initial cell culture) was used for in-solution tryptic digestion. .. Lyophilized peptide samples were re-suspended in an aqueous solution containing 0.1% v/v formic acid (FA) and 5% v/v acetonitrile (ACN) and analyzed using nano-Reverse Phase LC coupled to a Q ExactiveTM Hybrid Quadrupole - Orbitrap mass spectrometer through a nanoelectrospray ion source (Thermo Scientific, Germany).

    Liquid Chromatography:

    Article Title: Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling
    Article Snippet: .. Mass spectrometry (MS) and data analysis Acidified peptide mixtures were analyzed by nanoflow reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) on a nanoAcquity system (Waters) coupled to a Q-Exactive mass spectrometer equipped with a nanoelectrospray ion source for automated MS/MS. (Thermo Fisher Scientific). .. Peptide mixtures were loaded on a 20 mm trap column with 180 mm inner diameter (nanoAcquity UPLC 2 G-V/MTrap 5 mm Symmetry C18 ) at 1% buffer B, and separated by reverse-phase chromatography using a 150 mm column with 75 mm inner diameter (nanoAcquity UPLC 1.7 mm BEH130 C18 ) on a 60 min linear gradient set at a constant flow rate of 300 nL/min from 100% buffer A (0.1% formic acid, Milli-Q water) to 30% B (0.1% formic acid, acetonitrile).

    Tandem Mass Spectroscopy:

    Article Title: Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling
    Article Snippet: .. Mass spectrometry (MS) and data analysis Acidified peptide mixtures were analyzed by nanoflow reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) on a nanoAcquity system (Waters) coupled to a Q-Exactive mass spectrometer equipped with a nanoelectrospray ion source for automated MS/MS. (Thermo Fisher Scientific). .. Peptide mixtures were loaded on a 20 mm trap column with 180 mm inner diameter (nanoAcquity UPLC 2 G-V/MTrap 5 mm Symmetry C18 ) at 1% buffer B, and separated by reverse-phase chromatography using a 150 mm column with 75 mm inner diameter (nanoAcquity UPLC 1.7 mm BEH130 C18 ) on a 60 min linear gradient set at a constant flow rate of 300 nL/min from 100% buffer A (0.1% formic acid, Milli-Q water) to 30% B (0.1% formic acid, acetonitrile).

    Article Title: BubR1 Promotes Bub3-Dependent APC/C Inhibition during Spindle Assembly Checkpoint Signaling
    Article Snippet: Samples were then separated on a Thermo Fisher Scientific™ EASY-nLC 1000 HPLC system using a two hour gradient from 5%–60% with 0.1% formic acid and directly sprayed via a nanoelectrospray ion source (Proxeon Biosystems, now Thermo Fisher Scientific) in a quadrupole Orbitrap mass spectrometer (Q Exactive™, Thermo Fisher Scientific). .. The Q Exactive™ was operated in a data dependent mode acquiring one survey scan and subsequently ten MS/MS scans [ ].

    Article Title: Cell-based HTS identifies a chemical chaperone for preventing ER protein aggregation and proteotoxicity
    Article Snippet: LC-MS/MS analysis of the resultant peptides was carried out on a Dionex UltiMate 3000 UHPLC system connected to an Orbitrap Fusion mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). .. HCD MS/MS spectra were acquired at a resolution of 15,000, an AGC target of 5 × 104 , an isolation window of 4.0 m/z , a maximum injection time of 54 ms and a normalized collision energy of 30.

    Article Title: Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
    Article Snippet: An LTQ Orbitrap Velos system was equipped with an Agilent HPLC System 1100 Series (Agilent Technologies, Santa Clara, CA, USA) and a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA). .. Data were acquired in the Orbitrap analyzer with a resolution of 30,000 (m/z 400) for MS and 7,500 (m/z 400) for MS/MS scans.

