Masshunter data acquisition software

Manufactured by Agilent Technologies

Sourced in United States

MassHunter Data Acquisition software is a core component of Agilent's mass spectrometry solutions. It is designed to provide users with a streamlined interface for controlling and acquiring data from Agilent's mass spectrometers.

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MassHunter software (440 citations) MassHunter Workstation Data Acquisition software (32 citations) MassHunter Acquisition software (29 citations) Agilent MassHunter Workstation Data Acquisition software (6 citations) MassHunter Workstation LC/MS Data Acquisition software (4 citations) Agilent MassHunter data acquisition software (3 citations)

11 protocols using masshunter data acquisition software

Urine Metabolomics Profiling Protocol

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The D0, M1 and M6 samples from Stellenbosch University and the D0 and M1 samples from 14 patients of NAA2m study were used as discovery sets. Samples from all time points of the remaining 34 individuals of the NAA2m study were used as a qualification set. Samples used in the discovery phase (Figure
1) were sterilized by γ-irradiation. Those used in the down selection and qualification phase (Figure
1) were not γ-irradiated and additional biosafety measures were taken in handling these. The creatinine concentration of each sample was measured by an alkaline picrate based colorimetric assay (Oxford Biomedical Research, Oxford, MI). LC-MS analyses of urine samples were performed following the methods described in Mahapatra et al.
[22 (link)]. Positive-ion MS data in both centroid and profile modes were collected using the Agilent MassHunter Data Acquisition software. Data for the discovery samples sets were obtained in the 4 GHz high-resolution modes and that used in down selection and qualification was obtained in the 2 GHz extended dynamic range mode.

Mahapatra S., Hess A.M., Johnson J.L., Eisenach K.D., DeGroote M.A., Gitta P., Joloba M.L., Kaplan G., Walzl G., Boom W.H, & Belisle J.T. (2014). A metabolic biosignature of early response to anti-tuberculosis treatment. BMC Infectious Diseases, 14, 53.

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Ion Mobility-Mass Spectrometry Workflow

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Q-TOF instrument control and MS data acquisition
was accomplished via the MassHunter data acquisition software (ver.
9.00, Agilent). The SLIM IM module control and data acquisition utilized
a custom user interface (GAA Custom Engineering). IM-MS data were
viewed and processed using MassHunter IM-MS Browser (ver. 10). IM
traces were integrated across narrow m/z ranges and imported into Excel (Microsoft) for further analysis,
including peak fitting and peak metric calculations (arrival time
centroid, resolution, resolving power, percent valley, etc.). IM profile
data acquired for the assessment of the resolving power across various
SLIM IM conditions were extracted using IM-MS Browser and further
processed and visualized in the R statistical computing programming
environment (R Core Team, Vienna, Austria) using the tidyverse suite
of tools.^{40 (link)}

May J.C., Leaptrot K.L., Rose B.S., Moser K.L., Deng L., Maxon L., DeBord D, & McLean J.A. (2021). Resolving Power and Collision Cross Section Measurement Accuracy of a Prototype High-Resolution Ion Mobility Platform Incorporating Structures for Lossless Ion Manipulation. Journal of the American Society for Mass Spectrometry, 32(4), 1126-1137.

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Chromatography and Mass Spectrometry Analysis

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Chromatography was based on the
previously described method using an Agilent 1200 series high-performance
LC system (Agilent Technologies; Palo Alto, CA) coupled with an Atlantis
T3 reverse-phase C18 3.5 μm column (2.1 mm × 150 mm; Waters
Corp., Milford, MA).^{10 (link)} MS was performed
using an Agilent 6520 quadrupole time of flight LC–MS instrument
equipped with an Agilent electrospray ionization source that was operated
in the positive ionization mode. The operating conditions for the
mass spectrometer were: gas temperature, 300 °C; drying gas,
8 L/min; nebulizer, 45 lb/in.²; capillary voltage, 2000
V; fragmentation energy for MS and MS/MS, 120 V; fragmentation energy
to generate the m/z 100.0757 product
ion, 200 V; skimmer voltage, 60 V; and octapole RF setting, 750 V.
Specified ions were subjected to MS/MS fragmentation (isolation width
of 1.3 Da) by collision-induced dissociation at set collision energies
(5–40 V). Data were collected in the profile and centroid modes
at a scan rate of 2.0 spectra/s and a scan range of m/z 50–1700 using the Agilent MassHunter Data
Acquisition software.

Fitzgerald B.L., Mahapatra S., Farmer D.K., McNeil M.R., Casero RA J.r, & Belisle J.T. (2017). Elucidating the Structure of N1-Acetylisoputreanine: A Novel Polyamine Catabolite in Human Urine. ACS Omega, 2(7), 3921-3930.

