ultimate3000 nano hplc system  (Thermo Fisher)


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    Structured Review

    Thermo Fisher ultimate3000 nano hplc system
    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 <t>Ultimate3000</t> <t>nano</t> <t>HPLC</t> 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.
    Ultimate3000 Nano Hplc System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    ultimate3000 nano hplc system - by Bioz Stars, 2020-04
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    Images

    1) Product Images from "microRNA regulatory circuits in a mouse model of inherited retinal degeneration"

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

    Journal: Scientific Reports

    doi: 10.1038/srep31431

    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.
    Figure Legend 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.

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

    Related Articles

    High Performance Liquid Chromatography:

    Article Title: Queuosine‐modified tRNAs confer nutritional control of protein translation
    Article Snippet: The peptides were measured on a Q‐Exactive Plus mass spectrometer (Thermo Scientific) coupled to an Ultimate 3000 RSLCnano system (Thermo Scientific) in data‐dependent acquisition mode, selecting the top 12 peaks for higher energy collisional dissociation (HCD) fragmentation. .. A 90‐min gradient (solvent A: 0.1% formic acid; solvent B: HPLC grade acetonitrile in 0.1% formic acid) was applied using an Acclaim PepMap trap column (2 cm × 75 μm i.d., C18, 3 μm, 100 Å, Thermo Scientific) and an Acclaim PepMap RSLC analytical column (50 cm × 75 μm i.d., C18, 2 μm, 100 Å, Thermo Scientific).

    Flow Cytometry:

    Article Title: The N-Glycosylation of Mouse Immunoglobulin G (IgG)-Fragment Crystallizable Differs Between IgG Subclasses and Strains
    Article Snippet: Nanoliquid Chromatography Mass Spectrometry of Glycopeptides The 20 times diluted tryptic digests of the IgG samples were separated with an Ultimate 3000 RSLCnano system (Dionex/Thermo Scientific, Breda, the Netherlands) equipped with an Acclaim PepMap 100 trap column (100 μm × 20 mm, particle size 5 μm, Dionex/Thermo Scientific) and an Acclaim PepMap RSLC C18 nano-column (75 μm × 150 mm, particle size 2 μm, Dionex/Thermo Scientific). .. Two microliters of sample were injected and separated with a gradient from 97% solvent A (0.1% formic acid in water) and 3% solvent B (95% ACN) to 27% solvent B over 15 min, with a flow rate of 700 nL/min.

    Article Title: MS-based cross-linking analysis reveals the location of the PsbQ protein in cyanobacterial photosystem II
    Article Snippet: The peptide sample was loaded onto an Ultimate 3000 Nano LC system (Thermo Scientific Dionex) coupled with an LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific). .. The peptides were eluted at a flow rate of 260 nL/min, ramping a gradient from 5% to 60% solvent B (80% acetonitrile, 20% water, and 0.1% formic acid) in 110 min.

    Article Title: MHC-associated peptide proteomics enabling highly sensitive detection of immunogenic sequences for the development of therapeutic antibodies with low immunogenicity
    Article Snippet: Chromatographic separation was achieved using Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, Inc., Waltham, MA) with a C18 reversed phase nano-capillary column (3 μm, 75 μm x 120 mm) (Nikkyo Technos Co., Ltd., Tokyo, Japan), and the eluate was ionized under nano-electrospray, positive-ion mode and measured using an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific, Inc.). .. Peptides were separated on the column with a 2%-37% acetonitrile gradient containing 0.5% acetic acid for 69 or 138 min (only when evaluating the effects of gradient time for adalimumab samples) at 250 nL/min of flow rate.

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex). .. SHP-2 peptides were first trapped on a home-made precolumn (ReproSil-Pur 120 C18-AQ, 5 μm, Dr. Maisch GmbH; 100 μm × 5 cm) at 10 μl/ min of loading buffer (2% acetonitrile, 0.02% TFA in water) and then separated on an analytical column (ReproSil-Pur 120 C18-AQ, 1.9 μm, Dr. Maisch GmbH, 75 μm × 30 cm, self-packed) with a 40-min linear gradient ranging from 5% to 60% of buffer B (80% ACN/ 0.1% formic acid) and corresponding composition of Buffer A (0.1% formic acid in water) at a constant flow rate of 300 nl/min.

