Nanoacquity lc

Manufactured by Waters Corporation

Sourced in United States, United Kingdom

The NanoAcquity LC is a liquid chromatography system designed for high-performance separations. It features precise flow control, low dispersion, and exceptional sensitivity for demanding applications such as proteomics, metabolomics, and pharmaceutical analysis.

Automatically generated - may contain errors

Lab products found in correlation

Ltq velos, by Thermo Fisher Scientific (3 mentions) Superdex 200 10 300 gl column, by GE Healthcare (2 mentions) Orbitrap exploris, by Thermo Fisher Scientific (1 mentions) Freestyle v1, by Thermo Fisher Scientific (1 mentions) Xevo g2 mass spectrometer, by Waters Corporation (1 mentions) Synapt g2 mass spectrometer, by Waters Corporation (1 mentions) Tripletof 6600, by AB Sciex (1 mentions) Vivaspin centrifugal concentrator, by Sartorius (1 mentions) Ltq velos mass spectrometer, by Thermo Fisher Scientific (1 mentions) Ziptip, by Merck Group (1 mentions) Trypsin, by Merck Group (1 mentions) Mascot 2, by Matrix Science (1 mentions) Orbitrap fusion lumos, by Thermo Fisher Scientific (1 mentions) Silicatip emitter, by New Objective (1 mentions) Nanospray flex, by Thermo Fisher Scientific (1 mentions) Synapt g2 qtof, by Waters Corporation (1 mentions) 4000 qtrap, by Thermo Fisher Scientific (1 mentions) Mascot, by Matrix Science (1 mentions) Velos orbitrap elite, by Thermo Fisher Scientific (1 mentions) Beh c18 analytical column, by Waters Corporation (1 mentions)

Close spelling variants of this product

Waters NanoAcquity LC NanoAcquity ultra performance LC NanoAcquity LC system NanoAcquity ultra-high pressure LC system NanoACQUITY UltraPerformance LC system Waters nanoACQUITY Ultra Performance LC (UPLC) System Waters nanoACQUITY LC system NanoACQUITY Ultra Performance LC (UPLC) system NanoAcquity

15 protocols using nanoacquity lc

Phosphoprotein Quantification via LC-MS

Check if the same lab product or an alternative is used in the 5 most similar protocols

The protein solution at 1.2 μg/μl was diluted in water to 24 ng/μl. Ten μl was loaded (~240 ng) onto a Waters NanoAcquity LC with online desalting. Reversed phase separation was carried out on an in‐house packed C2 column (100 μm i.d., ~50 cm long, packing material SMTC2MEB2–3‐300 from Separation Methods Technologies, Newark, DE). Mobile phases were 0.2% formic acid in water (A) and 0.2% formic acid in acetonitrile (B). A linear gradient with a flow rate of 0.3 μl/min was run from 15% to 50% mobile phase B over 30 min. The protein eluted between 30%–40% mobile phase B. Mass spectrometry data were collected on a Thermo Orbitrap Exploris. The mass spectrum (120 k resolution, 5 microscans) across the elution window were summed, and deconvoluted with FreeStyle (v1.5, ThermoScientific) for estimating the relative abundance of the phosphorylated protein.

Buchko G.W., Zhou M., Vesely C.H., Tao J., Shaw W.J., Mehl R.A, & Cooley R.B. (2023). High‐yield recombinant bacterial expression of 13C‐, 15N‐labeled, serine‐16 phosphorylated, murine amelogenin using a modified third generation genetic code expansion protocol. Protein Science : A Publication of the Protein Society, 32(2), e4560.

+ Open protocol

+ Expand

GLP-1 Construct Deuterium Labeling

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

For analysis of exchange into the indicated GLP-1 constructs, the peptides were dissolved in 25% acetonitrile/water at 50 μM and kept on ice. Deuterium labeling was initiated with an 18-fold dilution into D2O buffer (10 mM potassium phosphate pD 7.01, 100 mM NaCl) at 21°C. After 10 seconds of labeling, the reaction was quenched with the addition of an equal volume of quenching buffer (150 mM sodium phosphate pH 2.48) at 0°C. Samples were then injected onto an in-house packed POROS 20-R2 trap for peptide trapping and desalting for 3 minutes. A Waters nanoACQUITY LC was used to elute each peptide from the trap with a 15%–70% gradient of acetonitrile over 6 minutes at a flow rate of 100 μL/min. Eluant was directed into a Waters Xevo G2 mass spectrometer operated in TOF-only mode for mass analysis. Data were analyzed as described^{31 (link)}. All mass spectra were processed manually using MagTran. The relative amount of deuterium in the GLP-1 constructs was determined by subtracting the centroid mass of the undeuterated form from the deuterated form, at each condition. Deuterium levels were not corrected for back exchange and thus reported as relative.

