Acquity uplc m class system

Manufactured by Waters Corporation

Sourced in United States

The ACQUITY UPLC M-Class system is a high-performance liquid chromatography (HPLC) instrument designed for analytical separations. It utilizes ultra-high pressure liquid chromatography (UPLC) technology to achieve efficient and rapid chromatographic separations. The system is capable of generating high pressures up to 15,000 psi, enabling the use of sub-2 micron particle size columns for improved resolution, sensitivity, and speed.

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Acquity UPLC system (1422 citations) Acquity UPLC (716 citations) UPLC system (190 citations) Acquity system (56 citations) UPLC-MS/MS (55 citations) UPLC-MS (45 citations) M-Class UPLC (14 citations) ACQUITY-UPLC CLASS system (6 citations) Acquity I-Class UPLC TQS-micro MS system (2 citations)

39 protocols using acquity uplc m class system

Proteomic and Peptidomic Characterization of A. hypochondriacus Seed

Cited 2 times

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LC-MS/MS data for bottom-up proteomic and top-down peptidomic characterization of A. hypochondriacus seed fractions were acquired using an Acquity M-class UPLC system (Waters, Milford, USA) coupled to a Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Scientific, Waltham, USA) as previously described (Al-Mohanna et al., 2021 (link)). Collected raw MS data (*.raw) were converted to Mascot Generic Files (*.mgf) using ProteoWizard (Chambers et al., 2012 (link)).
In vitro gastrointestinal digestion samples were analyzed using a nanoAcquity UPLC (Waters, Milford, USA) coupled to a TripleToF 5600 (Sciex, Framingham, USA), as previously described (Moyer et al., 2021 (link)).

Moyer T.B., Schug W.J, & Hicks L.M. (2021). Amaranthus hypochondriacus seeds as a rich source of cysteine rich bioactive peptides. Food chemistry, 377, 131959.

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Tryptic Peptide Analysis by QTOF MS

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The tryptic digests were analyzed on a Waters Xevo G2-XS quadrupole time-of-flight (QTOF) mass spectrometer coupled to a Waters Acquity M-class UPLC system with an ion-key ionization source. Samples were trapped on an M-class symmetry C18 column (300μM × 50mm packed with a 5μM particle), followed by separation on a peptide BEH (1.7 μM particle) ion-key column (150μM × 50mm). The liquid chromatography gradient proceeded from 3–50% acetonitrile/water (0.1% formic acid) over 20 minutes at a flowrate of 1.5 μL/min. Samples were ionized in positive mode with ESI parameters as follows: capillary voltage, 3 kV ; sampling cone voltage, 40 V; source temperature, 120°C; desolvation temperature, 600°C; cone gas flow, 25.0 L/hr. Full scan LC-MS data was acquired over a range of 400–2000 m/z in sensitivity mode with leucine enkephalin as a lockspray analyte. Fragmentation analysis for peptide identification was performed using MSMS mode for individual target ions and fast data dependent acquisition (fastDDA) over the range of 150–1400 m/z and 250–1500 m/z, respectively.

Nolte W.M., Tessman R.T, & Goldman J.L. (2020). Screening Trimethoprim Primary Metabolites for Covalent Binding to Albumin. Medicinal chemistry research : an international journal for rapid communications on design and mechanisms of action of biologically active agents, 29(7), 1238-1246.

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High-Resolution Mass Spectrometry of Biomolecules

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Samples were analyzed as previously described using an Acquity M-class UPLC system (Waters, Milford, MA, USA) coupled to a Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Scientific, Waltham, MA, USA) equipped with a Nanospray Flex source operated positive polarity mode [56 (link)]. Injections (4 μL) were made to a Symmetry C18 trap column (100 Å, 5 μm, 180 μm × 20 mm; Waters) and then separated on a HSS T3 C18 column (100 Å, 1.8 μm, 75 μm × 250 mm; Waters) resulting in an average peak width of 30 s. Data was acquired using a top 20 data-dependent acquisition mode with an isolation window of 1.5 m/z. Survey scans were collected with a scan range of 350–2000 m/z, 120,000 resolving power, an AGC target of 1 × 10⁶, and maximum injection time of 50 ms. Precursor ions were selected (isolation window of 1.5 m/z) for higher-energy collisional dissociation (HCD) collecting spectra with a scan range of 200–2000 m/z, resolving power of 30,000, AGC target of 3 × 105 and a maximum injection time of 100 ms. The total duty cycle of this method is 2.05 s producing approximately 15 survey scans across a chromatographic peak.

Moyer T.B., Purvis A.L., Wommack A.J, & Hicks L.M. (2021). Proteomic response of Escherichia coli to a membrane lytic and iron chelating truncated Amaranthus tricolor defensin. BMC Microbiology, 21, 110.

