Immunoprecipitation

	Immobilization to NH₂ group of protein	Immobilization with affinity binding	Immobilized with Avidin-biotin binding	Immobilization to SH group and NH₂ group of protein	Immobilization to His-tag of protein	Immobilization with click chemistry
It is possible to firmly immobilize the proteins by covalent bond to the beads. Since the NH₂ groups on the protein is randomly immobilized on the beads, the orientation of the antibodies becomes disjointed. NHS beads are recommended because they are easier to operate than COOH beads.	Only antibodies can be immobilized on beads. The Fc site of the antibody binds to the beads by affinity. The immobilization operation is easy.	Immobilizes to beads with strong affinity binding. Immobilization requires biotinlation of the ligand.	Ligand immobilization is possible with inexpensive beads. However, temperature tolerance of the protein at 37℃ is required.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.
（1）Antibody	◎	◎	◎	○	○	△
Recommended beads	COOH beads NHS beads	Protein A beads Protein G beads	Streptavidin beads NeutrAvidin beads	Epoxy beads	Ts beads	Azide beads Alkyne beads

	Immobilization to NH₂ group of protein	Immobilization with affinity binding	Immobilized with Avidin-biotin binding	Immobilization to SH group and NH₂ group of protein	Immobilization to His-tag of protein	Immobilization with click chemistry
It is possible to firmly immobilize the proteins by covalent bond to the beads. Since the NH₂ groups on the protein is randomly immobilized on the beads, the orientation of the antibodies becomes disjointed. NHS beads are recommended because they are easier to operate than COOH beads.	Only antibodies can be immobilized on beads. The Fc site of the antibody binds to the beads by affinity. The immobilization operation is easy.	Immobilizes to beads with strong affinity binding. Immobilization requires biotinlation of the ligand.	Ligand immobilization is possible with inexpensive beads. However, temperature tolerance of the protein at 37℃ is required.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.
（2）Antigen	◎	×	◎	○	○	△
Recommended beads	COOH beads NHS beads	Protein A beads Protein G beads	Streptavidin beads NeutrAvidin beads	Epoxy beads	Ts beads	Azide beads Alkyne beads

	Immobilization to NH₂ group of protein	Immobilization with affinity binding	Immobilized with Avidin-biotin binding	Immobilization to SH group and NH₂ group of protein	Immobilization to His-tag of protein	Immobilization with click chemistry
It is possible to firmly immobilize the proteins by covalent bond to the beads. Since the NH₂ groups on the protein is randomly immobilized on the beads, the orientation of the antibodies becomes disjointed. NHS beads are recommended because they are easier to operate than COOH beads.	Only antibodies can be immobilized on beads. The Fc site of the antibody binds to the beads by affinity. The immobilization operation is easy.	Immobilizes to beads with strong affinity binding. Immobilization requires biotinlation of the ligand.	Ligand immobilization is possible with inexpensive beads. However, temperature tolerance of the protein at 37℃ is required.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.
（3）Direct method	◎	◎	◎	○	○	△
Recommended beads	COOH beads NHS beads	Protein A beads Protein G beads	Streptavidin beads NeutrAvidin beads	Epoxy beads	Ts beads	Azide beads Alkyne beads

	Immobilization to NH₂ group of protein	Immobilization with affinity binding	Immobilized with Avidin-biotin binding	Immobilization to SH group and NH₂ group of protein	Immobilization to His-tag of protein	Immobilization with click chemistry
It is possible to firmly immobilize the proteins by covalent bond to the beads. Since the NH₂ groups on the protein is randomly immobilized on the beads, the orientation of the antibodies becomes disjointed. NHS beads are recommended because they are easier to operate than COOH beads.	Only antibodies can be immobilized on beads. The Fc site of the antibody binds to the beads by affinity. The immobilization operation is easy.	Immobilizes to beads with strong affinity binding. Immobilization requires biotinlation of the ligand.	Ligand immobilization is possible with inexpensive beads. However, temperature tolerance of the protein at 37℃ is required.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.
（4）Indirect method	×	△	◎	×	○	△
Recommended beads	COOH beads NHS beads	Protein A beads Protein G beads	Streptavidin beads NeutrAvidin beads	Epoxy beads	Ts beads	Azide beads Alkyne beads

