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: 92/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ultimate3000 nano hplc system/product/Thermo Fisher
    Average 92 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    ultimate3000 nano hplc system - by Bioz Stars, 2020-01
    92/100 stars

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    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, Mass Spectrometry, Mouse Assay, High Performance Liquid Chromatography, Expressing

    Related Articles

    Centrifugation:

    Article Title:
    Article Snippet: HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific). .. The monophosphorylated-peptide-enriched sample was then loaded onto a TSKgel Amide-80 HILIC 1 mm × 250 mm column (Tosoh Bioscience, Tokyo, Japan) using gradient elution from 90% ACN, 0.1% TFA to 60% ACN, 0.1% TFA for 35 min at 50 μl/min.

    Mass Spectrometry:

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    Article Snippet: LC-MS-MS and label-free quantification were performed as described . .. 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) . .. MS spectra were acquired in OrbitrapXL and up to 10 of the most abundant peptide ions selected for fragmentation in the linear ion trap.

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: Paragraph title: Sample preparation and MS-based proteomic analysis ... LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: Paragraph title: Mass spectrometry for identification of interacting proteins ... Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer.

    Article Title:
    Article Snippet: Paragraph title: Mass Spectrometry ... Briefly, every sample was automatically loaded onto an Ultimate3000 nano-HPLC system (Dionex) with a nano-trap column (300 μm inner diameter × 5 mm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; LC Packings) at a flow rate of 30 μl/min in HPLC buffer containing 0.1% TFA for 5 min. Peptides were separated on a reversed phase chromatography (PepMap, 25 cm, 75 μm inner diameter, 1 μm/100 Å pore size, LC Packings) over 80 or 140 min at a flow rate of 300 nl/min using increasing acetonitrile concentrations in 0.1% formic acid.

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously [ ]. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. The raw data were analyzed using Sequest (Thermo Fisher Scientific) or Mascot and Scaffold (Proteome Software) as described previously [ ].

    Article Title: Structural and functional protein network analyses predict novel signaling functions for rhodopsin
    Article Snippet: Database searches were performed using the Mascot software ( ). .. LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. Tryptic peptide mixtures were automatically injected and loaded with a flow rate of 30 μl/min in 95% buffer C (0.5% TFA in HPLC-grade water) and 5% buffer B (98% acetonitrile, 0.1% formic acid in HPLC-grade water) onto a nanotrap column (100 μm i.d.

    Article Title:
    Article Snippet: The peptides generated by tryptic digests were acidified and then subjected to LC-MS/MS as described elsewhere ( ). .. Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. Tryptic peptides were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm inner diameter × 2 cm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; Dionex).

    Article Title: Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously ( ). .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Tryptic peptide mixtures were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm i.d.

    Article Title:
    Article Snippet: Soluble phase was retrieved and used immediately for LC-MSMS analysis. .. LC-MSMS analysis was performed on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA) online coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Samples originating from in-solution digests of membrane fractions of retinal tissue were acidified with TFA and automatically loaded to the HPLC system equipped with a nano trap column (100 μm i.d.

    Construct:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: HEK293T cells transiently expressing the SF-TAP tagged constructs were lysed in lysis buffer containing 0.5% Nonidet-P40, protease inhibitor cocktail (Roche), and phosphatase inhibitor cocktails I and II (Sigma-Aldrich) in TBS (30 mM Tris-HCl, pH 7.4, and 150 mM NaCl) for 20 minutes at 4°C. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Incubation:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: The protein complexes were eluted by incubation for 10 minutes in Strep-elution buffer (IBA). .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Expressing:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: HEK293T cells transiently expressing the SF-TAP tagged constructs were lysed in lysis buffer containing 0.5% Nonidet-P40, protease inhibitor cocktail (Roche), and phosphatase inhibitor cocktails I and II (Sigma-Aldrich) in TBS (30 mM Tris-HCl, pH 7.4, and 150 mM NaCl) for 20 minutes at 4°C. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Derivative Assay:

    Article Title:
    Article Snippet: Protein samples derived from cellular fractions before Strep pull-down were processed via filter-aided sample preparation as described elsewhere ( ). .. Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    High Performance Liquid Chromatography:

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    Article Snippet: LC-MS-MS and label-free quantification were performed as described . .. 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) . .. MS spectra were acquired in OrbitrapXL and up to 10 of the most abundant peptide ions selected for fragmentation in the linear ion trap.

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: LC-MS/MS analyses were performed on an LTQ OrbitrapXL (Thermo Fisher Scientific, Bremen, Germany). .. Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer. .. Peptides were separated on a reversed phase chromatography over 140 min at a flow rate of 300 nl/min.