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GC-MS Analysis of MEROCTANE Impurities

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Control A and both MEROCTANE samples were analysed by GC–MS in triplicate. One µL of each sample was injected into a 7820A GC system gas chromatography (Agilent Technologies, USA), coupled to a 5977E MSD (Agilent Technologies, USA) single quadrupole mass spectrometer. For gas chromatographic separation a DB-Wax capillary column of 30 m × 0.25 mm × 0.25 μm (Agilent Technologies, USA) was used.
Detection and data acquisition were performed in scan mode from 20 to 700 Da. Data analysis was performed using Mass Hunter Data Acquisition software (Quantitative Analysis B.07.00, Agilent Technologies, USA) and tentative identification of the impurities was carried out using the NIST17 MS search 2.3 library and the EIC of the characteristic ions. The NIST MS Search parameter R. Match of the identified compounds was above 600 in all cases.

Coco-Martin R.M., Andrés-Iglesias C., Srivastava G.K., Lagos-Rodriguez J., Ruiz-Tevah M., Díaz-Cárdenas M.R., Fernandez-Bueno I., García-Serna J., García-Gutierrez M.T., García-Layana A, & Pastor J.C. (2021). Intraocular toxicity caused by MEROCTANE perfluorocarbon liquid. Scientific Reports, 11, 599.

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Peptide Purification and Mass Spectrometry

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An Agilent C-18 300Ǻ large capacity chip was used to load the previously de-salted peptides. The column was equilibrated using 0.1% FA in water (Buffer 1), and the peptides were eluted using an increasing gradient of 90% ACN in 0.1% FA (Buffer 2) using the following gradient: 3–50% Buffer 2 from 0–30 min, 50–95% Buffer 2 from 30–32 min, 95% Buffer 2 from 32–39 min, and 95–3% Buffer 2 from 39–47 min. The Q-TOF settings were as follows: positive polarity, fragmentor voltage at 300 V, capillary voltage at 2050 V, drying gas at a flow rate of 5 L/min, and a 300 °C gas temperature. Auto MS/MS mode was used to analyze the intact protein, with a range of 110–3000 m/z for the MS scan and a 50–3000 m/z range for the MS/MS scan. Agilent MassHunter data acquisition software was used to perform the spectrum analysis.

Chung Y.S., Ahmed P.K., Othman I, & Shaikh M.F. (2021). Orthosiphon stamineus Proteins Alleviate Hydrogen Peroxide Stress in SH-SY5Y Cells. Life, 11(6), 585.

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Monoclonal Antibody Denaturation and Tryptic Digestion

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Samples (100 μg)
were denatured using 8 M urea in tris buffer (0.4 M, pH 7.8). mAb
was incubated with 5 μL of DTT (200 mM) for 1 h, followed by
addition of 20 μL (200 mM) of IAA for 1 h. Furthermore, samples
were diluted 10-fold with 50 mM tris pH 7.8 and digested using MS
grade trypsin (1:20 w/w) with overnight incubation at 37 °C and
acidified with FA. Peptides obtained by trypsin digestion were injected
on the AdvanceBio peptide mapping C18 column (2.1 × 150 mm, 1.7
μm, Agilent Technologies) using a 1290 Infinity UHPLC system
coupled with AdvaceBio 6545XT Q-TOF system (Agilent Technologies).
The column was operated at a flow rate of 0.50 mL/min at 55 °C.
Mobile phase A consisted of 0.1% v/v FA in water, and mobile phase
B was 0.1% FA in acetonitrile. The peptide was eluted by a linear
gradient of mobile phase B (5–40%) for 30 min. The MS parameters
were drying gas at 300 °C, drying gas flow of 11 L/min, nebulizer
pressure of 35 psig, sheath gas temperature of 275 °C, sheath
gas flow of 10 L/min, nozzle voltage of 4000 V, and fragmentor voltage
of 175 V. MS–MS data were collected in the profile mode at
a rate of three spectra per second with a 50–1700 m/z range. Data were acquired using MassHunter data
acquisition software (Agilent Technologies). Data analysis was performed
with BioConfirm software version 10.0 (Agilent Technologies).

Sarin D., Krishna K., Nejadnik M.R., Suryanarayanan R, & Rathore A.S. (2024). Impact of Excipient Extraction and Buffer Exchange on Recombinant Monoclonal Antibody Stability. Molecular Pharmaceutics, 21(4), 1872-1883.

