Targetlynx v4

Manufactured by Waters Corporation

Sourced in United States

TargetLynx V4.2 is a software application developed by Waters Corporation for data processing and analysis of mass spectrometry data. It provides automated data processing capabilities, including peak detection, integration, and quantitation.

Automatically generated - may contain errors

Lab products found in correlation

Close spelling variants of this product

TargetLynx quantification application manager software (v4.1, TargetLynx

23 protocols using targetlynx v4

Data Acquisition and Statistical Analysis

Cited 1 time

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

Data acquisition and analyses including calibration curves were carried out using Waters TargetLynx V4.1 software. The homoeostatic model assessment percentage insulin sensitivity (HOMA2%S) was calculated using the iHOMA2 software, using default settings.
²² (link) Other statistical analyses were carried out using STATA 15.1 (STATACorp LLC). The distribution of parameters was assessed using kernel density plots and Q‐Q plots versus idealised normal distributions. A repeated‐measures linear mixed model was used for analysis of glucose, insulin and PYY concentrations as well as the area‐under‐concentration curve (AUC) analysis. GraphPad Prism 9.0.2 (GraphPad Software) was used for the calculation of AUC values using the trapezoid method. For the purposes of analysis, analyte concentrations smaller than the LLOQ were set at zero.

Kowalka A.M., Alexiadou K., Cuenco J., Clarke R.E., Minnion J., Williams E.L., Bech P., Purkayastha S., Ahmed A.R., Takats Z., Whitwell H.J., Romero M.G., Bloom S.R., Camuzeaux S., Lewis M.R., Khoo B, & Tan T.M. (2022). The postprandial secretion of peptide YY1‐36 and 3‐36 in obesity is differentially increased after gastric bypass versus sleeve gastrectomy. Clinical Endocrinology, 99(3), 272-284.

+ Open protocol

+ Expand

Quantification of Cyanotoxins by LC-MS/MS

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

Two different LC-MS/MS methods were used, i.e., a reverse-phase (RP, C18) UPLC-MS/MS method for the MCs (18), cylindrospermopsin, nodularin, and anatoxins (2), according to Pekar et al. [2 (link)], and an UP-HILIC MS/MS method for the polar saxitoxin and the analogues (ionized in ESI+ and ESI− modes) according to Boundy et al. [38 (link)]. All mass spectral analyses were performed using a Waters Xevo TQ-S triple quadrupole mass spectrometer coupled to a Waters Acquity UPLC i-Class with a flow-through needle sample manager. For quantitative analysis, a specific calibration curve was built for each of the toxin analogues using the TargetLynx v 4.1 software (Waters, Milford, MA, USA, 2011).

Dirks C., Cappelli P., Blomqvist M., Ekroth S., Johansson M., Persson M., Drakare S., Pekar H, & Zuberovic Muratovic A. (2024). Cyanotoxin Occurrence and Diversity in 98 Cyanobacterial Blooms from Swedish Lakes and the Baltic Sea. Marine Drugs, 22(5), 199.

+ Open protocol

+ Expand

UPLC-Q-TOF-MS Data Processing Workflow

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

The raw data files obtained from UPLC-Q-TOF-MS runs were analyzed using MassLynx v4.2, MarkerLynx v4.2, and Targetlynx v4.2 software (Waters). The extracted ion chromatograms were visualized using MarkerLynx. Markers at the range of 150 and 1500 Da were analyzed with an intensity threshold of 200 to 350 counts and with retention time and mass windows of 0.20 min and 0.050 Da, respectively. The noise level was set to 5.00. The replicate minimum was set to 50% for fractions B and C. The starting time interval was 0.8 min for fraction A and 0.4 min for fractions B and C. The end-time interval of the chromatograph was set to 11.20 for fractions A and B and 11.10 for fraction C. The variables in the dataset generated by Markerlynx were verified using Targetlynx software. The TargetLynx peak values were added to the dataset and the data were then normalized to total peak intensity before importing into SIMCA v17.0 (Umetrics, Umea, Sweden). Pareto scaling was applied before multivariate data analyses, including PCA and OPLS-DA, were performed.

Ribeiro T., Jónsdóttir K., Hernandez-Bautista R., Silva N.G., Sánchez-Astráin B., Samadi A., Eiriksson F.F., Thorsteinsdóttir M., Ussar S, & Urbatzka R. (2023). Metabolite Profile Characterization of Cyanobacterial Strains with Bioactivity on Lipid Metabolism Using In Vivo and In Vitro Approaches. Marine Drugs, 21(9), 498.