    Article Title:
    Article Snippet: LC-MS/MS analysis was performed as described previously on an LTQ OrbitrapXL (Thermo Fisher Scientific Inc.) ( – ). .. Briefly, every sample was automatically loaded onto an Ultimate3000 nano-HPLC system (Dionex) with a nano-trap column (300 μm inner diameter × 5 mm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; LC Packings) at a flow rate of 30 μl/min in HPLC buffer containing 0.1% TFA for 5 min. Peptides were separated on a reversed phase chromatography (PepMap, 25 cm, 75 μm inner diameter, 1 μm/100 Å pore size, LC Packings) over 80 or 140 min at a flow rate of 300 nl/min using increasing acetonitrile concentrations in 0.1% formic acid. .. Maximal injection time for MS spectra was 100 ms and for MS/MS spectra 500 ms. MS data were acquired using from the high resolution MS prescan the 10 most abundant peptide ions for fragmentation in the linear ion trap, if they were at least doubly charged and have an intensity of at least 200 counts, with a dynamic exclusion of 45 s and an isolation width of 2 atomic mass units.

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously [ ]. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. The raw data were analyzed using Sequest (Thermo Fisher Scientific) or Mascot and Scaffold (Proteome Software) as described previously [ ].

    Article Title: Structural and functional protein network analyses predict novel signaling functions for rhodopsin
    Article Snippet: LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Article Title:
    Article Snippet: Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. Tryptic peptides were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm inner diameter × 2 cm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; Dionex).

    Article Title:
    Article Snippet: The eluate was immediately concentrated by evaporation and adjusted to the starting conditions of HILIC chromatography (90% acetonitrile/0.1% TFA). .. HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific). .. The monophosphorylated-peptide-enriched sample was then loaded onto a TSKgel Amide-80 HILIC 1 mm × 250 mm column (Tosoh Bioscience, Tokyo, Japan) using gradient elution from 90% ACN, 0.1% TFA to 60% ACN, 0.1% TFA for 35 min at 50 μl/min.

    Article Title: Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously ( ). .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Tryptic peptide mixtures were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm i.d.

    Article Title:
    Article Snippet: Soluble phase was retrieved and used immediately for LC-MSMS analysis. .. LC-MSMS analysis was performed on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA) online coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Samples originating from in-solution digests of membrane fractions of retinal tissue were acidified with TFA and automatically loaded to the HPLC system equipped with a nano trap column (100 μm i.d.

    Flow Cytometry:

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: LC-MS/MS analyses were performed on an LTQ OrbitrapXL (Thermo Fisher Scientific, Bremen, Germany). .. Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer. .. Peptides were separated on a reversed phase chromatography over 140 min at a flow rate of 300 nl/min.

    Article Title:
    Article Snippet: LC-MS/MS analysis was performed as described previously on an LTQ OrbitrapXL (Thermo Fisher Scientific Inc.) ( – ). .. Briefly, every sample was automatically loaded onto an Ultimate3000 nano-HPLC system (Dionex) with a nano-trap column (300 μm inner diameter × 5 mm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; LC Packings) at a flow rate of 30 μl/min in HPLC buffer containing 0.1% TFA for 5 min. Peptides were separated on a reversed phase chromatography (PepMap, 25 cm, 75 μm inner diameter, 1 μm/100 Å pore size, LC Packings) over 80 or 140 min at a flow rate of 300 nl/min using increasing acetonitrile concentrations in 0.1% formic acid. .. Maximal injection time for MS spectra was 100 ms and for MS/MS spectra 500 ms. MS data were acquired using from the high resolution MS prescan the 10 most abundant peptide ions for fragmentation in the linear ion trap, if they were at least doubly charged and have an intensity of at least 200 counts, with a dynamic exclusion of 45 s and an isolation width of 2 atomic mass units.

    Article Title: Structural and functional protein network analyses predict novel signaling functions for rhodopsin
    Article Snippet: LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Article Title:
    Article Snippet: Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. Tryptic peptides were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm inner diameter × 2 cm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; Dionex).

    Article Title: Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice
    Article Snippet: LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source.

    Article Title:
    Article Snippet: LC-MSMS analysis was performed on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA) online coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Samples originating from in-solution digests of membrane fractions of retinal tissue were acidified with TFA and automatically loaded to the HPLC system equipped with a nano trap column (100 μm i.d.

    Chromatography:

    Article Title:
    Article Snippet: The eluate was immediately concentrated by evaporation and adjusted to the starting conditions of HILIC chromatography (90% acetonitrile/0.1% TFA). .. HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific).

