The International Protein Index: An integrated database for proteomics experiments

By Paul Julian Kersey, Jorge Duarte, Allyson Williams, Youla Karavidopoulou, Ewan Birney, Rolf Apweiler. Proteomics, 2004

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Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics*S (2005, neutral): “0, November 2004 for Samples 1 and 3) (30).”
The UniProt-GO Annotation database in 2011 (2011, methodology): “Previously, proteome sets defined by the now-defunct Integr8 (20) and IPI (21) projects were used by the UniProt-GOA project.”
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (2012, background): “Seven peptides derived from the SNV and six peptides derived from edited transcripts were unique to a single protein in the IPI database (Kersey et al., 2004) and classified as high confidence.”
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data (2012, methodology): “Human and mouse data were searched against International Protein Index [14] (IPI) protein sequences while the yeast data was searched against the protein translations in the Saccaromyces Genome Database [15] (SGD).”
Acquisition of the contractile phenotype by murine arterial smooth muscle cells depends on the Mir143/145 gene cluster. (2009, background): “SILAC quantification, and false positive rate determination (50).”
Interpretation of Shotgun Proteomic Data (2005, background): “A good balance between the completeness and the level of redundancy is found in the International Protein Index (IPI) database (46), which is available for a number of organisms including human and mouse.”