    Article Title: Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans
    Article Snippet: Nano-LC separation was carried out using a Ultimate 3000 RSLCnano System equipped with an Acclaim PepMap RSLC column (C18, 75 µm × 15 cm with 2 µm particles, Thermo Scientific) preceded by a 2 cm Acclaim PepMap100 guard column (Thermo Scientific). .. Peptides were eluted from the column with a multi-step gradient from 5% to 55% solvent B in 55 minutes (0–5 min 5%B, then in 15 min to 20%B and finally in 25 min till 55%B), at a constant flow rate of 300 nl min−1 .

    Article Title: Analyses of the Xylem Sap Proteomes Identified Candidate Fusarium virguliforme Proteinacious Toxins
    Article Snippet: The Orbitrap was interfaced with an UltiMate3000 RSLCnano system (Dionex, Sunnyvale, CA). .. The reconstituted peptides (2 µL) were injected under “User Defined Program” onto a PepMap C18 trap column (5 µm, 300 µm×5 mm, Dionex) at a 20 µL/min flow rate for on-line desalting and then separated on a PepMap C18 RP nano column (3 µm, 75 µm×15 cm, Dionex) which was installed in the “Plug and Play” device with a 10-µm spray emitter (New Objective, Woburn, MA) mounted in front of the Orbitrap orifice.

    Article Title: Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer
    Article Snippet: Data Acquisition Samples were analyzed using a UltiMate 3000 Nano LC system coupled to an Orbitrap Fusion Lumos Tribrid mass spectrometer equipped with an EasySpray Source (Thermo Fisher Scientific, San Jose, CA). .. Peptides were loaded onto a 500 mm C-18 EasySpray column (75 μm ID, 2 μm particles, 100 Å pore size) with 2% B at 300 nL/min flow rate for 11 min and eluted at 300 nL/min flow rate with a linear gradient from 2–40% B over 139 min.

    Article Title: Prevention of calpain-dependent degradation of STK38 by MEKK2-mediated phosphorylation
    Article Snippet: Nano liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) For the identification of phosphorylation sites, nanoLC-MS/MS was performed on an UltiMate 3000 RSLCnano system (Thermo Fisher Scientific) coupled to a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with nano ESI source. .. Peptides separation was performed using 60 min gradient of water containing 0.1% FA (mobile phase A) and acetonitrile containing 0.1% FA (mobile phase B) at a flow rate of 300 nL/min.

    Mass Spectrometry:

    Article Title: A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions
    Article Snippet: .. Each sample in the second TMT experiment (which incorporated homogenate centrifugations steps) was analysed using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) during a 90 min nano‐liquid chromatography separation using a Dionex UltiMate 3000 RSLCnano system (Thermo Fisher Scientific). .. Samples were analysed using an MS1 AGC target of 1 × 106 and maximum injection times of 100 ms. MS cycle time was set to 2 s, and MS runs used an exclusion duration of 45 s, a quadrupole isolation window of 1.2 m / z , and HCD fragmentation using a collision energy of 35% and a stepped collision energy of 5%.

    Article Title: The N-Glycosylation of Mouse Immunoglobulin G (IgG)-Fragment Crystallizable Differs Between IgG Subclasses and Strains
    Article Snippet: .. Nanoliquid Chromatography Mass Spectrometry of Glycopeptides The 20 times diluted tryptic digests of the IgG samples were separated with an Ultimate 3000 RSLCnano system (Dionex/Thermo Scientific, Breda, the Netherlands) equipped with an Acclaim PepMap 100 trap column (100 μm × 20 mm, particle size 5 μm, Dionex/Thermo Scientific) and an Acclaim PepMap RSLC C18 nano-column (75 μm × 150 mm, particle size 2 μm, Dionex/Thermo Scientific). .. Two microliters of sample were injected and separated with a gradient from 97% solvent A (0.1% formic acid in water) and 3% solvent B (95% ACN) to 27% solvent B over 15 min, with a flow rate of 700 nL/min.

