Technical Note 167

QFX Fluorometer vs. Qubit® Comparison

Introduction

The DeNovix® QFX Fluorometer and the Qubit® 3.0/Qubit® 4 Fluorometers are commonly used for fluorescence quantification of nucleic acids, proteins and other biomolecules. This note presents a comparison of instrument features and system performance of the QFX and the Qubit® 3.0/4. A performance comparison of DeNovix dsDNA Quantification Assays and Qubit® dsDNA Assays is also presented.

The DeNovix QFX Fluorometer enables precise fluorescence quantification using a proprietary optical core and a versatile set of four fluorescence channels. The QFX, along with the DeNovix family of dsDNA Fluorescence Assays, provides the highest sensitivity and widest dynamic range for quantification available. When compared to the Qubit® 3.0/4 and Qubit® dsDNA assays, the DeNovix QFX provides a lower detection limit 20X below Qubit’s and an upper range 2X higher.

DeNovix dsDNA Quantification Assays

DeNovix offers three dsDNA Fluorescence Quantification Kits that enable quick, sensitive and reproducible measurements of dsDNA, ranging from  0.5 pg/µL to 4000 ng/µL in a simple mix-and-measure protocol. DeNovix Broad Range, High Sensitivity and Ultra High Sensitivity Assays provide significantly enhanced dynamic range over the Qubit® Assays (Figures 1).

The DeNovix Ultra High Sensitivity dsDNA Assay delivers unmatched sensitivity, measuring concentrations as low as 0.5 pg/µL. Qubit® has no equivalent assay.

Due to DeNovix’s 20X greater sensitivity over the Qubit® HS dsDNA Assays, scientists are more equipped for research than ever. Single cell analysis, laser captured samples, circulating DNA and tumor heterogeneity studies are among the applications that can now benefit from faster and more accurate quantification.

Figure 1: Comparison of dsDNA Fluorescence Assay Concentration Ranges

Feature Comparison

The DeNovix QFX Fluorometer includes features equivalent or superior to Qubit® 3.0/4. Table 1 summarizes each system. The QFX provides scientists with the flexibility to choose DeNovix Assays or nearly any other fluorescence assay. Intuitive EasyApps® come preinstalled on this stand-alone instrument. The system includes a custom OS and a 7” HD touchscreen.

Table 1: Comparison of Key Feature of the QFX Fluorometer and Qubit® 3.0 / 4
FeatureDeNovix QFXQubit® 3.0/4
Fluorescence Channels4 (UV, Blue, Green, Red)2 (Blue, Red)
dsDNA Assay Concentration Range0.5 pg/μL – 4000 ng/μL*10 pg/μL – 2000 ng/μL**
Minimum Sample Volume1 μL (in 200 μL assay volume)1 μL (in 200 μL assay volume)
Measurement Time2 seconds5 seconds
Standard Curves Options2-point standard or 
customizable 2 – 8 standards2 or 3 point standard
Pre-Programmed AssaysCommonly used DeNovix, Qubit®, and Promega AssaysQubit® Assays
UV AssaysPossible including: Alexa Fluor 405, Hoechst 33258, DAPI, eBFP, 7-hydroxy 4- methylcoumarin and 4-Methylumbelliferyl B-D-Galactopyranoside None
Display7” HD Touchscreen5.7” Touchscreen
Password Protected AccountsYesNot Available
Method DevelopmentEasy method developmentRequires use of online tool & subsequent import
Accessory SupportUSB keyboard, mouse, 
barcode readerNot Available
Data ExportWiFi/ethernet to network drives, Email results, USB; LIMS compatibleUSB
NetworkingWiFi and EthernetNot Available
PrintingWiFi printing or local label printerNot Available
Onboard Sample Storage Capacity32 GB storage, > 8 million samples4 GB storage, 1000 samples
Software UpdatesWiFi, ethernet, USB; 
Automatic notificationsUSB
ColorsArctic White, Brazilian Blue, 
Tungsten Silver, Fire RedWhite
Warranty2 years1 year
Country of ManufactureUSAMalaysia

Methods

Comparison data for DeNovix dsDNA Quantification Assays and correlating Qubit® Quantification Assays were obtained on a DeNovix QFX Fluorometer and Qubit® 3.0 respectively. Each assay was prepared as described in the manufacturer’s protocol. Samples were mixed and incubated at room temperature for 5 minutes. Three replicate measurements were taken for each sample. The DeNovix Assays were measured on the DeNovix Fluorometer, and the Qubit® Assays were measured on the Qubit® 3.0 Fluorometer.