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UPLC-MS/MS Peptide Quantification Protocol

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Sample analysis was performed using a Waters Acquity M-class UPLC system (Waters Corporation, MA, USA), equipped with a Peptide BEH C 18 130 Å 1.7 m 150 m × 50 mm ionKey LC separation device (Waters Corporation) and interfaced to a triple quadrupole mass spectrometer (Xevo TQS, Waters Micromass, Manchester, UK) operated in positive ionization mode. iKey device was kept at 40 • C and sample manager was kept at 7 • C. Chromatographic separation was performed with gradient of A: H 2 O 0.01% HCOOH and B: MeOH 0.01% HCOOH, as follows: 0 min 30% B, 2 min 60% B, 2.10 min 90% B, 3.10 min 90% B, 3.20 min 30% B until 5.50 min for re-equilibrating the column for next injection. Flow rate was established at 3 L min -1 . Cone and nebulizer gas were dry nitrogen set to 250 L h -1 and 7 bar, respectively. For the operation of MS/MS mode, collision gas was argon 99.995% (Praxair, Madrid, Spain) set to 0.15 mL min -1 . Source temperature was kept at 120 • C and capillary voltage was established at 3.5 kV. All data was acquired and processed using MassLynx v4.1 software (Waters, Manchester, UK).

Celma A., Sancho J.V., Salgueiro-González N., Castiglioni S., Zuccato E., Hernández F, & Bijlsma L. (2019). Simultaneous determination of new psychoactive substances and illicit drugs in sewage: Potential of micro-liquid chromatography tandem mass spectrometry in wastewater-based epidemiology. Journal of chromatography. A, 1602.

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HDX-MS Analysis of Protein Dynamics

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The AI model was developed using previously obtained experimental
HDX-MS data for enolase, serum amyloid P component, barnase, and α-lactalbumin.^{11 (link)} Data were acquired on a Synapt G2Si HDMS equipped
with an Acquity UPLC M-Class system and automatic HDX-MS (Waters Corporation,
Manchester, U.K.). For each protein, isotope uptake was recorded for
7 different exposure times between 15 s and 8 h with data analysis
conducted using the ProteinLynx Global Server v3.0.2 and DynamX v3.0.0
(Waters Corporation, Manchester, U.K.). Separate data acquisitions
were obtained for back and forward exchange controls of each protein.
Briefly, all back exchange controls were obtained using fully exchanged
protein samples with data acquired using a labeling time point of
15 s. Forward exchange controls were obtained for each protein using
a reference, i.e., unlabeled acquisition, but with the quench buffer
containing 50% D₂O to match the ¹H:²H ratio in the experimental quench solutions. After calculation of
the relative fractions uptake (RFU) of all experimental time points
and the control data, the experimental data sets of each protein were
corrected for exchange artifacts.

Salmas R.E, & Borysik A.J. (2024). Deep Learning Enables Automatic Correction of Experimental HDX-MS Data with Applications in Protein Modeling. Journal of the American Society for Mass Spectrometry, 35(2), 197-204.

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Zeno SWATH MS-Based Discovery Proteomics

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Discovery proteomics using Zeno SWATH MS (preprint: Wang et al, 2022b (link)) Tryptic digests were analyzed on a 7600 ZenoTOF mass spectrometer system (SCIEX), coupled to an ACQUITY UPLC M‐Class system (Waters). 2 μl of each sample (360 ng sample + 0.02 μl PQ500, Biognosys) were loaded on a HSS T3 column (300 μm × 150 mm, 1.8 μm, Waters) heated to 35°C, then chromatographically separated with a 20‐min gradient using a flow rate of 5 μl/min (Zelezniak et al, 2018 (link)). A Zeno SWATH acquisition scheme with 85 variable‐size windows and 11‐ms accumulation time with 1.4 s cycle time was used (preprint: Wang et al, 2022b (link)) which allows for MS detection for average 7 points per chromatographic peak with the chosen chromatography.

Wang Z., Tober‐Lau P., Farztdinov V., Lemke O., Schwecke T., Steinbrecher S., Muenzner J., Kriedemann H., Sander L.E., Hartl J., Mülleder M., Ralser M, & Kurth F. (2022). The human host response to monkeypox infection: a proteomic case series study. EMBO Molecular Medicine, 14(11), e16643.

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Peptide Separation and Mass Spectrometry

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Peptides from pooled samples of each condition were separated with a linear gradient from 3 to 35% B (eluent A: 0.1% FA in water and eluent B: 0.1% FA in ACN) on an in-house packed 40 cm × 0.75 μm C18 column (1.9-μm C18 beads, Dr. Maisch Reprosil-Pur) connected to an Acquity UPLC M-Class system (Waters). Samples were acquired on an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific) at a normalized AGC target of 200% for both MS1 and MS2. The scan range was set to 350 to 1150 m/z, RF lens was set to 30%, and the maximum injection time was 100 ms for MS1 and 54 ms for MS2. Cycle time was 3 s, and the dynamic exclusion was set to 60 s. Charge states between 2 and 7 were acquired, and the Orbitrap resolution for MS1 was set to 120,000 and 30,000 for MS2. Peptides were fragmented with higher-energy collisional dissociation (HCD) at a collision energy of 30%. The total method length was 165 min.

