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Tandem affinity purification (TAP) tagging fuses a two-part affinity tag to a protein of interest so that the protein, and the complex it sits in, can be pulled out of a cell extract in two successive purification steps under native conditions. It was introduced in 1999 and first developed in yeast.
Short answer
TAP tagging attaches a dual-affinity tag to the N- or C-terminus of a target protein. Two sequential affinity steps then isolate the tagged protein together with its binding partners, without needing to know the complex’s composition in advance. Researchers use it to identify what a protein physically associates with, typically followed by mass spectrometry.
Definition and scope
The TAP method was described by Rigaut and colleagues in 1999 as a generic procedure to purify proteins expressed at their natural level under native conditions, using a novel tandem affinity purification tag (Nature Biotechnology 17(10):1030-2, PMID 10504710). A 2001 methods paper by Puig and colleagues describes it as a general procedure of protein complex purification that allows rapid purification of complexes under native conditions, even when expressed at their natural level, and notes that prior knowledge of complex composition or function is not required (Methods 24(3):218-29, PMID 11403571).
In scope: purification of native protein complexes for composition analysis. Out of scope for this page: bench step lists and any claims about yield or purity, which depend on the protein, organism and conditions.
How it is used in practice
According to Puig et al., the method requires fusing the TAP tag to the target protein at either its N-terminus or its C-terminus. Active macromolecular complexes can then be isolated starting from a relatively small number of cells and used for multiple downstream applications.
An introductory article from Bitesize Bio (checked 2026-10-29) describes the tag as two IgG-binding domains of Staphylococcus aureus Protein A, a calmodulin-binding peptide (CBP), and a TEV protease cleavage site placed between them. In that description, the tagged protein first binds IgG beads through the Protein A domains; after washing, TEV protease cleaves the tag and releases the protein, which still carries the calmodulin-binding peptide; a second purification on calmodulin resin, followed by washing and elution, completes the process. The two stages are the “tandem” in the name.
The purified material is commonly characterised by proteomic methods; see the CASRAI guide What is proteomics for the wider context.
Related concepts
TAP sits within the family of affinity-based approaches to finding protein interactions. Puig et al. state that variations of the method can specifically purify complexes containing two given components, or subtract undesired complexes, and that although it was initially developed in yeast it can be adapted to various organisms.
A common alternative route to the same question is co-immunoprecipitation, which uses an antibody rather than a fused tag; see co-immunoprecipitation controls, lysis conditions and interpretation. Tagged proteins can also be produced in heterologous hosts, for example in the baculovirus expression system.
Where it matters for labs: a sourced checklist
| Consideration | What the sources say | Source |
|---|---|---|
| Construct | The target protein must be fused to the TAP tag at the N- or C-terminus. | Puig et al. 2001 |
| Prior knowledge | No prior knowledge of complex composition or function is required. | Puig et al. 2001 |
| Expression level | Designed for proteins expressed at their natural level, under native conditions. | Rigaut et al. 1999 |
| Starting material | Can start from a relatively small number of cells. | Puig et al. 2001 |
| Host organism | Developed in yeast; adaptable to other organisms. | Puig et al. 2001 |
| Tag interference | The tag may disrupt the protein’s function or its interactions. | Bitesize Bio |
| Stringency | Near-physiological conditions that are not stringent enough can leave non-specific proteins in the preparation. | Bitesize Bio |
The checklist is a planning aid for deciding whether the method fits a question. Tag placement and controls should be settled against the primary literature for the specific protein and organism.
Common misunderstandings
“TAP needs to know the partners in advance”
It does not. Puig et al. state that prior knowledge of complex composition or function is not required, which is why it is used for exploration.
“A tandem purification guarantees a clean result”
Two steps reduce background but do not remove it. Conditions that stay near-physiological can carry non-specific proteins through, so identifications need the same critical reading as any interaction data.
“The tag is neutral”
A tag is an addition to the protein and may affect function or interactions, which is why N- versus C-terminal placement is a design decision.
FAQ
What is a TAP tag?
A dual-affinity tag fused to a target protein. In the Bitesize Bio description it combines two Protein A IgG-binding domains, a TEV protease cleavage site and a calmodulin-binding peptide.
What is the TEV protease site for?
Per the same description, TEV cleavage between the two affinity elements releases the protein from the first affinity matrix so it can be captured in the second step.
Who developed the method?
Rigaut, Shevchenko, Rutz, Wilm, Mann and Seraphin, published in Nature Biotechnology in 1999 (PMID 10504710).
Sources
- Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999;17(10):1030-2. https://pubmed.ncbi.nlm.nih.gov/10504710/ (date checked: 2026-10-29).
- Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, Bragado-Nilsson E, Wilm M, Seraphin B. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods. 2001;24(3):218-29. https://pubmed.ncbi.nlm.nih.gov/11403571/ (date checked: 2026-10-29).
- Bitesize Bio. An Introduction to Tandem Affinity Purification. https://bitesizebio.com/8208/an-introduction-to-tandem-affinity-purification/ (date checked: 2026-10-29); tag components, workflow and cautions are attributed to this article.