    Article Title: MS-based cross-linking analysis reveals the location of the PsbQ protein in cyanobacterial photosystem II
    Article Snippet: .. The peptide sample was loaded onto an Ultimate 3000 Nano LC system (Thermo Scientific Dionex) coupled with an LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific). .. The peptides were trapped by a guard column (Acclaim PepMap100, 100 µm × 2 cm, C18, 5 µm, 100 Å; Thermo Scientific Dionex) through which solvent A (water with 0.1% formic acid; Sigma-Aldrich) was pumped at 6 µL/min.

    Article Title: MHC-associated peptide proteomics enabling highly sensitive detection of immunogenic sequences for the development of therapeutic antibodies with low immunogenicity
    Article Snippet: .. Chromatographic separation was achieved using Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, Inc., Waltham, MA) with a C18 reversed phase nano-capillary column (3 μm, 75 μm x 120 mm) (Nikkyo Technos Co., Ltd., Tokyo, Japan), and the eluate was ionized under nano-electrospray, positive-ion mode and measured using an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific, Inc.). .. Peptides were separated on the column with a 2%-37% acetonitrile gradient containing 0.5% acetic acid for 69 or 138 min (only when evaluating the effects of gradient time for adalimumab samples) at 250 nL/min of flow rate.

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex). .. SHP-2 peptides were first trapped on a home-made precolumn (ReproSil-Pur 120 C18-AQ, 5 μm, Dr. Maisch GmbH; 100 μm × 5 cm) at 10 μl/ min of loading buffer (2% acetonitrile, 0.02% TFA in water) and then separated on an analytical column (ReproSil-Pur 120 C18-AQ, 1.9 μm, Dr. Maisch GmbH, 75 μm × 30 cm, self-packed) with a 40-min linear gradient ranging from 5% to 60% of buffer B (80% ACN/ 0.1% formic acid) and corresponding composition of Buffer A (0.1% formic acid in water) at a constant flow rate of 300 nl/min.

    Article Title: Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans
    Article Snippet: Nano-LC separation was carried out using a Ultimate 3000 RSLCnano System equipped with an Acclaim PepMap RSLC column (C18, 75 µm × 15 cm with 2 µm particles, Thermo Scientific) preceded by a 2 cm Acclaim PepMap100 guard column (Thermo Scientific). .. MS analysis was performed employing a maXis Impact UHR-TOF-MS (Bruker Daltonics, Bremen, Germany) in data dependent MS/MS mode in the m/z 150–2200 range.

    Article Title: Queuosine‐modified tRNAs confer nutritional control of protein translation
    Article Snippet: .. The peptides were measured on a Q‐Exactive Plus mass spectrometer (Thermo Scientific) coupled to an Ultimate 3000 RSLCnano system (Thermo Scientific) in data‐dependent acquisition mode, selecting the top 12 peaks for higher energy collisional dissociation (HCD) fragmentation. .. A 90‐min gradient (solvent A: 0.1% formic acid; solvent B: HPLC grade acetonitrile in 0.1% formic acid) was applied using an Acclaim PepMap trap column (2 cm × 75 μm i.d., C18, 3 μm, 100 Å, Thermo Scientific) and an Acclaim PepMap RSLC analytical column (50 cm × 75 μm i.d., C18, 2 μm, 100 Å, Thermo Scientific).

    Article Title: Analyses of the Xylem Sap Proteomes Identified Candidate Fusarium virguliforme Proteinacious Toxins
    Article Snippet: The tryptic digests were reconstituted in 2% acetonitrile (ACN) with 0.5% formic aid (FA) for nano LC-ESI-MS/MS analysis, which was carried out using an LTQ-Orbitrap Velos (Thermo-Fisher Scientific, San Jose, CA) mass spectrometer equipped with “Plug and Play” nano ion source device (CorSolutions LLC, Ithaca, NY). .. The Orbitrap was interfaced with an UltiMate3000 RSLCnano system (Dionex, Sunnyvale, CA).

