Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics
- PMID: 37450153
- DOI: 10.1007/978-1-0716-3327-4_22
Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics
Abstract
Protein-protein interactions (PPIs) are the physical interactions formed among proteins. These interactions are primarily functional, i.e., they arise from specific biomolecular events, and each interaction interface serves a specific purpose. A significant number of methods have been developed for protein interactions in the field of proteomics in the last decade. Advanced mass spectrometry technology significantly contributed to the development of these methods. The rapid advancement of groundbreaking MS technology has greatly aided the mapping of protein interaction from large-data sets comprehensively. This chapter describes the affinity purification (AP) mass spectrometry (MS)-based methods combined with chemical cross-linking (XL) of protein complexes. This chapter includes sample preparation methods involving cell culture, cell treatments with ligands, drugs, and cross-linkers, protein extractions, affinity purification, sodium dodecyl sulfate (SDS) polyacrylamide gel separation, in-solution or in-gel digestion, liquid-chromatography, and mass spectrometry analysis of samples (LC-MS/MS). Application of a cleavable cross-linker, dual cleavable cross-linking technology (DUCCT) in combination with the affinity purification (AP) method has also been described. Methods for data analysis using unmodified and cross-linked peptide analysis are discussed.
Keywords: AP-MS; Cross-linking; Mass spectrometry; Protein; Proteomics; SDS polyacrylamide gel technique; protein interactions.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Similar articles
-
In vivo cross-linking-based affinity purification and mass spectrometry for targeting intracellular protein-protein interactions.Anal Chim Acta. 2023 Jul 18;1265:341273. doi: 10.1016/j.aca.2023.341273. Epub 2023 May 4. Anal Chim Acta. 2023. PMID: 37230567
-
High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL.J Am Soc Mass Spectrom. 2020 Feb 5;31(2):173-182. doi: 10.1021/jasms.9b00111. Epub 2020 Jan 2. J Am Soc Mass Spectrom. 2020. PMID: 32031390
-
A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein-protein interactions.Nat Protoc. 2018 Dec;13(12):2864-2889. doi: 10.1038/s41596-018-0068-8. Nat Protoc. 2018. PMID: 30382245
-
Divide and conquer: cleavable cross-linkers to study protein conformation and protein-protein interactions.Anal Bioanal Chem. 2017 Jan;409(1):33-44. doi: 10.1007/s00216-016-9941-x. Epub 2016 Oct 12. Anal Bioanal Chem. 2017. PMID: 27734140 Review.
-
XL-MS: Protein cross-linking coupled with mass spectrometry.Methods. 2015 Nov 1;89:54-63. doi: 10.1016/j.ymeth.2015.06.010. Epub 2015 Jun 12. Methods. 2015. PMID: 26079926 Review.
References
-
- Ijaz M, Ansari M-u-R, Iqbal M (2018) Introductory chapter: protein-protein interactions and assays. Protein-Protein Interaction Assays. https://doi.org/10.5772/INTECHOPEN.77337 - DOI
-
- MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289(5485):1760–1763. https://doi.org/10.1126/SCIENCE.289.5485.1760 - DOI - PubMed
-
- Purcell S, Neale B, Todd-Brown K et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575. https://doi.org/10.1086/519795 - DOI - PubMed - PMC
-
- Ewing RM, Chu P, Elisma F et al (2007) Large-scale mapping of human protein–protein interactions by mass spectrometry. Mol Syst Biol 3(1):89. https://doi.org/10.1038/msb4100134 - DOI - PubMed - PMC
-
- Zacharias AO, Fang Z, Rahman A et al (2021) Affinity and chemical enrichment strategies for mapping low-abundance protein modifications and protein-interaction networks. J Sep Sci 44(1):310–322. https://doi.org/10.1002/JSSC.202000930 - DOI - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources