Extracting high confidence protein interactions from affinity purification data: at the crossroads

Journal of Proteomics
Shuye PuShoshana J Wodak

Abstract

Deriving protein-protein interactions from data generated by affinity-purification and mass spectrometry (AP-MS) techniques requires application of scoring methods to measure the reliability of detected putative interactions. Choosing the appropriate scoring method has become a major challenge. Here we apply six popular scoring methods to the same AP-MS dataset and compare their performance. The comparison was carried out for six distinct datasets from human, fly and yeast, which focus on different biological processes and differ in their coverage of the proteome. Results show that the performance of a given scoring method may vary substantially depending on the dataset. Disturbingly, we find that the high confidence (HC) PPI networks built by applying the six scoring methods to the same raw AP-MS dataset display very poor overlap, with only 1.7-4.1% of the HC interactions present in all the networks built, respectively, from the proteome-wide human, fly or yeast datasets. Various properties of the shared versus unique interactions in each network, including biases in protein abundance, suggest that current scoring methods are able to eliminate only the most obvious contaminants, but still fail to reliably single out specific i...Continue Reading

References

Jun 14, 2001·Methods : a Companion to Methods in Enzymology·O PuigB Séraphin
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Sang-Won LeeRichard D Smith
Mar 14, 2003·Nature·Ruedi Aebersold, Matthias Mann
Oct 17, 2003·Nature·Sina GhaemmaghamiJonathan S Weissman
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
May 9, 2006·Current Opinion in Lipidology·John B Massey
Aug 30, 2006·Genome Biology·Johannes Goll, Peter Uetz
Dec 5, 2006·Biophysical Journal·Ramzi Alsallaq, Huan-Xiang Zhou
Jan 4, 2007·Molecular & Cellular Proteomics : MCP·Sean R CollinsNevan J Krogan
Mar 9, 2007·Bioinformatics·James Z WangChin-Fu Chen
Apr 19, 2008·PLoS Computational Biology·Jian Qiu, William Stafford Noble
May 2, 2008·Current Opinion in Structural Biology·Emmanuel D Levy, Jose B Pereira-Leal
Sep 19, 2008·Molecular & Cellular Proteomics : MCP·Shoshana J WodakBertrand Séraphin
Oct 4, 2008·Science·Lars Juhl Jensen, Peer Bork
Dec 9, 2008·Nature Methods·Kavitha VenkatesanMarc Vidal
Mar 6, 2009·Science Signaling·Emmanuel D LevyStephen W Michnick
Mar 25, 2009·FEBS Letters·Chanchal Kumar, Matthias Mann
Apr 8, 2009·Trends in Genetics : TIG·Christian R LandryStephen W Michnick
Jul 21, 2009·Cell·Mathew E SowaJ Wade Harper
Sep 26, 2009·PLoS Computational Biology·Xueping YuJaques Reifman
Nov 10, 2009·Nucleic Acids Research·Arnaud CeolGianni Cesareni
May 22, 2010·Science·Ashton BreitkreutzMike Tyers
Aug 25, 2010·The Journal of Cell Biology·Tobias C Walther, Matthias Mann
Sep 2, 2010·Nature Methods·Tommy NilssonJohn J M Bergeron
Oct 14, 2010·Database : the Journal of Biological Databases and Curation·Brian TurnerShoshana J Wodak
Dec 2, 2010·Journal of Proteome Research·Mathieu Lavallée-AdamMathieu Blanchette
Dec 4, 2010·Science·Sourav BandyopadhyayTrey Ideker
Dec 7, 2010·Nature Methods·Hyungwon ChoiAlexey I Nesvizhskii
Apr 1, 2011·Molecular & Cellular Proteomics : MCP·Sven-Eric SchelhornElena Zotenko
May 10, 2011·Nature Biotechnology·Andrei L TurinskyShoshana J Wodak
Nov 1, 2011·Cell·K G GuruharshaSpyros Artavanis-Tsakonas
Nov 29, 2011·Nature Cell Biology·John C ChristiansonRon R Kopito
Jan 19, 2012·Molecular Systems Biology·Trey Ideker, Nevan J Krogan
Apr 27, 2012·Molecular & Cellular Proteomics : MCP·M WangC von Mering
Aug 15, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Emmanuel D LevyChristian R Landry

❮ Previous
Next ❯

Citations

Dec 1, 2015·Journal of Proteome Research·Kevin TitecaSven Eyckerman
Dec 29, 2015·Mass Spectrometry Reviews·Pieter MeysmanKris Laukens
Apr 14, 2016·Chemical Reviews·Ozlem KeskinAttila Gursoy
Apr 6, 2017·Journal of Proteome Research·Stefano SalaChristophe Ampe
Jan 27, 2017·Molecular BioSystems·Spencer HavisSteven J Bark
Mar 18, 2019·Journal of Molecular Biology·Mauricio Macossay-CastilloShoshana J Wodak
Mar 22, 2016·Journal of Proteome Research·Zhou YiMarie-Hélène Mucchielli-Giorgi
Aug 19, 2021·Chemical Reviews·Rivkah Rogawski, Michal Sharon
Sep 3, 2021·Cellular & Molecular Immunology·Xin WangZheng Zhang

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.