Nanoacquity liquid chromatography system

Manufactured by Waters Corporation

The NanoACQUITY liquid chromatography system is a high-performance liquid chromatography (HPLC) instrument designed for the separation and analysis of small-volume samples. It features a compact design and advanced technology to provide precise and efficient liquid chromatography performance.

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Lab products found in correlation

Thermo velos orbitrap mass spectrometer, by Thermo Fisher Scientific (2 mentions) Sypro ruby, by Thermo Fisher Scientific (2 mentions) Ltq orbitrap velos mass spectrometer, by Thermo Fisher Scientific (2 mentions) Xevo qtof mass spectrometer, by Waters Corporation (1 mentions) Tsq quantiva, by Thermo Fisher Scientific (1 mentions) Micro bicinchoninic acid assay, by Thermo Fisher Scientific (1 mentions) Pinpoint 1, by Thermo Fisher Scientific (1 mentions)

Close spelling variants of this product

NanoAcquity (157 citations) NanoAcquity system (49 citations) NanoACQUITY ultra-performance liquid chromatography system (25 citations) Liquid chromatography system (19 citations) NanoAcquity Ultra-high pressure liquid chromatography system (6 citations) NanoAcquity chromatography system (4 citations)

8 protocols using nanoacquity liquid chromatography system

Protein Peptide Analysis by Mass Spectrometry

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Protein‐derived peptides were analyzed by the LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific Inc) coupled with a nanoAcquity liquid chromatography system (Waters). Peptide separation was performed using solution A (0.1% formic acid in liquid chromatography and mass spectrometry [MS]–grade water) and solution B (0.1% formic acid in liquid chromatography–MS acetonitrile) as mobile phases. Gradient runs from 2% to 30% solution B in 100 minutes and from 30% to 60% in 10 minutes were followed by a final 10‐minute wash at 85% solution B.
Full MS scans were acquired in the Orbitrap mass analyzer over the range m/z 375 to 1500 with a mass resolution of 30 000. Tandem MS (MS/MS) was acquired using top 7 data‐dependent acquisition with high‐energy collision dissociation (40%). The gas‐phase fractionation method was applied to acquire MS/MS scans.

Afzal T.A., Luong L.A., Chen D., Zhang C., Yang F., Chen Q., An W., Wilkes E., Yashiro K., Cutillas P.R., Zhang L, & Xiao Q. (2016). NCK Associated Protein 1 Modulated by miRNA‐214 Determines Vascular Smooth Muscle Cell Migration, Proliferation, and Neointima Hyperplasia. Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, 5(12), e004629.

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Nanoscale Proteomics Analysis Protocol

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The trypsin digested samples were analyzed using a Waters Xevo QTOF mass spectrometer equipped with a nanospray source, coupled to a Waters NanoAcquity liquid chromatography system. The samples were injected onto an Acquity UPLC Symmetry C18 10 K 2 g V/M trapping column, and eluted onto an Acquity UPLC peptide BEH C18 column 130 A, 1.7, 75 µm × 250 mm. In-line fractionation was done using a two-phase gradient system. Solvent A was 2% acetonitrile (ACN) in 0.1% formic acid and (solvent B)100% ACN was 0.1% formic acid. The mass spectrum acquisition was done in positive-ion survey mode using a data-dependent method. The mass acquisition window was set for 100 −1990m/z in full MS mode. The detector was set to positive ions in continuum mode. An intensity threshold was set for 50 counts /sec with a scan time of 0.9 sec. MS/MS mode was set with a mass window of 50–1990 m/z. Three MSMS scans were collected for each MS peak with charge state peak selection from +1 to +4. The collision energy was ramped according to charge.

Hicks W., Meng F., Kassa T, & Alayash A.I. (2020). Effects of α subunit substitutions on the oxidation of βCys93 and the stability of sickle cell hemoglobin. Redox Report : Communications in Free Radical Research, 25(1), 95-103.

