Four hundred nanograms of 8 AM and 8 MN peptide digests were randomized with blanks between and loaded on a column in a 14 μL injection for a total of 16 LC/MS/MS runs. Resulting data was acquired on an OrbitrapVelos Elite mass spectrometer (Thermo Electron, San Jose, CA) equipped with a Waters nanoACQUITY LC system (Waters, Taunton, MA). Peptides were desalted in a trap column (180 μm × 20 mm, packed with C18 Symmetry, 5 μm, 100A, Waters, Taunton, MA) and subsequently resolved in a reversed phase column (75 μm × 250 mm nano column, packed with C18 BEH130, 1.7 μm, 130A (Waters, Taunton, MA). LC was carried out at ambient temperature at a flow rate of 300 nL/min using a gradient mixture of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B). The gradient employed ranged from 4 to 44% solvent B over 210 min. Peptides eluting from the capillary tip were introduced into the nanospray mode with a capillary voltage of 2.4 kV. A full scan was obtained for eluted peptides in the range of 380–1800 amu followed by 25 data dependent MS/MS scans. MS/MS spectra were generated by collision-induced dissociation of the peptide ions at normalized collision energy of 35% to generate a series of b- and y-ions as major fragments. In addition a one-hour wash was included between each sample.
Waters nanoacquity lc system
Manufactured by Waters Corporation
Sourced in United States
The Waters nanoACQUITY LC system is a high-performance liquid chromatography (HPLC) instrument designed for the analysis of nanoscale samples. It utilizes nanoflow technology to enable the separation and detection of minute quantities of analytes with high sensitivity and resolution.
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5 protocols using waters nanoacquity lc system
1
Shotgun Proteomics Analysis of Peptide Digests
2
Comprehensive Proteomic Analysis of Cercarial Heads and Tails
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Sample injections of 11 μL containing 600 ng digested peptide was loaded with blank runs intervening between each sample. The cercarial heads and tails were run in triplicate. The Orbitrap Velos Elite mass spectrometer (Thermo Electron, San Jose, CA) equipped with the Waters nanoACQUITY LC system (Waters, Taunton, MA) was used for acquisition. Peptides were desalted in a trap column (180 μm × 20 mm, packed with C18 Symmetry, 5 μm, 100 Å, Waters, Taunton, MA) and subsequently resolved in a reversed-phase column (75 μm × 250 mm nano column, packed with C18 BEH130, 1.7 μm, 130 Å (Waters, Taunton, MA). Liquid chromatography was carried out at ambient temperature at a flow rate of 300 nL/min using a gradient mixture of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B). The gradient employed ranged from 4 to 44% solvent B over 210 min. Peptides eluting from the capillary tip were introduced into the nanospray mode with a capillary voltage of 2.4 kV. A full scan was obtained for eluted peptides in the range of 380–1800 atomic mass units, followed by twenty-five data-dependent MS/MS scans. MS/MS spectra were generated by collision-induced dissociation of the peptide ions at a normalized collision energy of 35% to create a series of b- and y-ions as major fragments. A one-hour wash was included between each sample.
3
Sensitive DIA-MS Proteomics Analysis
4
Peptide Identification via Orbitrap Mass Spectrometry
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For each sample, 400ng of AM and MN peptide digests were loaded on a column in a 14μL injection. Samples were randomized and blanks were added between samples. Resulting data was acquired on an Orbitrap Velos Elite mass spectrometer (Thermo Electron, San Jose, CA) equipped with a Waters nanoAcquity LC system (Waters, Taunton, MA). Peptides were desalted in a trap column (180 μm × 20 mm, packed with C18 Symmetry, 5μm, 100Å, Waters, Taunton, MA) and subsequently resolved in a reversed phase column (75μm x 250 mm nano column, packed with C18 BEH130, 1.7μm, 130Å (Waters, Taunton, MA)). Liquid chromatography was carried out at ambient temperature at a flow rate of 300 nL/min using a gradient mixture of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B). The gradient employed ranged from 4 to 44% solvent B over 210 min. Peptides eluting from the capillary tip were introduced into the nanospray mode with a capillary voltage of 2.4 kV. A full scan was obtained for eluted peptides in the range of 380–1800 atomic mass units followed by twenty-five data dependent MS/MS scans. MS/MS spectra were generated by collision-induced dissociation of the peptide ions at normalized collision energy of 35% to generate a series of b- and y-ions as major fragments. A one-hour wash was included between each sample.
5
Proteomic Analysis of Cercarial Parasites
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Sample injections of 11 μL containing 600 ng digested peptide was loaded with blank runs intervening between each sample. The cercarial heads and tails were run in triplicate. The Orbitrap Celos Elite mass spectrometer (Thermo Electron, San Jose, CA) equipped with the Waters nanoACQUITY LC system (Waters, Taunton, MA) was used for acquisition. Peptides were desalted in a trap column (180 μm × 20 mm, packed with C18 Symmetry, 5μm, 100Å, Waters, Taunton, MA) and subsequently resolved in a reversed-phase column (75μm x 250 mm nano column, packed with C18 BEH130, 1.7μm, 130Å (Waters, Taunton, MA). Liquid chromatography was carried out at ambient temperature at a flow rate of 300 nL/min using a gradient mixture of 0.1% formic acid in water (solvent A) and 0.1% formic acid in acetonitrile (solvent B). The gradient employed ranged from 4 to 44% solvent B over 210 min. Peptides eluting from the capillary tip were introduced into the nanospray mode with a capillary voltage of 2.4 kV. A full scan was obtained for eluted peptides in the range of 380-1800 atomic mass units followed by twenty-five data-dependent MS/MS scans. MS/MS spectra were generated by collision-induced dissociation of the peptide ions at a normalized collision energy of 35% to create a series of b-and y-ions as major fragments. A one-hour wash was included between each sample.
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