NOPdb: Nucleolar Proteome Database

Abstract

The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain structures and relevant protein homologues across species, as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of approximately 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints, highlighted by visualization means in the NOPdb, provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/uncharacterized proteins. The NOPdb (http://www.lamondlab.com/NOPdb) is searchable by either gene names, nucleotide or protein sequences, Gene Ontology terms or motifs, or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink, OMIM and PubMed).

Figure 1

Snapshots of the NOPdb (). The database was searched against molecular weights between 65 and 70 kDa and here we show an overview page for the PES1 protein (pescadillo) documenting its motif distribution, its GO annotations, its identification history by multiple MS analysis and its quantitative data from SILAC analyses. Proteins of similar kinetic profiles based on correlation coefficient are identified for future investigation. The kinetic profiles are ranked according to the Pearson's correlation coefficients for the log value of the peak intensities of multiple peptides at a particular timepoint normalized to the respective peak intensities at zero timepoints.