sigma anti-flag M2 antibody is very good.

For pulldown assay, however, i do suggest to use magnetic beads than the agarose beads. Agarose beads are usually porous and could result in higher background than magnetic beads. Plus, the process of using magnetic beads is much straightforward.

I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?

A highly recommended rabbit-produced antibody for immunoprecipitation (IP) and subsequent western blotting of FLAG-tagged proteins in mouse-derived chondrocyte cell lines is the Anti-FLAG® M2 antibody from Sigma-Aldrich. This antibody demonstrates high affinity and specificity for FLAG-tagged proteins, making it suitable for capturing and detecting these proteins in various applications, including IP and western blotting [1][2][3][4]. The Anti-FLAG® M2 monoclonal antibody is widely used due to its ability to bind both N-terminal and C-terminal FLAG tags without requiring calcium-dependent conditions, ensuring reliable and consistent results [5][6].

Reference

[1] Brizzard, B., Chubet, R., & Vizard, D. (1994). Immunoaffinity purification of FLAG epitope-tagged bacterial alkaline phosphatase using a novel monoclonal antibody and peptide elution.. BioTechniques, 16 4, 730-5 .

[2] Knappik, A., & Plückthun, A. (1994). An improved affinity tag based on the FLAG peptide for the detection and purification of recombinant antibody fragments.. BioTechniques, 17 4, 754-61 .

[3] Ferrando, R., Newton, K., Chu, F., Webster, J., & French, D. (2015). Immunohistochemical Detection of FLAG-Tagged Endogenous Proteins in Knock-In Mice. Journal of Histochemistry & Cytochemistry, 63, 244 - 255.

[4] Verhagen, A. (2006). Using FLAG Epitope-Tagged Proteins for Coimmunoprecipitation of Interacting Proteins.. CSH protocols, 2006 5.

[5] Itakura, E., Chen, C., & Bono, M. d. (2017). Purification of FLAG-tagged Secreted Proteins from Mammalian Cells.. Bio-protocol, 7 15.

[6] Zhang, L., Uder, S., Juehne, T., Brizzard, B., & Song, K. (2002). Nonradioactive assay of FLAG-tagged MAPK using ANTI-FLAG antibody-coated multiwell plates.. BioTechniques, 32 2, 442-7 .

A commonly recommended FLAG antibody produced in rabbit for immunoprecipitation (IP) is the Anti-FLAG® M2 Affinity Gel (Sigma-Aldrich). This antibody is well-regarded for its high specificity and affinity for the FLAG epitope, making it suitable for IP experiments.

Another good option is the Rabbit Monoclonal Anti-DDDDK (FLAG) Antibody (Cell Signaling Technology, Cat. #2368). This antibody is also known for its high specificity and is widely used in various applications, including IP.

When selecting an antibody, consider factors such as your experimental conditions, the species of your samples, and the availability of published protocols and reviews related to your specific application. Additionally, checking product reviews and published literature can provide insights into the antibody's performance in IP experiments.