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Mass Spectrometry Analysis of Membrane Proteins

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Proteins isolated from membranes, or membrane proteins that bind to PIP₃-coated beads, were dissolved in Laemmli buffer as described above, and separated in one dimension on 1% SDS, 4–12% acrylamide gradient gels. They were then stained with SYPRO Ruby (Thermo-Fisher) or Coomassie Blue to visualize total protein, and 1-mm slices were excised. Proteins were digested in situ with trypsin, and peptides analyzed by high-resolution LC-MS/MS with a Thermo-Velos Orbitrap mass spectrometer (ThermoFisher) coupled to a nanoACQUITY liquid chromatography system (Waters, Milford MA) as described previously (Ayyadevara et al., 2016a (link); Ayyadevara et al., 2016b (link)). Proteins were identified by MASCOT software www.matrixscience.com) matching of peptide fragmentation patterns to a database of previously observed fragment patterns (Ayyadevara et al., 2016a (link); Ayyadevara et al., 2016b (link)).

Ayyadevara S., Ganne A., Hendrix R.D., Balasubramaniam M., Shmookler Reis R.J, & Barger S.W. (2018). Functional assessments through novel proteomics approaches: Application to insulin/IGF signaling in neurodegenerative disease. Journal of neuroscience methods, 319, 40-46.

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Quantifying HER2 Protein Levels by SRM Mass Spectrometry

Cited 1 time

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HER2 protein level was quantified by SRM mass spectrometry as previously described [9–11 (link)]. Briefly, one section was cut for hematoxylin and eosin (H&E) staining, and multiple sections were cut on to Director® microdissection slides and stained with eosin. The H&E was used to guide tumor area selection on the slide sections, which were then microdissected (Molecular Machines & Industries, Eching, Germany). Collected tumor tissue was solubilized using Liquid Tissue® according to manufacturer’s instructions. Total protein concentration from each sample was measured by a micro bicinchoninic acid assay (Thermo Fisher Scientific Inc, Waltham, MA).
A mixture of stable isotope-labeled synthetic peptides was added to the liquefied tumor samples as internal standards. All samples were analyzed in triplicate using a triple quadrupole mass spectrometer (TSQ Quantiva™, Thermo Scientific, Waltham, MA) interfacing with a nanoACQUITY liquid chromatography system (Waters Corporation, Milford, MA). A 100 µm inner diameter chromatographic column packed with C18 resin (ProntoSIL 200-5-C18AQ; Bischoff Chromatography, Germany) was used for peptide separation before mass spectrometry analysis. For protein quantitation, peak areas from each endogenous and internal standard peptide were calculated and ratios were determined using PinPoint 1.3 (Thermo Scientific, Waltham, MA).

An E., Ock C.Y., Kim T.Y., Lee K.H., Han S.W., Im S.A., Kim T.Y., Liao W.L., Cecchi F., Blackler A., Thyparambil S., Kim W.H., Burrows J., Hembrough T., Catenacci D.V., Oh D.Y, & Bang Y.J. (2016). Quantitative proteomic analysis of HER2 expression in the selection of gastric cancer patients for trastuzumab treatment. Annals of Oncology, 28(1), 110-115.

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Proteomic Analysis of Aortic Proteins

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Proteomics studies and data analysis were conducted as described in our previous studies.^{18 (link),29 (link),32 (link),40 (link)} Briefly, the loosely bound newly synthesized proteins in aorta were specifically extracted and enriched using a similar method reported by Didangelos et al^{41 (link),42} from both WT and NE-KO mice that received an Ang II infusion for 2 weeks. The extracted aortic proteins were digested using trypsin, and protein-derived peptides were analyzed by the LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific, Inc) coupled with a nanoAcquity liquid chromatography system (Waters) as detailed in our previous study.^{40 (link)} The fold changes of protein expressions between WT and NE-KO aortas were transformed using the log₂ function, while the P values were −log10 transformed for volcano plot analysis.