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Comprehensive Epidermal Lipid Analysis

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LC-HRMS data were acquired and deconvoluted using the MassHunter Data Acquisition Software (B.09.00, Agilent Technologies). Chromatographic and spectral investigation was conducted on MassHunter Workstation Qualitative Analysis software (version 10.0, Agilent Technologies); quantitative analysis of candidate epidermal lipid species on QCs was conducted on MassHunter Workstation Profinder (version 10.0, Agilent Technologies). LipidCreator Lifs tool (version 1.1.0) was used for in silico spectral library support and CERs comprehensive characterization^{23 (link)}. The multivariate statistical analysis was performed by the software Agilent MassHunter Mass Profiler Professional (MPP, version 15.1, Agilent Technologies).

Maiellaro M., Bottillo G., Cavallo A, & Camera E. (2024). Comparison between ammonium formate and ammonium fluoride in the analysis of stratum corneum lipids by reversed phase chromatography coupled with high resolution mass spectrometry. Scientific Reports, 14, 40.

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Automated Compound Identification Protocol

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The single or mixed standard solutions at individual concentrations of 100 ng/mL each were injected in the LC/Q-TOF-HRMS system to collect retention time data, MS and MS/MS accurate masses of target ions. A Microsoft Excel spreadsheet was created containing compound name, molecular formula, retention time, exact mass, collision energy and fragment ions for each analyte, and was converted into comma-separated values format for retrospective library searching by the Agilent MassHunter Data Acquisition software (version B.07.00). The raw data of a sample run can then be automatically matched against the database within a defined tolerance for retention time (±0.1 min) and exact mass (±5 ppm) by the MassHunter software (European Commission, 2021 , European Commission, 2021 , European Commission, 2019 ).

Bai M., Tang R., Li G., She W., Chen G., Shen H., Zhu S., Zhang H, & Wu H. (2022). High-throughput screening of 756 chemical contaminants in aquaculture products using liquid chromatography/quadrupole time-of-flight mass spectrometry. Food Chemistry: X, 15, 100380.

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Proteomic Analysis of SH-SY5Y Cells

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An Olympus CKX41 inverted trinocular microscope (Manila, Philippines) connected to an Olympus UIS2 optical system camera and AnalySIS 1.5 software were used for the microscopic examination of SH-SY5Y cells.
In the protein expression study, an Agilent 1200 series HPLC paired with an Agilent 6550 iFunnel quadrupole time of flight (Q-TOF) LC/MS, a C-18 300Ǻ large capacity chip, and Agilent MassHunter data acquisition software (all from Agilent Technologies, USA) were used to determine the differentially expressed proteins. Additionally, version 8.0 of PEAKS^®Studio software (Bioinformatics Solution, Waterloo, ON, Canada) and the UniProtKB database (organism: Homo sapiens) were used to analyze the results of the mass-spectrometry-based label-free quantitative proteomics (LFQ). Cytoscape software, with version 3.7.2 of the BiNGO plugin, was used for Gene Ontology (GO)-annotated information (Cytoscape Consortium, California, USA). Reactome Pathway Browser version 3.7 and Reactome Database Release 72 (organism: Homo sapiens) were utilized for the investigation into protein–protein interactions, functional annotations, and systemic pathway enrichment analysis.

Chung Y.S., Ahmed P.K., Othman I, & Shaikh M.F. (2021). Orthosiphon stamineus Proteins Alleviate Hydrogen Peroxide Stress in SH-SY5Y Cells. Life, 11(6), 585.

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Quantification of Endogenous Compounds in Blood

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Data acquisition was performed with MassHunter Data Acquisition software (B.08.02, Agilent Technologies, Waldbronn, Germany). Data analysis was performed with Quantitative Analysis software (version 10.1, Agilent Technologies, Waldbronn, Germany). Peak areas corresponding to the endogenous concentrations of studied compounds in blood used to prepare calibration curves were subtracted from the values obtained for the calibration solutions (Vishwanathan et al., 2000 (link)). The concentration obtained at each step of the study was divided by the concentration obtained at step 1 (at rest before exercise) to obtain a change of magnitude factors. The means of the change of magnitude factors obtained at each step were compared with a one-way ANOVA test for data with a normal distribution and a Friedman test for data not satisfying the normality test. These statistical analyzes were performed using GraphPad prism 6 and as well as the construction of the different graphs. Results of prevalidation were computed with e-noval 4.1 software (Pharmalex, Mont-Saint-Guibert, Belgium).

Nix C., Hemmati M., Cobraiville G., Servais A.C, & Fillet M. (2021). Blood Microsampling to Monitor Metabolic Profiles During Physical Exercise. Frontiers in Molecular Biosciences, 8, 681400.

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