    Ligation:

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: PL3 -labeled samples were instead conjugated to EZ-Link™ Phosphine-PEG3 -Biotin (Sigma Aldrich) via Staudinger ligation (0.2 mM per 1 ml sample, 2 mg protein, 4 h at 37°C, then 20 h at 25°C). .. LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Protease Inhibitor:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: HEK293T cells transiently expressing the SF-TAP tagged constructs were lysed in lysis buffer containing 0.5% Nonidet-P40, protease inhibitor cocktail (Roche), and phosphatase inhibitor cocktails I and II (Sigma-Aldrich) in TBS (30 mM Tris-HCl, pH 7.4, and 150 mM NaCl) for 20 minutes at 4°C. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Liquid Chromatography:

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    Article Snippet: LC-MS-MS and label-free quantification were performed as described . .. 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) . .. MS spectra were acquired in OrbitrapXL and up to 10 of the most abundant peptide ions selected for fragmentation in the linear ion trap.

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: LC-MS/MS analyses were performed on an LTQ OrbitrapXL (Thermo Fisher Scientific, Bremen, Germany). .. Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer.

    Article Title:
    Article Snippet: LC-MS/MS analysis was performed as described previously on an LTQ OrbitrapXL (Thermo Fisher Scientific Inc.) ( – ). .. Briefly, every sample was automatically loaded onto an Ultimate3000 nano-HPLC system (Dionex) with a nano-trap column (300 μm inner diameter × 5 mm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; LC Packings) at a flow rate of 30 μl/min in HPLC buffer containing 0.1% TFA for 5 min. Peptides were separated on a reversed phase chromatography (PepMap, 25 cm, 75 μm inner diameter, 1 μm/100 Å pore size, LC Packings) over 80 or 140 min at a flow rate of 300 nl/min using increasing acetonitrile concentrations in 0.1% formic acid. .. Maximal injection time for MS spectra was 100 ms and for MS/MS spectra 500 ms. MS data were acquired using from the high resolution MS prescan the 10 most abundant peptide ions for fragmentation in the linear ion trap, if they were at least doubly charged and have an intensity of at least 200 counts, with a dynamic exclusion of 45 s and an isolation width of 2 atomic mass units.

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously [ ]. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. The raw data were analyzed using Sequest (Thermo Fisher Scientific) or Mascot and Scaffold (Proteome Software) as described previously [ ].

    Article Title: Structural and functional protein network analyses predict novel signaling functions for rhodopsin
    Article Snippet: Database searches were performed using the Mascot software ( ). .. LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. Tryptic peptide mixtures were automatically injected and loaded with a flow rate of 30 μl/min in 95% buffer C (0.5% TFA in HPLC-grade water) and 5% buffer B (98% acetonitrile, 0.1% formic acid in HPLC-grade water) onto a nanotrap column (100 μm i.d.

    Article Title:
    Article Snippet: The peptides generated by tryptic digests were acidified and then subjected to LC-MS/MS as described elsewhere ( ). .. Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source. .. Tryptic peptides were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm inner diameter × 2 cm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; Dionex).

    Article Title:
    Article Snippet: HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific). .. Fractions were collected in a 96-well plate, evaporated by vacuum centrifugation, and redissolved in 5 μl of 0.1% formic acid.

    Article Title: Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously ( ). .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Tryptic peptide mixtures were automatically injected and loaded at a flow rate of 30 μl/min in 95% buffer C (0.5% trifluoroacetic acid in HPLC-grade water) and 5% buffer B (98% actetonitrile and 0.1% formic acid in HPLC-grade water) onto a nano trap column (100 μm i.d.

    Article Title:
    Article Snippet: Soluble phase was retrieved and used immediately for LC-MSMS analysis. .. LC-MSMS analysis was performed on an Ultimate3000 nano HPLC system (Dionex, Sunnyvale, CA) online coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nano spray ion source. .. Samples originating from in-solution digests of membrane fractions of retinal tissue were acidified with TFA and automatically loaded to the HPLC system equipped with a nano trap column (100 μm i.d.

    Sedimentation:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: After sedimentation of nuclei at 10,000 g for 10 minutes, the cleared lysates were transferred to Strep-Tactin-Superflow beads (IBA) and incubated for 1 hour before the resin was washed 3 times with wash buffer (TBS containing 0.1% NP-40 and phosphatase inhibitor cocktails I and II). .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Generated:

    Article Title:
    Article Snippet: The peptides generated by tryptic digests were acidified and then subjected to LC-MS/MS as described elsewhere ( ). .. Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Tandem Mass Spectroscopy:

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer. .. Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer.

    Injection:

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer. .. Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer.