Yang M., Zhou X., Pearce S.W., Yang Z., Chen Q., Niu K., Liu C., Luo J., Li D., Shao Y., Zhang C., Chen D., Wu Q., Cutillas P.R., Zhao L., Xiao Q, & Zhang L. (2023). Causal Role for Neutrophil Elastase in Thoracic Aortic Dissection in Mice. Arteriosclerosis, Thrombosis, and Vascular Biology, 43(10), 1900-1920.

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Peptide Analysis by Orbitrap Velos Mass Spectrometry

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The peptide mixtures were resuspended (1% FA, 2% ACN) and the volume corresponding to 500 ng of protein was analysed by an LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific). Peptide mixtures were injected into the capillary column (75 μm × 25 cm) in full loop mode and separated by a 5 μm C18 column using a nanoacquity liquid chromatography system (Waters). Peptides were eluted with a linear gradient of 1-35% buffer B (0.1% FA, 100% ACN) for 150 min, followed by 35-45% buffer A for 20min (A: 0.1% FA). The mass spectrometer was operated in positive ion mode (source voltage 2000V) and data-dependent manner. The full MS scans were performed in the Orbitrap at the range of 300-1,700 m/z at a resolution of 60,000. For MS/MS scans, the 15 most abundant ions with multiple charge states were selected for collision-induced dissociation (CID) fragmentation following one MS full scan.

Karri V., Schuhmacher M P.r.o.f.e.s.s.o.r, & Kumar V. (2020). A systems toxicology approach to compare the heavy metal mixtures (Pb, As, MeHg) impact in neurodegenerative diseases. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 139.

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Membrane Protein Identification by Mass Spectrometry

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Proteins isolated from membranes, or membranes followed by PIP₃-coated beads, were dissolved in Laemmli buffer as described above, and separated in one dimension on 1% SDS, 4–12% acrylamide gradient gels. They were then stained with SYPRO Ruby (ThermoFisher) or Coomassie Blue to visualize total protein, and 1-mm slices were excised. Proteins were digested in situ with trypsin, and peptides analyzed by high-resolution LC-MS/MS with a Thermo-Velos Orbitrap mass spectrometer (ThermoFisher) coupled to a nanoACQUITY liquid chromatography system (Waters, Milford MA) as previously reported [20 (link)]. Proteins were identified by MASCOT (www.matrixscience.com) matching of peptide fragmentation patterns to a database of previously observed fragment patterns [20 (link)].

Ayyadevara S., Balasubramaniam M., Johnson J., Alla R., Mackintosh S.G, & Shmookler Reis R.J. (2016). PIP3-binding proteins promote age-dependent protein aggregation and limit survival in C. elegans. Oncotarget, 7(31), 48870-48886.

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Peptide Separation and Identification by LC-MS/MS

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The peptide mixtures were resuspended (1% FA, 2% ACN) and the volume corresponding to 500 ng of protein was analyzed by an LTQ-Orbitrap velos mass spectrometer (Thermo Fisher Scientific). Peptide mixtures were injected into the capillary column (75 μm × 25 cm) in full loop mode and separated by a 5 μm C18 column using a nano-acquity liquid chromatography system (Waters). Peptides were eluted with a linear gradient of 1-35% buffer B (0.1% FA, 100% ACN) for 150 min, followed by 35-45% buffer A for 20 min (0.1% A). The mass spectrometer was operated in positive ion mode (source voltage 2000 V) and data-dependent manner. The full MS scans were performed in the Orbitrap at the range of 300-1700 m/z at a resolution of 60,000. For MS/MS scans, the 15 most abundant ions with multiple charge states were selected for collision induced dissociation (CID) fragmentation following one MS full scan.

Karri V., Ramos D., Martinez J.B., Odena A., Oliveira E., Coort S.L., Evelo C.T., Mariman E.C.M., Schuhmacher M, & Kumar V. (2018). Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases. Journal of proteomics, 187.

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