From pull-down data to protein interaction networks and complexes with biological relevance

B Zhang, BH Park, T Karpinets, NF Samatova - Bioinformatics, 2008 - academic.oup.com
Motivation: Recent improvements in high-throughput Mass Spectrometry (MS) technology
have expedited genome-wide discovery of protein–protein interactions by providing a …

[HTML][HTML] Inferring protein-protein interaction networks from mass spectrometry-based proteomic approaches: a mini-review

K Yugandhar, S Gupta, H Yu - Computational and structural biotechnology …, 2019 - Elsevier
Studying protein-protein interaction networks provide key evidence for the underlying
molecular mechanisms. Mass spectrometry-based proteomic approaches have been …

[HTML][HTML] Predicting co-complexed protein pairs using genomic and proteomic data integration

LV Zhang, SL Wong, OD King, FP Roth - BMC bioinformatics, 2004 - Springer
Background Identifying all protein-protein interactions in an organism is a major objective of
proteomics. A related goal is to know which protein pairs are present in the same protein …

What do we learn from high-throughput protein interaction data?

B Titz, M Schlesner, P Uetz - Expert review of proteomics, 2004 - Taylor & Francis
The biological significance of protein interactions, their method of generation and reliability
is briefly reviewed. Protein interaction networks adopt a scale-free topology that explains …

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

AI Nesvizhskii - Proteomics, 2012 - Wiley Online Library
Analysis of protein interaction networks and protein complexes using affinity purification and
mass spectrometry (AP/MS) is among most commonly used and successful applications of …

[HTML][HTML] Computational approaches for detecting protein complexes from protein interaction networks: a survey

X Li, M Wu, CK Kwoh, SK Ng - BMC genomics, 2010 - Springer
Background Most proteins form macromolecular complexes to perform their biological
functions. However, experimentally determined protein complex data, especially of those …

Computational analyses of high-throughput protein-protein interaction data

Y Chen, D Xu - Current protein and peptide science, 2003 - ingentaconnect.com
Protein-protein interactions play important roles in nearly all events that take place in a cell.
High-throughput experimental techniques enable the study of protein-protein interactions at …

[HTML][HTML] Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry

RM Kaake, X Wang, L Huang - Molecular & cellular proteomics, 2010 - ASBMB
Protein-protein interactions are important for nearly all biological processes, and it is known
that aberrant protein-protein interactions can lead to human disease and cancer. Recent …

[HTML][HTML] Building protein-protein interaction networks with proteomics and informatics tools

ME Sardiu, MP Washburn - Journal of Biological Chemistry, 2011 - ASBMB
The systematic characterization of the whole interactomes of different model organisms has
revealed that the eukaryotic proteome is highly interconnected. Therefore, biological …

[HTML][HTML] Large scale chemical cross-linking mass spectrometry perspectives

BL Zybailov, GV Glazko, M Jaiswal… - Journal of proteomics & …, 2013 - ncbi.nlm.nih.gov
The spectacular heterogeneity of a complex protein mixture from biological samples
becomes even more difficult to tackle when one's attention is shifted towards different protein …