	Immobilization to NH₂ group of protein	Immobilization with affinity binding	Immobilized with Avidin-biotin binding	Immobilization to SH group and NH₂ group of protein	Immobilization to His-tag of protein	Immobilization with click chemistry
It is possible to firmly immobilize the proteins by covalent bond to the beads. Since the NH₂ groups on the protein is randomly immobilized on the beads, the orientation of the antibodies becomes disjointed. NHS beads are recommended because they are easier to operate than COOH beads.	Only antibodies can be immobilized on beads. The Fc site of the antibody binds to the beads by affinity. The immobilization operation is easy.	Immobilizes to beads with strong affinity binding. Immobilization requires biotinlation of the ligand.	Ligand immobilization is possible with inexpensive beads. However, temperature tolerance of the protein at 37℃ is required.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.	It is necessary to introduce His-tag into the protein. The beads also bind to the NH₂ groups on the protein.
（1）Antibody	◎	◎	◎	○	○	△
（2）Antigen	◎	×	◎	○	○	△
（3）Direct method	◎	◎	◎	○	○	△
（4）Indirect method	×	△	◎	×	○	△
Recommended beads	COOH beads NHS beads	Protein A beads Protein G beads	Streptavidin beads NeutrAvidin beads	Epoxy beads	Ts beads	Azide beads Alkyne beads

Protocol
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Catalog

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FG winds issue 5

Immunoprecipitation(1)
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FG winds issue 6

Immunoprecipitation(2)
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FG winds issue 7

Immunoprecipitation (3)
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FG winds issue 8

Immunoprecipitation (4)
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Chromatin immunoprecipitation 1

unichi Yamamoto, Tokyo Medical University
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Chromatin immunoprecipitation 2

obuo Horikoshi, Houston Methodist Research Institute Weill Cornell Medical College
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Protein A beads / Protein G beads

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Papers

Jingyun Jin et al.(2023)

The N‑terminal disordered region of ChsB regulates its efcient
Current Genetics (2023) 69:175–188
Takahata et al.(2023)

Immuno-Mass Spectrometry Workflow for Quantification of Serum α-Fetoprotein Using Antibody-Immobilized Magnetic Beads and Modified Eluents.
Mass Spectrom (Tokyo). 2023;12(1):A0122.
Dozen et al.(2022)

Tumor Suppressive Role of the PRELP Gene in Ovarian Clear Cell Carcinoma
J. Pers. Med. 2022, 12(12), 1999; https://doi.org/10.3390/jpm12121999
Kamiya et al.(2022)

Targeting necroptosis in muscle fibers ameliorates inflammatory myopathies
Nature Communications volume 13, Article number: 166 (2022)
Hamada et al.(2022)

An oncogenic splice variant of PDGFRα in adult glioblastoma as a therapeutic target for selective CDK4/6 inhibitors
Scientifc Reports (2022) 12:1275
Fujii et al.(2022)

α1,4- Linked N- acetylglucosamine suppresses gastric cancer development by inhibiting Mucin-1-mediated signaling.
Cancer Science. 2022;00:1–12
Amina Bolatkan et al.(2022)

Downregulation of METTL6 mitigates cell progression, migration, invasion and adhesion in hepatocellular carcinoma by inhibiting cell adhesion molecules
INTERNATIONAL JOURNAL OF ONCOLOGY 60: 4, 2022
Hosoya et al.(2022)

Chondroprotective effects of CDK4/6 inhibition via enhanced ubiquitin-dependent degradation of JUN in synovial fibroblasts
Rheumatology 2022;61:3427–3438
Kazuma et al.(2022)

ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells
Scientific Reports volume 12, Article number: 2278 (2022)
Kambe et al.(2021)