    Article Title: Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes
    Article Snippet: .. Peptide mixtures (6 μl) were separated on a self-packed C18 (1.9 μm Dr Maisch, Germany) fused silica column (25 cm × 75 μM internal diameter (ID); New Objective, Woburn, MA, USA) by a Dionex Ultimate 3000 RSLCNano and monitored on a Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific , San Jose, CA, USA). ..

    Article Title: Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer
    Article Snippet: .. Data Acquisition Samples were analyzed using a UltiMate 3000 Nano LC system coupled to an Orbitrap Fusion Lumos Tribrid mass spectrometer equipped with an EasySpray Source (Thermo Fisher Scientific, San Jose, CA). ..

    Article Title: Altered secretion patterns and cell wall organization caused by loss of PodB function in the filamentous fungus Aspergillus nidulans
    Article Snippet: .. LC-MS/MS analysis NanoLC-MSMS analyses were carried out using a UltiMate™ 3000 RSLCnano system interfaced to an orbitrap Fusion Lumos tribrid mass spectrometer (Thermo Scientific, San Jose, CA). ..

    Article Title: Prevention of calpain-dependent degradation of STK38 by MEKK2-mediated phosphorylation
    Article Snippet: .. Nano liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) For the identification of phosphorylation sites, nanoLC-MS/MS was performed on an UltiMate 3000 RSLCnano system (Thermo Fisher Scientific) coupled to a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with nano ESI source. .. The nanoLC system was equipped with a trap column (C18 PepMap 100, 0.3 mm × 5 mm, 5 μm, Thermo Fisher Scientific) and an analytical column (NTCC-360/75-3-125, Nikkyo Technos, Tokyo, Japan).

    Chromatography:

    Article Title: A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions
    Article Snippet: .. Each sample in the second TMT experiment (which incorporated homogenate centrifugations steps) was analysed using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) during a 90 min nano‐liquid chromatography separation using a Dionex UltiMate 3000 RSLCnano system (Thermo Fisher Scientific). .. Samples were analysed using an MS1 AGC target of 1 × 106 and maximum injection times of 100 ms. MS cycle time was set to 2 s, and MS runs used an exclusion duration of 45 s, a quadrupole isolation window of 1.2 m / z , and HCD fragmentation using a collision energy of 35% and a stepped collision energy of 5%.

    Article Title: The N-Glycosylation of Mouse Immunoglobulin G (IgG)-Fragment Crystallizable Differs Between IgG Subclasses and Strains
    Article Snippet: .. Nanoliquid Chromatography Mass Spectrometry of Glycopeptides The 20 times diluted tryptic digests of the IgG samples were separated with an Ultimate 3000 RSLCnano system (Dionex/Thermo Scientific, Breda, the Netherlands) equipped with an Acclaim PepMap 100 trap column (100 μm × 20 mm, particle size 5 μm, Dionex/Thermo Scientific) and an Acclaim PepMap RSLC C18 nano-column (75 μm × 150 mm, particle size 2 μm, Dionex/Thermo Scientific). .. Two microliters of sample were injected and separated with a gradient from 97% solvent A (0.1% formic acid in water) and 3% solvent B (95% ACN) to 27% solvent B over 15 min, with a flow rate of 700 nL/min.

    Isolation:

    Article Title: A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions
    Article Snippet: Each sample in the second TMT experiment (which incorporated homogenate centrifugations steps) was analysed using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) during a 90 min nano‐liquid chromatography separation using a Dionex UltiMate 3000 RSLCnano system (Thermo Fisher Scientific). .. Samples were analysed using an MS1 AGC target of 1 × 106 and maximum injection times of 100 ms. MS cycle time was set to 2 s, and MS runs used an exclusion duration of 45 s, a quadrupole isolation window of 1.2 m / z , and HCD fragmentation using a collision energy of 35% and a stepped collision energy of 5%.

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex). .. Pre-defined precursor ions of interest were isolated by the quadrupole and fragmented in the higher-energy collisional dissociation (HCD) cell.