DeNovix Broad Range, High Sensitivity and Ultra High Sensitivity Assays

A series of dilutions of calf thymus DNA was prepared in TE buffer. Working solution (190 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube (DeNovix cat #TUBE-PCR-0.5-500). dsDNA (10 µL) was added to each tube in the standard range, and volume was adjusted for total mass in the extended range.

For Ultra High Sensitivity, working solution (200 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube. dsDNA (10 µL) was added to each tube.

Qubit® Broad Range and High Sensitivity Assays

A series of dilutions from phage lambda DNA was prepared in TE buffer. Working solution (190 µL) was added to a thin-walled, clear UV-transparent 0.5 mL PCR tube. dsDNA (10 µL) was added to each standard tube, and volume was adjusted for total mass within the core range of the assay. The extended range of the Qubit® Assays extends the total mass limitations of the assay. The appropriate total mass for the extended range was added to each assay tube using 200 µL total volumes.

Performance Data

Table 2: Broad Range Fluorescence Assay Performance Data
Broad Range dsDNA Assay
ExpectedDeNovix Assay measured on QFXQubit® Assay measured on Qubit®
ng/µLng/µL%CVng/µL%CV
40003551.610.010Out of Assay Range
30003123.240.008Out of Assay Range
20001974.530.0071826.333.340
10001050.920.007896.671.897
400358.080.073481.332.288
200195.700.140196.671.471
100106.100.08990.532.053
5053.750.09545.202.341
2526.830.11221.001.905
12.513.480.12612.371.683
6.256.650.3015.912.493
22.390.4602.040.980
11.121.3390.8102.506
0.50.5420.0000.6251.293
0.20.2374.6410.3456.083
0.10.1164.310Measured Out of Range
Table 3: High Sensitivity Fluorescence Assay Performance Data
High Sensitivity dsDNA Assay
ExpectedDeNovix Assay measured on QFXQubit® Assay measured on Qubit®
ng/µLng/µL%CVng/µL%CV
250261.620.006Out of Assay Range
10098.070.027112.671.025
2524.780.01626.331.096
1010.570.36010.131.140
33.040.1973.172.026
10.7900.1011.4760.889
0.30.2450.1630.7030.164
0.10.0700.0000.1191.788
0.030.0190.0000.0721.520
0.010.0052.0000.0192.859
0.0050.0045.0000.0084.619
Table 4: Ultra High Sensitivity Fluorescence Assay Performance Data
Ultra High Sensitivity dsDNA Assay
ExpectedDeNovix Assay measured on QFXQubit Assay measured on Qubit
pg/µLpg/µL%CVng/µLStDev
300304.400.108No Equivalent Assay
150142.910.182
5045.180.398
108.5191.056
21.8322.238
11.0858.750
0.50.3606.890

Summary

The combination of the DeNovix QFX and DeNovix dsDNA Quantification Assays provides fast and accurate measurement with unmatched sensitivity. The QFX and DeNovix Assays enable superior accuracy, higher sensitivity and a broader range of dsDNA quantification (0.5 pg/µL – 4000 ng/µL) compared to the Qubit® 3.0/4,  and Qubit® Assay range (10 pg/µL – 2000 ng/µL).

DeNovix dsDNA Quantification Assays are available for purchase at denovix.com and through DeNovix authorized distributors.

Qubit® is a registered trademarks of Thermo Fisher Scientific. 

Revised 19 Oct 2020