Enhanced β2-microglobulin binding of a “navigator” molecule bearing a single-chain variable fragment antibody for artificial switching of metabolic processing pathways
Biomater. Sci., 2021, 9, 5551–5558
S. Kageyama et al. (2021)

Identification of the mutation signature of the cancer genome caused by irradiation
Radiotherapy and Oncology 155 (2021) 10
Suzuki et al.(2021)

A PX-BAR protein Mvp1/SNX8 and a dynamin-like GTPase Vps1 drive endosomal recycling
eLife 2021;10:e69883.
Kaneko et al.(2021)

Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential
Cancers 2021, 13, 2126
Ozawa et al.(2021)

Exploiting ubiquitin ligase cereblon as a target for small-molecule compounds in medicine and chemical biology
Cell Chemical Biology 28, July 15, 2021
Takahashi et al.(2020)

A Human DUB Protein Array for Clarification of Linkage Specificity of Polyubiquitin Chain and Application to Evaluation of Its Inhibitors
Biomedicines 2020, 8, 152
Kang et al.(2020)

Comprehensive analysis on the whole Rho-GAP family reveals that ARHGAP4 suppresses EMT in epithelial cells under negative regulation by Septin9
The FASEB Journal. 2020;34:8326-8340
Obara et al.(2020)

N-glycosylation of Rim21 at an unconventional site fine-tunes its behavior in the plasma membrane
Cell Structure and Function 2020, https://doi.org/10.1247/csf.19021
M. Sekino et al. (2020)

Development of an automatic magnetic immunostaining system for rapid intraoperative diagnosis of cancer metastasis
AIP Advances 10, 015106 (2020)
Y. Kambe et al. (2020)

Artificial switching of the metabolic processing pathway of an etiologic factor, β2-microglobulin, by a “navigator” molecule
Journal of Controlled Release 327 (2020) 8–18
Tomioka et al.(2020)

TORC1 inactivation stimulates autophagy of nucleoporin and nuclear pore complexes
Journal of Cell Biology 2020 Vol. 219 No. 7 e201910063
Meguro et al.(2020)

Pex3 confines pexophagy receptor activity of Atg36 to peroxisomes by regulating Hrr25-mediated phosphorylation and proteasomal degradation
J. Biol. Chem. (2020) 295(48) 16292–16298
K. Akiyoshi et al. (2020)

Wash-free detection of biological target using cluster formation of magnetic markers
Journal of Magnetism and Magnetic Materials 500 (2020) 166356
Mochida et al.(2020)

Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes
NATURE COMMUNICATIONS (2020) 11:3306
Federspiel et al.(2019)

Hdac4 Interactions in Huntington’s Disease Viewed Through the Prism of Multiomics
Molecular & Cellular Proteomics 18, S92–S113 (2019)
Suzuki et al.(2019)

A bipartite sorting signal ensures specificity of retromer complex in membrane protein recycling
J. Cell Biol. 2019 Vol. 218 No. 9 2876–2886
Fujimori et al.(2019)

Mismatch repair dependence of replication stress-associated DSB recognition and repair
Heliyon 5 (2019) e03057
Y. Kabe et al. (2019) [ExoCounter]

Application of high-performance magnetic nanobeads to biological sensing devices.
Aal. Bioanal. Chem., doi: 10.1007/s00216-018-1548-y (2019).
T. Onishi et al. (2019)

Magnetically Promoted Rapid Immunofluorescence Staining for Frozen Tissue Sections
J. Histochem. Cytochem., Epub 2019 Apr 8
K. Harada et al. (2019)

Two distinct mechanisms target the autophagy-related E3 complex to the pre-autophagosomal structure
Elife, 8, e43088(2019)
Myouga et al.(2018)

Stable Accumulation of Photosystem II Requires ONE-HELIX PROTEIN1 (OHP1) of the Light Harvesting-Like Family
Plant Physiology, Volume 176, Issue 3, March 2018, Pages 2277–2291
Yamagami et al.(2018)

ISGF3 with reduced phosphorylation is associated with constitutive expression of interferon-induced genes in aging cells
npj Aging and Mechanisms of Disease (2018)4:11
T. Fujii et al. (2018)