+ Open protocol

+ Expand

Quantitative Amino Acid Uptake Analysis

Cited 1 time

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

Waters TargetLynx V4.2 software (Waters, Milford, MA, USA) was used to fit calibration curves based on 1/x²-weighted linear regressions of the peak area ratios of [¹³C₆, ¹⁵N]-L-leucine and the IS. GraphPad Prism 9 software (version 9.3.1) was used for data visualization, statistical analysis (unpaired t-test), and to determine the IC₅₀ values of JPH203 and BCH (nonlinear regression, log(inhibitor) vs. response with variable slope (four parameters)). The obtained IC₅₀ values were converted to the corresponding inhibition constant K_i with the IC-50-to-K_i web-based tool [49 (link)]. Therefore, the mean of reported K_m values for L-leucine uptake by LAT-1_HD (32 µM) was used [1 (link),2 (link),50 (link)], and classical competitive inhibition was assumed. Microsoft Excel 2010 (Mountain View, CA, USA) was used for general calculations and for the normalization of the [¹³C₆, ¹⁵N]-L-leucine cell homogenate amount of substance to protein content [pmol/mg]. Western blot band intensities were quantified with Fiji (Fiji is just ImageJ 2.0.0) [54 (link)].

Bay C., Bajraktari-Sylejmani G., Haefeli W.E., Burhenne J., Weiss J, & Sauter M. (2022). Functional Characterization of the Solute Carrier LAT-1 (SLC7A5/SLC2A3) in Human Brain Capillary Endothelial Cells with Rapid UPLC-MS/MS Quantification of Intracellular Isotopically Labelled L-Leucine. International Journal of Molecular Sciences, 23(7), 3637.

+ Open protocol

+ Expand

Quantitative Analysis of Aflatoxins by UPLC-MS/MS

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

Detection was performed
using a UPLC Acquity H-class PLUS system, coupled with a TQ-S micro
triple quadrupole mass spectrometer (Waters, Milford, MA). Chromatographic
separation of AFB1, AFB2, AFG1, and AFG2 was carried out with an ACQUITY
UPLC BEH C₁₈ analytical column (1.7 μm, 2.1 mm ×
100 mm) (Waters). The autosampler was set at 10 °C. The flow
rate of the mobile phase was fixed to 0.45 mL/min, and the injection
volume for the UPLC system was 2 μL. The column oven was maintained
at 45 °C. The mobile phase consisted of eluent A (H₂O, 5 mM ammonium formate, 0.1% formic acid) and eluent B (MeOH).
The gradient elution started at 98% eluent A for 0.25 min with a linear
increase to 99% eluent B in 8 min. Then, the column was re-equilibrated
with initial conditions for 2 min.
For MS/MS detection, the
electrospray ionization (ESI) interface was used in positive polarity
with the following settings: capillary voltage, 4 kV; ESI source temperature,
150 °C; desolvation gas temperature, 450 °C; cone gas flow,
1 L/h; and desolvation gas flow, 990 L/h. The acquisition of data
was performed by applying the multiple reaction monitoring (MRM) mode
with a dwell time of 0.025 s. Masslynx and Targetlynx V 4.2 software
(Waters Corp., Milford, MA) were employed for data acquisition and
processing.

Ouakhssase A., Fatini N, & Ait Addi E. (2021). Chemometric Approach Based on Accuracy Profile and Data Chronological Distribution as a Tool to Detect Performance Degradation and Improve the Analytical Quality Control for Aflatoxins’ Analysis in Almonds Using UPLC–MS/MS. ACS Omega, 6(19), 12746-12754.

+ Open protocol

+ Expand

Quantitative Analysis of DNA Adducts

Cited 1 time

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

The analyses were performed using a Waters Xevo G2-XS quadrupole-time
of flight mass spectrometer for compound characterization in HR (Supporting
Information, section “Supplementary Results,” MS And MS/MS Characterization) and a Waters Xevo TQ-XS
(triple quadrupole) mass spectrometer both equipped with Z-spray (electrospray)
ionization and step-wave source optimization, and controlled under
MassLynx v4.2 (Waters) as fully described previously.^{13 (link)} The Waters Xevo G2-XS was used for the compounds characterization
in HR, in full-scan, and in quadrupole selection mode without or with
increasing collision energy up to 35 V for fragment generation. The
Waters Xevo TQ-XS was used for the implementation of the MRM method
as detailed in Supporting Information, section “Supplementary Results” and Table S1. The final
MRM transitions for O6-m2dGO and 2dGO analyses are given in Table 2 with expected LC
retention times of each compound and selected MRM transitions for
LC method optimization.
MassLynx and TargetLynx v.4.2 (Waters) were used for
rapid chromatogram
and spectra evaluation and for the construction of calibration curves
and the computing of quantification data, respectively. As only 60
μL out of 65 μL was taken from each sample for analysis
and CALs were prepared as 60 μL-samples, calculated concentrations
were corrected by a factor 1.083 to retrieve real concentrations in
the samples.

