Fluorescent Labeling Proteins

Phycobiliproteins are photosynthetic accessory pigments isolated from cyanobacteria and red algae. Their exceptional fluorescence properties—high extinction coefficients, excellent quantum yields, and broad absorption spectra—make them ideal labels for detecting rare cell populations and weakly expressed markers in flow cytometry and immunoassay applications.

The three major phycobiliproteins—PE, APC, and PerCP—offer distinct spectral properties optimized for different laser configurations and panel designs. Extinction coefficient (ε) and quantum yield (QY) together contribute to fluorophore brightness; their product (ε × QY) provides a commonly used relative brightness metric for comparing detection sensitivity under similar optical conditions.

Key Advantages of Fluorescent Labeling Proteins

High extinction coefficients (up to ~1,960,000 cm⁻¹M⁻¹ for PE) for maximum light absorption
Excellent quantum yields for efficient photon conversion
Multiple excitation options spanning common 488 nm, 561 nm, and 633–640 nm laser lines
Tandem conjugates extending emission to 820 nm for expanded panel design
Available as raw proteins, preactivated formats, and complete labeling kits

Protein	Ex (nm)	Em (nm)	ε (cm⁻¹M⁻¹)	QY	Relative Brightness	Laser Lines
R-Phycoerythrin (PE)	565	574	1,960,000	0.82	1,607,200	488, 561 nm
Allophycocyanin (APC)	651	660	700,000	0.68	476,000	633, 640 nm
PerCP	477	678	406,000	0.40	162,400	488 nm

PE delivers ~3.4× greater brightness than APC and ~10× greater than PerCP, making it the preferred choice for detecting low-abundance antigens. However, PerCP's exceptionally large Stokes shift (~200 nm) enables far-red emission from blue laser excitation, a unique capability for single-laser multicolor panels.

Tandem Conjugates

Tandem dyes combine a phycobiliprotein donor with an organic dye acceptor via FRET, extending emission wavelengths while maintaining the donor's excitation properties. The extinction coefficient of each tandem equals that of its phycobiliprotein donor, since the donor is responsible for light absorption.

The table below provides an overview of the available tandem dyes. Please click the category links to learn more about a particular phycobiliprotein tandem series.

Category	Example Tandems	Emission Range (nm)	ε (cm⁻¹M⁻¹)	Laser
PE Tandems	PE-Texas Red, PE-Cy5, PE-Cy5.5, PE-Cy7, PE-iFluor® 594 to PE-iFluor® 780	606–800	1,960,000	488, 561 nm
APC Tandems	APC-Cy5.5, APC-Cy7, APC-iFluor® 700 to APC-iFluor® 800	700–819	700,000	633, 640 nm
PerCP Tandems	PerCP-Cy5.5, PerCP-Cy7, PerCP-iFluor® 700 to PerCP-iFluor® 780	695–806	350,000	488 nm

Preactivated Proteins

Preactivated phycobiliproteins are ready for direct conjugation to antibodies without additional crosslinker chemistry. These are provided in three variations. Amine-reactive formats target lysine residues and N-termini, affording higher yield than SMCC chemistry, while bypassing the need for antibody reduction. Thiol-reactive (maleimide) formats target free sulfhydryl groups in the hinge region of antibodies for site-directed conjugation. Finally, ammonium sulfate-free proteins benefit from being ready for immediate labeling without dialysis.

Buccutite™ Rapid Antibody Labeling Kits

Buccutite™ technology uses two unique crosslinkers—Buccutite™ MTA and Buccutite™ FOL—that rapidly react upon mixing, achieving 100% conjugation yield without purification. This approach reduces the risk of antibody aggregation and activity loss that can occur with traditional SMCC-based conjugation under suboptimal conditions.

Workflow

Add Buccutite™ MTA linker to antibody → Incubate 30 min
Add FOL-activated PE, APC, PerCP, or tandem dye → Incubate 60 min
Conjugate ready to use in less than 2 hours—no purification needed

Fig. 1

Buccutite™ Rapid Antibody Labeling Kit workflow

Selecting the Optimal Phycobiliprotein

The following tables offer selection guides that can assist in selecting the optimal phycobiliproteins for a given experiment.

This document (01.0201.251203r1) was last updated on Thu Feb 12 2026. All trademarks and registered trademarks mentioned herein are the property of their respective owners.