Bird G.H., Fu A., Escudero S., Godes M., Opoku-Nsiah K., Wales T.E., Cameron M.D., Engen J.R., Danial N.N, & Walensky L.D. (2020). Hydrocarbon-stitched Peptide Agonists of Glucagon-Like Peptide-1 Receptor. ACS chemical biology, 15(6), 1340-1348.

+ Open protocol

+ Expand

Proteomic Analysis of Protein Samples

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The detailed method was described previously with modifications [14 (link)]. The proteins from SDS-PAGE gels were separated and performed on a Waters NanoAcquity LC with a binary buffer system. The samples were loaded onto the trap column and then separated by an initial linear gradient of buffer B. The MS was operated in Data-Dependent MS/MS Scan mode, with one full scan acquisition in the Orbitrap with an Automatic Gain Control (AGC) target value of 1× 10⁶ ions. The 20 most intensive ions with a charge >1 were selected for MS/MS analysis. CID (collision-induced dissociation) scans were collected at an AGC target value of 5,000 with a maximum injection time of 25s, and dynamic exclusion was set to 30s. The MS/MS spectra were searched on Sorcerer-SEQUEST (version 4.0.4 build, Sage-N Research, Inc.) against a composite target/decoy database. Searching parameters consisted of semitryptic restriction, fixed modification of Cys (+57.0215 Da, alkylation by iodoacetamide) and dynamic modification of oxidized Met (+15.9949 Da). Mass tolerance was set to ±20 ppm. Peptide matches were filtered by a minimal peptide length of 6 amino acids.

Zhu Y.P., Peng Z.G., Wu Z.Y., Li J.R., Huang M.H., Si S.Y, & Jiang J.D. (2015). Host APOBEC3G Protein Inhibits HCV Replication through Direct Binding at NS3. PLoS ONE, 10(3), e0121608.

+ Open protocol

+ Expand

Comparative Proteomics of AIEX-Derived Extracellular Vesicles

Check if the same lab product or an alternative is used in the 5 most similar protocols

Three biological replicates of AIEX EVs isolated from peak 1 and peak 2, were analysed in triplicate for label free LC-MS/MS. EVs were lysed in 6 M urea. Protein was precipitated using acetone, digested using 1 µg trypsin, reduced using 100 mM DTT and alkylated using 150 mM iodoacetamide followed by an overnight digest with 1 µg of trypsin, all of the above reactions were in 50 mM ammonium bicarbonate, pH 8.0. Samples were acidified using 0.1% formic acid/5% acetonitrile and cleaned up using Pierce C18 spin columns following manufacturer’s instructions. Peptides were eluted with 0.1% formic acid/5% acetonitrile, dried and reconstituted in 0.1% formic acid. Yeast alcohol dehydrogenase tryptic digest was spiked in to allow for quantification. 4 µl of each sample (normalised to 0.8 µg protein/µl) was run in triplicate on a NanoAcquity LC coupled to a Synapt G2 mass spectrometer (Waters). A 90-minute reversed phase gradient was run for each sample and ion mobility MS^E data was collected. Data was analysed using Waters Prognesis QI for Proteomic software searching against the Human Uniprot database.

Heath N., Grant L., De Oliveira T.M., Rowlinson R., Osteikoetxea X., Dekker N, & Overman R. (2018). Rapid isolation and enrichment of extracellular vesicle preparations using anion exchange chromatography. Scientific Reports, 8, 5730.

+ Open protocol

+ Expand

Glycopeptide Separation and Identification

Check if the same lab product or an alternative is used in the 5 most similar protocols

Glycopeptide separation was achieved on a Nanoacquity LC (Waters, Milford, MA) using capillary trap, 180 μm x 0.5 mm, and analytical 75 μm x 150 mm Atlantis DB C18, 3 μm, 300 A columns (Waters) interfaced with the 6600 TripleTOF (Sciex, Framingham, MA). A 3 min trapping step using 2% ACN, 0.1% formic acid at 15 μl/min was followed by chromatographic separation at 0.4 μl/min as follows: starting conditions 5% ACN, 0.1% formic acid; 1-55 min, 5–50% ACN, 0.1% formic acid; 55-60 min, 50–95% ACN, 0.1% formic acid; 60-70 min 95% ACN, 0.1% formic acid followed by equilibration to starting conditions for additional 20 min. For all runs, we have injected 1 μl (0.02 μg of protein) of tryptic digest directly on column. We have used an Information Dependent Acquisition (IDA) workflow with one MS1 full scan (400-1800 m/z) and 50 MS/MS fragmentations (100-1800 m/z), isolation window (0.7 Da), with rolling collision energy using different slope CE calculation for Low CE and High CE fragmentation. MS/MS mass spectra were recorded in the range 100-1800 m/z with resolution 30,000 and mass accuracy less than 15 ppm using the following experimental parameters: declustering potential 80 V, curtain gas 30, ion spray voltage 2,300 V, ion source gas-1 11, interface heater 180°C, entrance potential 10 V, collision exit potential 11 V.