    Avidin-Biotin Assay:

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: Upon avidin-bead enrichment, samples were reduced with 5 mM TCEP (1 h at 37°C), alkylated using 10 mM IAA (30 min at 25°C) and quenched with 10 mM DTT (30 min at 25°C) on-bead. .. LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Labeling:

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: PL3 -labeled samples were instead conjugated to EZ-Link™ Phosphine-PEG3 -Biotin (Sigma Aldrich) via Staudinger ligation (0.2 mM per 1 ml sample, 2 mg protein, 4 h at 37°C, then 20 h at 25°C). .. LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Size-exclusion Chromatography:

    Article Title: Interaction of septin 7 and DOCK8 in equine lymphocytes reveals novel insights into signaling pathways associated with autoimmunity
    Article Snippet: Briefly, peptides were loaded onto an Ultimate3000 nano HPLC system (Dionex, Idstein, Germany) equipped with a nano trap column at a flow rate of 30 µl/min in HPLC-buffer. .. MS spectra were recorded within a mass range from 200–2000 Da at a resolution of 60,000 full-width half-maximum.

    Lysis:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: HEK293T cells transiently expressing the SF-TAP tagged constructs were lysed in lysis buffer containing 0.5% Nonidet-P40, protease inhibitor cocktail (Roche), and phosphatase inhibitor cocktails I and II (Sigma-Aldrich) in TBS (30 mM Tris-HCl, pH 7.4, and 150 mM NaCl) for 20 minutes at 4°C. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Purification:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: After purification, the samples were precipitated with chloroform and methanol and subjected to in-solution tryptic cleavage as described previously [ ]. .. LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Affinity Purification:

    Article Title: The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
    Article Snippet: Paragraph title: Affinity purification of protein complexes ... LC-MS/MS analysis was performed on an Ultimate3000 nano HPLC system (Dionex) coupled to a LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Software:

    Article Title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration
    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) . .. MS spectra were acquired in OrbitrapXL and up to 10 of the most abundant peptide ions selected for fragmentation in the linear ion trap.

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific). .. Data were acquired using Xcalibur software version 3.0sp2 (Thermo Fisher Scientific).

    Hydrophilic Interaction Liquid Chromatography:

    Article Title:
    Article Snippet: The eluate was immediately concentrated by evaporation and adjusted to the starting conditions of HILIC chromatography (90% acetonitrile/0.1% TFA). .. HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific). .. The monophosphorylated-peptide-enriched sample was then loaded onto a TSKgel Amide-80 HILIC 1 mm × 250 mm column (Tosoh Bioscience, Tokyo, Japan) using gradient elution from 90% ACN, 0.1% TFA to 60% ACN, 0.1% TFA for 35 min at 50 μl/min.

    Sample Prep:

    Article Title: Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics
    Article Snippet: Paragraph title: Sample preparation and MS-based proteomic analysis ... LC-MS/MS analysis was performed with an Ultimate3000 Nano-HPLC system (Thermo Fisher Scientific) coupled to an Orbitrap Fusion instrument (Thermo Fisher Scientific).

    Article Title:
    Article Snippet: Protein samples derived from cellular fractions before Strep pull-down were processed via filter-aided sample preparation as described elsewhere ( ). .. Briefly, LC-MS/MS analysis was performed on an Ultimate3000 nano-HPLC system (Dionex, Sunnyvale, CA) coupled to an LTQ OrbitrapXL mass spectrometer (Thermo Fisher Scientific) by a nanospray ion source.

    Article Title:
    Article Snippet: Paragraph title: Sample Preparation for Phosphoproteomics ... HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific).

    Evaporation:

    Article Title:
    Article Snippet: The eluate was immediately concentrated by evaporation and adjusted to the starting conditions of HILIC chromatography (90% acetonitrile/0.1% TFA). .. HILIC separation was performed using a Dionex UltiMate3000 nano HPLC system (Thermo Fisher Scientific).

    Reversed-phase Chromatography:

    Article Title:
    Article Snippet: LC-MS/MS analysis was performed as described previously on an LTQ OrbitrapXL (Thermo Fisher Scientific Inc.) ( – ). .. Briefly, every sample was automatically loaded onto an Ultimate3000 nano-HPLC system (Dionex) with a nano-trap column (300 μm inner diameter × 5 mm, packed with Acclaim PepMap100 C18, 5 μm, 100 Å; LC Packings) at a flow rate of 30 μl/min in HPLC buffer containing 0.1% TFA for 5 min. Peptides were separated on a reversed phase chromatography (PepMap, 25 cm, 75 μm inner diameter, 1 μm/100 Å pore size, LC Packings) over 80 or 140 min at a flow rate of 300 nl/min using increasing acetonitrile concentrations in 0.1% formic acid. .. Maximal injection time for MS spectra was 100 ms and for MS/MS spectra 500 ms. MS data were acquired using from the high resolution MS prescan the 10 most abundant peptide ions for fragmentation in the linear ion trap, if they were at least doubly charged and have an intensity of at least 200 counts, with a dynamic exclusion of 45 s and an isolation width of 2 atomic mass units.

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