    Article Title: Over-expression, purification, and confirmation of Bacillus anthracis transcriptional regulator NprR
    Article Snippet: Trypsin digestion was performed to cleave the proteins into peptides, and the peptide mixture was subjected to LC-MS/MS analysis using a Linear Trap Quadrupole (LTQ) ion-trap mass spectrometer equipped with a nanoelectrospray ion source (Thermo Electron), high-performance liquid chromatography pump, and an auto-sampler (LC Packings). .. A full-scan MS (m/z 320 1800) experiment was performed, followed by MS/MS experiments on abundant ions detected in the full-MS scan.

    Article Title: Absolute quantification of microbial proteomes at different states by directed mass spectrometry
    Article Snippet: The hybrid LTQ-FT-ICR mass spectrometer was interfaced to a nanoelectrospray ion source (both Thermo Electron, Bremen, Germany) coupled online to a Tempo 1D-plus nanoLC (Applied Biosystems/MDS Sciex, Foster City, CA). .. Each survey scan acquired in the ICR cell at 100 000 FWHM was followed by MS/MS scans of the three most intense precursor ions in the linear ion trap with enabled dynamic exclusion for 60 s. Charge state screening was employed to select for ions with at least two charges and rejecting ions with undetermined charge state.

    Sequencing:

    Article Title: Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
    Article Snippet: Proteins were digested with 105 mM sequencing grade modified porcine trypsin (Promega, Madison, WI, USA) at 58°C for 1 h. Digestion products were first extracted with a solution of 1% formic acid and 2% acetonitrile, then with a solution of 1% formic acid and 50% acetonitrile. .. The samples were then transferred on a Thermo Surveyor MS pump connected to a LTQ linear ion trap mass spectrometer (Thermo Electron, San Jose, CA, USA) equipped with a nanoelectrospray ion source (Thermo Electron).

    Article Title: Oncogenic epithelial cell-derived exosomes containing Rac1 and PAK2 induce angiogenesis in recipient endothelial cells
    Article Snippet: Individual samples were excised, destained (50 mM ammonium bicarbonate/acetonitrile), reduced (10 mM DTT (Calbiochem) for 30 min), alkylated (50 mM iodoacetic acid (Fluka) for 30 min) and trypsinized (0.2 μg trypsin (Promega Sequencing Grade) for 16 h at 37°C). .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    Article Title: Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation
    Article Snippet: Individual samples were excised (single gel bands and multi-band excision) and destained (50 mM ammonium bicarbonate/acetonitrile), reduced (10 mM DTT, Calbiochem, for 30 min), alkylated (50 mM iodoacetic acid, Fluka, for 30 min) and trypsinized (0.2 μg trypsin, Promega Sequencing Grade, for 16 h at 37°C), as described [ ]. .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    Injection:

    Article Title: Cell-based HTS identifies a chemical chaperone for preventing ER protein aggregation and proteotoxicity
    Article Snippet: LC-MS/MS analysis of the resultant peptides was carried out on a Dionex UltiMate 3000 UHPLC system connected to an Orbitrap Fusion mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). .. HCD MS/MS spectra were acquired at a resolution of 15,000, an AGC target of 5 × 104 , an isolation window of 4.0 m/z , a maximum injection time of 54 ms and a normalized collision energy of 30.

    Article Title: Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns *
    Article Snippet: The nanoelectrospray ion source (Thermo Fisher Scientific) was used with a spray voltage of 1.9 kV. .. MS survey scans were obtained for the m/z range of 700–1200 in the orbitrap with maximum ion injection time of 50 ms, auto gain control target 5 × 105 , resolution 60,000 and 10 microscans per each full MS event.

    Binding Assay:

    Article Title: Perturbations to the Ubiquitin Conjugate Proteome in Yeast ?ubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition *
    Article Snippet: Mass spectrometry experiments were performed on an EASY-nLC (Thermo Scientific) connected to a hybrid LTQ-Orbitrap Classic with a nanoelectrospray ion source (Thermo Scientific) using a setup and settings ( ) very similar to those previously described ( ). .. Binding and separation of the peptides took place on a 15 cm silica analytical column (75 μm ID) packed in-house with reversed phase ReproSil-Pur C18AQ 3 μm resin (Dr Maisch GmbH, Ammerbuch-Entringen, Germany).