Sanda M., Benicky J, & Goldman R. (2020). Low collision energy fragmentation in structure-specific glycoproteomics analysis. Analytical chemistry, 92(12), 8262-8267.

+ Open protocol

+ Expand

Production and Purification of Recombinant Proteins

Check if the same lab product or an alternative is used in the 5 most similar protocols

Full length human TLL-215 (link) was used to generate constructs encoding TLL2-TC4, TLL2-TE2 and TLL2-TC3 by PCR. The constructs were ligated into a modified pCEP-Pu vector30 (link) and transfected into HEK 293-EBNA cells cultured as described previously16 (link). Constructs encoding mTLD-C1C2E1, TLL1-C1C2E1, TLL2-C1C2E1, mTLD-C4C5, TLL1-C4C5 and TLL2-C4C5 were generated at the Oxford Protein Production Facility (OPPF-UK), Harwell, UK in a pOPINTTGneo expression vector31 (link) provided by OPPF and transfected into HEK 293S cells. ΔN-chordin was generated as previously described32 (link). For all constructs a 6x histidine tag was incorporated at the C-terminus. Conditioned media was concentrated and buffer exchanged into 10 mM HEPES, 500 mM NaCl, 10 mM imidazole, 2 mM CaCl₂, pH 7.4 using tangential flow ultrafiltration (Pall Life Sciences). All recombinant proteins were then purified by nickel affinity chromatography followed by size-exclusion chromatography on an AKTA purifier HPLC using a Superdex200 10/300GL column (GE Healthcare) in 10 mM HEPES, 500 mM NaCl, 2 mM CaCl₂, pH 7.4. Where needed, proteins were concentrated using Vivaspin centrifugal concentrators (Sartorius). Protein identities were confirmed by in-gel trypsin digestion and liquid chromatography tandem mass spectrometry (LC-MS/MS) using a NanoAcquity LC (Waters) coupled to a LTQ Velos (Thermo Fisher Scientific).

Bayley C.P., Ruiz Nivia H.D., Dajani R., Jowitt T.A., Collins R.F., Rada H., Bird L.E, & Baldock C. (2016). Diversity between mammalian tolloid proteinases: Oligomerisation and non-catalytic domains influence activity and specificity. Scientific Reports, 6, 21456.

+ Open protocol

+ Expand

Quantitative NfL Peptide Analysis by PRM

Check if the same lab product or an alternative is used in the 5 most similar protocols

Extracted digests were reconstituted with 25 µl of 0.1% formic acid/0% acetonitrile
(ACN). A 4.5 µl aliquot of each digest was then injected into nano-Acquity LC for MS
analysis. The nano-Acquity LC (Waters Corporation, Milford, MA, USA) was fitted with HSS
T3 75 μm × 100 μm, 1.8 μm column and a flow rate of 0.5 μl/min of a gradient of solutions
A and B was used to separate the peptides. Solution A was composed of 0.1% formic acid in
MS-grade water and solution B was composed of 0.1% formic acid in ACN. Samples were
analysed in positive ion mode, with a spray voltage of 2200 V and ion transfer tube
temperature of 275°C. Data were collected with parallel reaction monitoring (PRM) for
endogenous (N14) and isotopically labelled (Lys, Arg: ¹³C ¹⁵N)
peptides. Tryptic peptides specific to NfL were identified via the Blast search, and those
with good ionization were included in the qualitative PRM, designed to optimize sequence
coverage. The quantitative method was optimized for assay precision, and multiplexing was
reduced to the analysis of six NfL peptides across various NfL domains and their
corresponding ISTDs (Supplementary
Table 3).

Budelier M.M., He Y., Barthelemy N.R., Jiang H., Li Y., Park E., Henson R.L., Schindler S.E., Holtzman D.M, & Bateman R.J. (2022). A map of neurofilament light chain species in brain and cerebrospinal fluid and alterations in Alzheimer’s disease. Brain Communications, 4(2), fcac045.