Fresnais M., Jung I., Klein U.B., Theile D., Liang S., Haefeli W.E., Burhenne J, & Longuespée R. (2023). Quantification of Biologically Active DNA Alkylation in Temozolomide-Exposed Glioblastoma Cell Lines by Ultra-Performance Liquid Chromatography–Tandem Mass Spectrometry: Method Development and Recommendations for Validation. ACS Omega, 8(26), 23695-23705.

+ Open protocol

+ Expand

Pharmacokinetic Analysis of Exenatide

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

Calibration curves were calculated with weighted linear regressions (1/x²) from the peak area ratios of the analyte and IS of calibration samples using Waters TargetLynx V4.2 software (Waters, Milford, MA, USA). Non-compartmental pharmacokinetic parameters were determined utilizing Thermo Kinetica Version 5.0 (Thermo Fisher Scientific, Waltham, MA, USA); maximum plasma concentration (C_max) and time to C_max (t_max) was directly obtained from the raw data, terminal elimination half-life (t_½), AUC extrapolated to infinity, apparent volume of distribution at steady state (V_ss/F), and apparent oral clearance (Cl/F) were calculated by a mixed log-linear model. Absolute exenatide bioavailability was calculated as AUC(nasal) ÷ AUC(intravenous) × Dose(intravenous) ÷ Dose(nasal) × 100%. Standard calculations were performed with Microsoft Office Excel 2010 (Mountain View, CA, USA).

Sauter M., Uhl P., Burhenne J, & Haefeli W.E. (2020). Ultra-sensitive bioanalysis of the therapeutic peptide exenatide for accurate pharmacokinetic analyses at effective plasma concentrations utilizing UPLC-MS/MS. Journal of Pharmaceutical Analysis, 10(3), 233-239.

+ Open protocol

+ Expand

LC-MS Data Processing Workflow

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

After the LC–MS analysis, data were processed by Waters TargetLynx V4.2 (Massachusetts, USA). Peaks were smoothed using the moving average filter. After smoothing, peaks of each target analyte were detected by its distinctive MRM pair and retention time. For the construction of calibration curves, weighted linear regression models were applied accordingly.

Mak S.Y., Chen S., Fong W.J., Choo A, & Ho Y.S. (2024). A simple and highly sensitive LC–MS workflow for characterization and quantification of ADC cleavable payloads. Scientific Reports, 14, 11018.

+ Open protocol

+ Expand

Pharmacokinetic Analysis Methods

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

Calibration curves were determined with 1/x² weighted linear regression using peak area ratios of the analyte to IS. This calculation was performed using the software TargetLynx V4.2 (Waters, Milford, MA, USA). Plasma pharmacokinetics were determined with the software Kinetica (v 5.0; Thermo Fisher Scientific, Waltham, MA, USA). Standard calculations were performed using Microsoft Office Excel 2010 (Mountain View, CA, USA). Concentration–response curves and IC₅₀ values were calculated by GraphPad Prism version 9.0.0 (GraphPad Software Inc., La Jolla, CA, USA) according to a sigmoid E_max model.

Benzel J., Bajraktari-Sylejmani G., Uhl P., Davis A., Nair S., Pfister S.M., Haefeli W.E., Weiss J., Burhenne J., Pajtler K.W, & Sauter M. (2021). Investigating the Central Nervous System Disposition of Actinomycin D: Implementation and Evaluation of Cerebral Microdialysis and Brain Tissue Measurements Supported by UPLC-MS/MS Quantification. Pharmaceutics, 13(9), 1498.

+ Open protocol

+ Expand

Quantification of MTX, DAMPA, and 7-OH-MTX in Fecal and Urine Samples

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

The quantification
of MTX,
DAMPA and 7-OH-MTX by UPLC-MS was achieved using a linear calibration
curve and a log transformation of the axis, using TargetLynx V 4.2
(Waters). The R² for the calibration curve
of each of the standards was greater than 0.98 (Figure S1). As the fecal samples were prepared in duplicate,
concentrations of each of the analytes were averaged. As the total
volume of urine samples collected was recorded, it was possible to
calculate the total amount of MTX excreted in the urine. However,
the total weight of the fecal samples was not recorded and so the
quantification of MTX and its metabolites excreted in feces are reported
as the mass of the analytes (μg) per 50 mg of wet fecal sample.

Letertre M.P., Munjoma N., Wolfer K., Pechlivanis A., McDonald J.A., Hardwick R.N., Cherrington N.J., Coen M., Nicholson J.K., Hoyles L., Swann J.R, & Wilson I.D. (2020). A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague–Dawley Rats. Journal of Proteome Research, 19(8), 3326-3339.

+ 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!