    Article Title: Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes
    Article Snippet: Peptide mixtures (6 μl) were separated on a self-packed C18 (1.9 μm Dr Maisch, Germany) fused silica column (25 cm × 75 μM internal diameter (ID); New Objective, Woburn, MA, USA) by a Dionex Ultimate 3000 RSLCNano and monitored on a Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific , San Jose, CA, USA). .. The MS scans (400–1,600 m/z range, 200,000 AGC, 50 ms maximum ion time) were collected at a resolution of 120,000 at m/z 200 in profile mode and the HCD MS/MS spectra (2 m/z isolation width, 30% collision energy, 10,000 AGC target, 35 ms maximum ion time) were detected in the ion trap.

    Size-exclusion Chromatography:

    Article Title: Altered secretion patterns and cell wall organization caused by loss of PodB function in the filamentous fungus Aspergillus nidulans
    Article Snippet: LC-MS/MS analysis NanoLC-MSMS analyses were carried out using a UltiMate™ 3000 RSLCnano system interfaced to an orbitrap Fusion Lumos tribrid mass spectrometer (Thermo Scientific, San Jose, CA). .. Data dependent MS2 and MS3 were carried with top of speed setting, cycle time is 3 sec. Full scan MS1 spectra were recorded in the range of m/z 400–1600 in the orbitrap at R = 120,000 (m/z 200).

    SDS-Gel:

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: After InstantBlue Coomassie staining, the corresponding immunoprecipitated SHP-2 band on the SDS gel was collected. .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex).

    Immunoprecipitation:

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: After InstantBlue Coomassie staining, the corresponding immunoprecipitated SHP-2 band on the SDS gel was collected. .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex).

    Incubation:

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: Gel slices were washed twice with 25 mM ABC buffer, destained in 25 mM ABC/50% acetonitrile (ACN) at 26 °C for 15 min, resuspended in 25 mM ABC buffer containing 0.05% Rapigest (Waters) plus 0.1 μg trypsin (sequencing grade, Promega), and then incubated at 37 °C for overnight. .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex).

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: MS-based cross-linking analysis reveals the location of the PsbQ protein in cyanobacterial photosystem II
    Article Snippet: The peptide samples were analyzed by using our LC-MS proteomics workflow ( ). .. The peptide sample was loaded onto an Ultimate 3000 Nano LC system (Thermo Scientific Dionex) coupled with an LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific).

    Article Title: MHC-associated peptide proteomics enabling highly sensitive detection of immunogenic sequences for the development of therapeutic antibodies with low immunogenicity
    Article Snippet: Paragraph title: Identification of HLA-DR-associated peptides with LC/MS ... Chromatographic separation was achieved using Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, Inc., Waltham, MA) with a C18 reversed phase nano-capillary column (3 μm, 75 μm x 120 mm) (Nikkyo Technos Co., Ltd., Tokyo, Japan), and the eluate was ionized under nano-electrospray, positive-ion mode and measured using an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific, Inc.).

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex). .. SHP-2 peptides were first trapped on a home-made precolumn (ReproSil-Pur 120 C18-AQ, 5 μm, Dr. Maisch GmbH; 100 μm × 5 cm) at 10 μl/ min of loading buffer (2% acetonitrile, 0.02% TFA in water) and then separated on an analytical column (ReproSil-Pur 120 C18-AQ, 1.9 μm, Dr. Maisch GmbH, 75 μm × 30 cm, self-packed) with a 40-min linear gradient ranging from 5% to 60% of buffer B (80% ACN/ 0.1% formic acid) and corresponding composition of Buffer A (0.1% formic acid in water) at a constant flow rate of 300 nl/min.

    Tandem Mass Spectroscopy:

    Article Title: A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions
    Article Snippet: Only peptides with charge states from +2 to +8 were selected for MS/MS using an exclusion duration of 40 s. Each phosphopeptide fraction was run in duplicate. .. Each sample in the second TMT experiment (which incorporated homogenate centrifugations steps) was analysed using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) during a 90 min nano‐liquid chromatography separation using a Dionex UltiMate 3000 RSLCnano system (Thermo Fisher Scientific).