+ Open protocol

+ Expand

Tryptic Digestion and LC-MS/MS Analysis of Xenopus Mucins

Check if the same lab product or an alternative is used in the 5 most similar protocols

Samples were exchanged into 2 M urea (50 mM ammonium bicarbonate) using Vivaspin columns and digested overnight in trypsin (1 μg, Sigma). The tryptic peptides were purified using ZipTips (Millipore) and solubilised in 0.1% formic acid. Tryptic peptides were separated by reverse phase liquid chromatography (LC) and analysed by tandem mass spectrometry (LC-MS/MS) using a NanoAcquity LC (Waters, Manchester, UK) coupled to a LTQ Velos mass spectrometer (Thermo Fisher Scientific). MS/MS data were searched using Mascot 2.4 (Matrix Science, UK) software against a custom database consisting of the SWISSPROT database with additional predicted Xenopus tropicalis-specific mucin sequences (Lang et al., 2007 (link)). The parameters were as follows: Carbamidomethyl (C) as fixed modification, Oxidation (M) as variable modification, peptides mass tolerance of 1.2 Da, fragments mass tolerance 0.6 Da, 1 missed cleavage maximum.

Dubaissi E., Rousseau K., Lea R., Soto X., Nardeosingh S., Schweickert A., Amaya E., Thornton D.J, & Papalopulu N. (2014). A secretory cell type develops alongside multiciliated cells, ionocytes and goblet cells, and provides a protective, anti-infective function in the frog embryonic mucociliary epidermis. Development (Cambridge, England), 141(7), 1514-1525.

+ Open protocol

+ Expand

Nano-LC-MS/MS for Peptide Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

A 5 μL aliquot of the peptide resuspension was injected into nano-Acquity LC for MS analysis. The nano-Acquity LC (Waters Corporation, Milford, MA, USA) was fitted with HSS T3 75 μm × 100 μm, 1.8 μm column and a flow rate of 0.5 μL/min of a gradient of solution A and B was used to separate the peptides. Solution A was composed of 0.1% formic acid in MS grade water and solution B was composed of 0.1% formic acid in acetonitrile. Peptides were eluted from the column with a gradient of 2%–20% of solution B in 28 min, then 20%–40% solution B for another 13 min before ramping up to 85% solution B in another 3 min to clean the column. The Orbitrap Fusion Lumos was equipped with a Nanospray Flex electrospray ion source (Thermo Fisher Scientific, San Jose, CA, USA). Peptide ions sprayed from a 10 μm SilicaTip emitter (New Objective, Woburn, MA, USA) into the ion source were targeted and isolated in the quadrupole. These were then fragmented by HCD and ion fragments were detected in the Orbitrap (resolution of 60,000, mass range 150–1,200 m/z). Monitoring of hydrophilic peptides (SSRcalc <9, all without leucine) for peptide profiling was performed on a HSS T3 300 μm × 100 μm, 1.8 mm column at a flow rate of 4 μl/min with an elution occurring with a 2%–12% solution B gradient and a spray operating on a 30 mm SilicaTip emitter.

Barthélemy N.R., Mallipeddi N., Moiseyev P., Sato C, & Bateman R.J. (2019). Tau Phosphorylation Rates Measured by Mass Spectrometry Differ in the Intracellular Brain vs. Extracellular Cerebrospinal Fluid Compartments and Are Differentially Affected by Alzheimer’s Disease. Frontiers in Aging Neuroscience, 11, 121.

+ Open protocol

+ Expand

Quantitative LC/MS Metabolite Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

A protocol was developed in collaboration with the Duke University Core Proteomics and Metabolomics Shared Resource using LC/MS on a high-resolution accurate-mass instrument. Recovery was optimized via the addition of urea to the homogenization buffer (suggesting tight binding to protein target in the intracellular matrix), and cleaned up using Oasis HLB extraction. After extraction, samples were dried down in Speed Vac and reconstituted in 25 uL of 1% ACN/0.1% TFA/0.02% HFBA and analyzed using a nanoAcquity LC (Waters) coupled to a Synapt G2 Q-ToF (Waters). Quantitative data was extracted as selected ion chromatograms for both the native ((M + 2H)²⁺at m/z 357.7 and heavy-labeled form CN-105 at m/z 362.7). Quantitation was accomplished by using a ratio of the peak area of the analyte and internal standard which was fit to a 7-point calibration curve (plasma R² = 0.997 and brain R² = 0.999).

Lei B., James M.L., Liu J., Zhou G., Venkatraman T.N., Lascola C.D., Acheson S.K., Dubois L.G., Laskowitz D.T, & Wang H. (2016). Neuroprotective pentapeptide CN-105 improves functional and histological outcomes in a murine model of intracerebral hemorrhage. Scientific Reports, 6, 34834.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!