A Novel Autoantibody against Plexin D1 in Patients with Neuropathic Pain
Ann. Neurol., 84, 200 (2018).
Sekiguchi et al.(2018)

MHC-associated peptide proteomics enabling highly sensitive detection of immunogenic sequences for the development of therapeutic antibodies with low immunogenicity
MABS 2018, VOL. 10, NO. 8, 1168–1181
K. Enpuku et al. (2018)

Wash-free detection of C-reactive protein based on third-harmonic signal measurement of magnetic markers.
Jpn. J. Appl. Phys., 57, 112, 090309 (2018).
T. Kotani et al. (2018)

The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation
Proc. Natl. Acad. Sci. USA, 115, 10363(2018)
Wang et al.(2017)

Transport Granules Bound with Nuclear Cap Binding Protein and Exon Junction Complex Are Associated with Microtubules and Spatially Separated from eIF4E Granules and P Bodies in Human Neuronal Processes
Front. Mol. Biosci. 4:93. doi: 10.3389/fmolb.2017.00093
Uematsu et al.(2017)

Accumulation of undegraded autophagosomes by expression of dominant-negative STX17 (syntaxin 17) mutants
Autophagy, 13:8 (2017), 1452-1464
Nishimura et al.(2017)

Autophagosome formation is initiated at phosphatidylinositol synthase-enriched ER subdomains
The EMBO Journal (2017)36:1719-1735
Y. Nishiya et al. (2017)

A new efficient method of generating photoaffinity beads for drug target identification
Bioorg. Med. Chem. Lett., 27, 834 (2017).
K. Nakata et al. (2017)

A proteomics method using immunoaffinity fluorogenic derivatization-liquid chromatography/tandem mass spectrometry (FD‐LC‐MS/MS) to identify a set of interacting proteins.
Biomedical Chromatography, DOI: 10.1002/bmc.4063 (2017).
Kakumu et al.(2017)

Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3
Genes to Cells (2017) 22, 310–327
S. Tsubota et al. (2017)

PRC2-Mediated Transcriptomic Alterations at the Embryonic Stage Govern Tumorigenesis and Clinical Outcome in MYCN-Driven Neuroblastoma
Cancer Res., DOI: 10.1158 (2017)
Saito et al.(2017)

TLR7 mediated viral recognition results in focal type I interferon secretion by dendritic cells
NATURE COMMUNICATIONS 8: 1592
Duarte et al.(2016)

Generation of Immunity against Pathogens via Single-Domain Antibody–Antigen Constructs
J Immunol December 15, 2016, 197 (12) 4838-4847
A. Kimura et al. (2016)

N-Myristoylation of the Rpt2 subunit of the yeast 26S proteasome is implicated in the subcellular compartment?specific protein quality control system
Journal of Proteomics, 130, 33 (2016)
M. Takeshita et al. (2016)

Alteration of matrix metalloproteinase-3 O-glycan structure as a biomarker for disease activity of rheumatoid arthritis
Arthritis Research & Therapy, 18, 112 (2016).
Y. Atsumi et al. (2015)

ATM and SIRT6/SNF2H Mediate Transient H2AX Stabilization When DSBs Form by Blocking HUWE1 to Allow Efficient γH2AX Foci Formation
Cell Reports, 13, 2728 (2015).
S. Yamauchi et al. (2015)

Opt2 mediates the exposure of phospholipids during cellular adaptation to altered lipid asymmetry
J Cell Sci (2015) 128 (1): 61–69.
S. Masaki et al. (2015)

Identification of the Specific Interactors of the Human Lariat RNA Debranching Enzyme 1 Protein
Int. J. Mol. Sci., 16, 3705 (2015).
S. Sakamoto et al. (2014)

Magnetically Promoted Rapid Immunoreactions Using Functionalized Fluorescent Magnetic Beads:A Proof of Principle
Clinical Chemistry, 60:4 (2014).

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（1）Antibody

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（2）Antigen

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（3）Direct method

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