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex). .. The MS instrument was operated in a targeted parallel reaction monitoring (PRM) mode comprised of a MS1 scan covering m/z range from 430 to 755 with resolution of 120,000 and several targeted MS/MS scans with resolution of 30,000.

    Article Title: Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans
    Article Snippet: Nano-LC separation was carried out using a Ultimate 3000 RSLCnano System equipped with an Acclaim PepMap RSLC column (C18, 75 µm × 15 cm with 2 µm particles, Thermo Scientific) preceded by a 2 cm Acclaim PepMap100 guard column (Thermo Scientific). .. MS analysis was performed employing a maXis Impact UHR-TOF-MS (Bruker Daltonics, Bremen, Germany) in data dependent MS/MS mode in the m/z 150–2200 range.

    Article Title: Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes
    Article Snippet: Peptide mixtures (6 μl) were separated on a self-packed C18 (1.9 μm Dr Maisch, Germany) fused silica column (25 cm × 75 μM internal diameter (ID); New Objective, Woburn, MA, USA) by a Dionex Ultimate 3000 RSLCNano and monitored on a Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific , San Jose, CA, USA). .. The MS scans (400–1,600 m/z range, 200,000 AGC, 50 ms maximum ion time) were collected at a resolution of 120,000 at m/z 200 in profile mode and the HCD MS/MS spectra (2 m/z isolation width, 30% collision energy, 10,000 AGC target, 35 ms maximum ion time) were detected in the ion trap.

    Sequencing:

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: Gel slices were washed twice with 25 mM ABC buffer, destained in 25 mM ABC/50% acetonitrile (ACN) at 26 °C for 15 min, resuspended in 25 mM ABC buffer containing 0.05% Rapigest (Waters) plus 0.1 μg trypsin (sequencing grade, Promega), and then incubated at 37 °C for overnight. .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex).

    Sonication:

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: Peptides were extracted from the gels by sonication in 5% trifluoroacetic acid (TFA)/50% ACN, and vacuum-dried for MS analysis. .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex).

    Injection:

    Article Title: A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions
    Article Snippet: These phosphopeptide fractions were also analysed with MS maximum injection times set at 50 ms for MS scans and 250 ms for MS/MS. .. Each sample in the second TMT experiment (which incorporated homogenate centrifugations steps) was analysed using an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific) during a 90 min nano‐liquid chromatography separation using a Dionex UltiMate 3000 RSLCnano system (Thermo Fisher Scientific).

    Article Title: The N-Glycosylation of Mouse Immunoglobulin G (IgG)-Fragment Crystallizable Differs Between IgG Subclasses and Strains
    Article Snippet: Nanoliquid Chromatography Mass Spectrometry of Glycopeptides The 20 times diluted tryptic digests of the IgG samples were separated with an Ultimate 3000 RSLCnano system (Dionex/Thermo Scientific, Breda, the Netherlands) equipped with an Acclaim PepMap 100 trap column (100 μm × 20 mm, particle size 5 μm, Dionex/Thermo Scientific) and an Acclaim PepMap RSLC C18 nano-column (75 μm × 150 mm, particle size 2 μm, Dionex/Thermo Scientific). .. Two microliters of sample were injected and separated with a gradient from 97% solvent A (0.1% formic acid in water) and 3% solvent B (95% ACN) to 27% solvent B over 15 min, with a flow rate of 700 nL/min.

    Article Title: MHC-associated peptide proteomics enabling highly sensitive detection of immunogenic sequences for the development of therapeutic antibodies with low immunogenicity
    Article Snippet: The peptide mixtures obtained were reconstituted in acidic water containing 2% acetonitrile, and approximately one-third of the sample volume was injected onto a nano-LC/MS system. .. Chromatographic separation was achieved using Ultimate 3000 RSLCnano system (Thermo Fisher Scientific, Inc., Waltham, MA) with a C18 reversed phase nano-capillary column (3 μm, 75 μm x 120 mm) (Nikkyo Technos Co., Ltd., Tokyo, Japan), and the eluate was ionized under nano-electrospray, positive-ion mode and measured using an Orbitrap Elite mass spectrometer (Thermo Fisher Scientific, Inc.).