    Isolation:

    Article Title: Cell-based HTS identifies a chemical chaperone for preventing ER protein aggregation and proteotoxicity
    Article Snippet: LC-MS/MS analysis of the resultant peptides was carried out on a Dionex UltiMate 3000 UHPLC system connected to an Orbitrap Fusion mass spectrometer through a nanoelectrospray ion source (Thermo Fisher Scientific). .. HCD MS/MS spectra were acquired at a resolution of 15,000, an AGC target of 5 × 104 , an isolation window of 4.0 m/z , a maximum injection time of 54 ms and a normalized collision energy of 30.

    Size-exclusion Chromatography:

    Article Title: Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
    Article Snippet: Analyzed parent ions were sent to a dynamic exclusion list for 15 sec to get an MS2 spectrum at the chromatographic peak apex (minimum peak width throughout the gradient was about 30 s). .. An LTQ Orbitrap Velos system was equipped with an Agilent HPLC System 1100 Series (Agilent Technologies, Santa Clara, CA, USA) and a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA).

    Purification:

    Article Title: Over-expression, purification, and confirmation of Bacillus anthracis transcriptional regulator NprR
    Article Snippet: Purified AqsR was then applied to 4 12% NuPAGE Bis-Tris gels (Novex). .. Trypsin digestion was performed to cleave the proteins into peptides, and the peptide mixture was subjected to LC-MS/MS analysis using a Linear Trap Quadrupole (LTQ) ion-trap mass spectrometer equipped with a nanoelectrospray ion source (Thermo Electron), high-performance liquid chromatography pump, and an auto-sampler (LC Packings).

    Article Title: Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation
    Article Snippet: Proteomic analysis Proteomic analyses were performed for cell lysates and purified EXOs (10 μg protein) as previously described [ ] with modifications. .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    Staining:

    Article Title: Oncogenic epithelial cell-derived exosomes containing Rac1 and PAK2 induce angiogenesis in recipient endothelial cells
    Article Snippet: Briefly, exosomes from each cell line (10 μg) were lysed in SDS sample buffer (4% (w/v) SDS, 20% (v/v) glycerol, 0.01% (v/v) bromophenol blue, 0.125 M Tris-HCl, pH 6.8), and proteins separated by SDS-PAGE, and visualized by Imperial™ Protein Stain (Invitrogen). .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    Article Title: Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation
    Article Snippet: Samples were lysed in SDS sample buffer, electrophoresed by SDS-PAGE and visualized by Imperial™ Protein Stain (Thermo Fisher Scientific). .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    SDS Page:

    Article Title: Oncogenic epithelial cell-derived exosomes containing Rac1 and PAK2 induce angiogenesis in recipient endothelial cells
    Article Snippet: Briefly, exosomes from each cell line (10 μg) were lysed in SDS sample buffer (4% (w/v) SDS, 20% (v/v) glycerol, 0.01% (v/v) bromophenol blue, 0.125 M Tris-HCl, pH 6.8), and proteins separated by SDS-PAGE, and visualized by Imperial™ Protein Stain (Invitrogen). .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    Article Title: Podoplanin is a component of extracellular vesicles that reprograms cell-derived exosomal proteins and modulates lymphatic vessel formation
    Article Snippet: Samples were lysed in SDS sample buffer, electrophoresed by SDS-PAGE and visualized by Imperial™ Protein Stain (Thermo Fisher Scientific). .. A nanoflow UPLC instrument (Ultimate 3000 RSLCnano, Thermo Fisher Scientific) was coupled on-line to an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific) with a nanoelectrospray ion source (Thermo Fisher Scientific).