Qi C., Lavriha P., Bayraktar E., Vaithia A., Schuster D., Pannella M., Sala V., Picotti P., Bortolozzi M, & Korkhov V.M. (2023). Structures of wild-type and selected CMT1X mutant connexin 32 gap junction channels and hemichannels. Science Advances, 9(35), eadh4890.

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Profiling Albumin Isoforms in Human Plasma

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The relative composition of albumin isoforms in human plasma samples was evaluated by direct infusion of diluted plasma (500-fold dilution) using the Xevo TQ-S micro triple-quadrupole mass spectrometer coupled with the ACQUITY UPLC^® M-Class system (Waters Corporation, Milford, CT, USA), as previously described [17 (link)]. After data deconvolution with the MaxEnt1 function on the MassLynx software (Waters Corporation, Milford, CT, USA), HSA-SH, thiolated albumin (+120 ± 2 Da, Thio-HSA), and glycated albumin (Gly-HSA, +160 ± 2 Da) were detected, and their intensities were used to calculate the relative abundances as previously described [13 (link)].

Brioschi M., Gianazza E., Andreini D., Mushtaq S., Cavallotti L., Veglia F., Tedesco C.C., Colombo G.I., Pepi M., Polvani G., Tremoli E., Parolari A, & Banfi C. (2022). Mercaptoalbumin Is Associated with Graft Patency in Patients Undergoing Coronary Artery Bypass Grafting. Antioxidants, 11(4), 702.

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FIE-FTICR MS-based Metabolic Profiling of hPSC-CMs

Cited 3 times

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Metabolites were reconstituted in 1:1 methanol:water. FIE-FTICR MS-based metabolic fingerprinting was performed using a Waters ACQUITY UPLC M-Class System (Waters Corporation, Milford, MS, USA) coupled to a Bruker solariX 12T FTICR mass spectrometer (Bruker Daltonics, Bremen, Germany) without an LC column as described previously.^{23 (link)} MS data were processed using MetaboScape v2021 and feature assignments were manually validated using DataAnalysis v4.3 (both Bruker Daltonics, Bremen, Germany). Bucket lists for data collected in positive and negative ionization modes were generated using the T-Rex 2D algorithm and combined to create one merged bucket list using a mass error tolerance of < 1.0 ppm. Features were annotated by SmartFormula in MetaboScape as described previously^{23 (link)} and by accurate mass using the Mass Bank of North America, Human Metabolome Database (HMDB)^{24 (link)}, LipidBlast^{25 (link)}, and METLIN databases^{26 (link)} with an error tolerance ≤ 3.0 ppm. See Supplemental File 1 for MetaboScape output. Overlap in metabolite features between hPSC-CMs was visualized using BioVenn.^{27 (link)} Metabolites were mapped to networks using MetScape plugin in CytoScape v 3.8.1.^{28 (link)}

Bayne E.F., Simmons A.D., Roberts D.S., Zhu Y., Aballo T.J., Wancewicz B., Palecek S.P, & Ge Y. (2021). A Multi-omics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes. Journal of proteome research, 20(10), 4646-4654.

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UPLC-MS/MS Peptide Identification Protocol

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An ACQUITY UPLC M-Class system (Waters, Milford, MA, USA) with an ACQUITY UPLC M-Class Peptide BEH C18 column (Waters, 75 μm × 150 mm, 1.7 μm, 300 Å) was coupled to a Q Exactive HF mass spectrometer (Thermo Fisher Scientific) for peptide separation and identification; details of its operation are presented below. Mobile phase A (0.1%FA in water) and mobile phase B (0.1% FA in ACN) were used for gradient separation. Peptides were automatically loaded onto the C18 column and flushed with 2% mobile phase B for 12 min at a flow rate of 0.5 μL/min, then followed by the 2-hour gradient: 12–102 min, 2–30% B; 102–106 min, 30–88% B; 106–110 min, 88% B; 110–111 min, 88-2% B; 111–120 min, 2% B. For samples prepared from different numbers of MCF-7 cells, a 4-hour gradient was used: 12–222 min, 2–30% B; 222–226 min, 30–88% B; 226–230 min, 88% B; 230–231 min, 88-2% B; 231–240 min, 2% B. The eluted peptides from the C18 column were pumped through a capillary tip for electrospray.

Zhang Z., Dubiak K.M., Huber P.W, & Dovichi N.J. (2020). Miniaturized filter-aided sample preparation (MICRO-FASP) method for high throughput, ultrasensitive proteomics sample preparation reveals proteome asymmetry in Xenopus laevis embryos. Analytical chemistry, 92(7), 5554-5560.

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