    Article Title: Queuosine‐modified tRNAs confer nutritional control of protein translation
    Article Snippet: The peptides were measured on a Q‐Exactive Plus mass spectrometer (Thermo Scientific) coupled to an Ultimate 3000 RSLCnano system (Thermo Scientific) in data‐dependent acquisition mode, selecting the top 12 peaks for higher energy collisional dissociation (HCD) fragmentation. .. A volume of 3 μl sample was injected and the peptides eluted with 90 min gradients of 2–35% solvent B at flowrates of 0.3 μl/min.

    Article Title: Analyses of the Xylem Sap Proteomes Identified Candidate Fusarium virguliforme Proteinacious Toxins
    Article Snippet: The Orbitrap was interfaced with an UltiMate3000 RSLCnano system (Dionex, Sunnyvale, CA). .. The reconstituted peptides (2 µL) were injected under “User Defined Program” onto a PepMap C18 trap column (5 µm, 300 µm×5 mm, Dionex) at a 20 µL/min flow rate for on-line desalting and then separated on a PepMap C18 RP nano column (3 µm, 75 µm×15 cm, Dionex) which was installed in the “Plug and Play” device with a 10-µm spray emitter (New Objective, Woburn, MA) mounted in front of the Orbitrap orifice.

    Liquid Chromatography:

    Article Title: Prevention of calpain-dependent degradation of STK38 by MEKK2-mediated phosphorylation
    Article Snippet: .. Nano liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) For the identification of phosphorylation sites, nanoLC-MS/MS was performed on an UltiMate 3000 RSLCnano system (Thermo Fisher Scientific) coupled to a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with nano ESI source. .. The nanoLC system was equipped with a trap column (C18 PepMap 100, 0.3 mm × 5 mm, 5 μm, Thermo Fisher Scientific) and an analytical column (NTCC-360/75-3-125, Nikkyo Technos, Tokyo, Japan).

    Derivative Assay:

    Article Title: Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes
    Article Snippet: Derived peptides were resuspended in peptide 20 μl of loading buffer (0.1% formic acid, 0.03% trifluoroacetic acid, 1% acetonitrile). .. Peptide mixtures (6 μl) were separated on a self-packed C18 (1.9 μm Dr Maisch, Germany) fused silica column (25 cm × 75 μM internal diameter (ID); New Objective, Woburn, MA, USA) by a Dionex Ultimate 3000 RSLCNano and monitored on a Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific , San Jose, CA, USA).

    Staining:

    Article Title: S-nitrosylation of endogenous protein tyrosine phosphatases in endothelial insulin signaling
    Article Snippet: After InstantBlue Coomassie staining, the corresponding immunoprecipitated SHP-2 band on the SDS gel was collected. .. All LC-MS analysis was performed on a Q Exactive HF (Thermo Fisher Scientific) mass spectrometer coupled with Ultimate 3000 RSLCnano System (Dionex).

    Article Title: Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans
    Article Snippet: After overnight staining using a Colloidal Blue Staining Kit (Thermo Scientific), destained gel lanes were processed into 31 slices per lane. .. Nano-LC separation was carried out using a Ultimate 3000 RSLCnano System equipped with an Acclaim PepMap RSLC column (C18, 75 µm × 15 cm with 2 µm particles, Thermo Scientific) preceded by a 2 cm Acclaim PepMap100 guard column (Thermo Scientific).

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  • 99
    Thermo Fisher ultimate3000 rslc nano hplc system
    Ultimate3000 Rslc Nano Hplc System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 2 article reviews
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    94
    Thermo Fisher ultimate3000 nano hplc system
    Ultimate3000 Nano Hplc System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 10 article reviews
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    94
    Thermo Fisher nano high pressure liquid chromatography system
    Nano High Pressure Liquid Chromatography System, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nano high pressure liquid chromatography system/product/Thermo Fisher
    Average 94 stars, based on 8 article reviews
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    nano high pressure liquid chromatography system - by Bioz Stars, 2020-04
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