    Software:

    Article Title: BubR1 Promotes Bub3-Dependent APC/C Inhibition during Spindle Assembly Checkpoint Signaling
    Article Snippet: Samples were then separated on a Thermo Fisher Scientific™ EASY-nLC 1000 HPLC system using a two hour gradient from 5%–60% with 0.1% formic acid and directly sprayed via a nanoelectrospray ion source (Proxeon Biosystems, now Thermo Fisher Scientific) in a quadrupole Orbitrap mass spectrometer (Q Exactive™, Thermo Fisher Scientific). .. Data were analyzed with the quantitative proteomics software MaxQuant (version 1.5.2.18) [ ] and further processed in Perseus (version 1.5.1.5) [ ].

    Article Title: Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
    Article Snippet: The samples were then transferred on a Thermo Surveyor MS pump connected to a LTQ linear ion trap mass spectrometer (Thermo Electron, San Jose, CA, USA) equipped with a nanoelectrospray ion source (Thermo Electron). .. Xcalibure 2.0 software was used for mass spectra acquisition.

    Article Title: Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns *
    Article Snippet: MS was controlled by Xcalibur software (Thermo Fisher Scientific). .. The nanoelectrospray ion source (Thermo Fisher Scientific) was used with a spray voltage of 1.9 kV.

    Selection:

    Article Title: Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
    Article Snippet: MS1 acquisition parameters were 300–1250 m/z mass range for analysis and subsequent ion selection for MS2 analysis and 250 ms signal accumulation time. .. An LTQ Orbitrap Velos system was equipped with an Agilent HPLC System 1100 Series (Agilent Technologies, Santa Clara, CA, USA) and a nanoelectrospray ion source (Thermo Scientific, Waltham, MA, USA).

    Concentration Assay:

    Article Title: Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
    Article Snippet: The protein solution was initially diluted into urea (2 M final concentration in 50 mM Ammonium Bicarbonate solution (ABS), followed by reduction of cysteines with 1 mM DTT (45 min; 56°C), alkylation [10 mM Iodoacetamide (IAA); 45 min; 22°C; dark] and digestion (0.015 μg Trypsin per 1.5 μg sample protein) (Trypsin Gold, Promega, United States; ratio trypsin/protein 1/100; overnight; 37°C). .. Lyophilized peptide samples were re-suspended in an aqueous solution containing 0.1% v/v formic acid (FA) and 5% v/v acetonitrile (ACN) and analyzed using nano-Reverse Phase LC coupled to a Q ExactiveTM Hybrid Quadrupole - Orbitrap mass spectrometer through a nanoelectrospray ion source (Thermo Scientific, Germany).

    Fractionation:

    Article Title: Perturbations to the Ubiquitin Conjugate Proteome in Yeast ?ubx Mutants Identify Ubx2 as a Regulator of Membrane Lipid Composition *
    Article Snippet: Paragraph title: Fractionation and Liquid Chromatography-tandem MS (LC-MS/MS) ... Mass spectrometry experiments were performed on an EASY-nLC (Thermo Scientific) connected to a hybrid LTQ-Orbitrap Classic with a nanoelectrospray ion source (Thermo Scientific) using a setup and settings ( ) very similar to those previously described ( ).

    Reversed-phase Chromatography:

    Article Title: Suppressor of cytokine signaling (SOCS)5 ameliorates influenza infection via inhibition of EGFR signaling
    Article Snippet: Mass spectrometry (MS) and data analysis Acidified peptide mixtures were analyzed by nanoflow reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) on a nanoAcquity system (Waters) coupled to a Q-Exactive mass spectrometer equipped with a nanoelectrospray ion source for automated MS/MS. (Thermo Fisher Scientific). .. Peptide mixtures were loaded on a 20 mm trap column with 180 mm inner diameter (nanoAcquity UPLC 2 G-V/MTrap 5 mm Symmetry C18 ) at 1% buffer B, and separated by reverse-phase chromatography using a 150 mm column with 75 mm inner diameter (nanoAcquity UPLC 1.7 mm BEH130 C18 ) on a 60 min linear gradient set at a constant flow rate of 300 nL/min from 100% buffer A (0.1% formic acid, Milli-Q water) to 30% B (0.1% formic acid, acetonitrile).

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    Thermo Fisher nanoelectrospray ion source
    Nanoelectrospray Ion Source, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 310 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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