Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling

Supplemental data for the article: Characterization of functional reprogramming during osteoclast development using quantitative proteomics and mRNA profiling Eunkyung An, Manikandan Narayanan, and Aleksandra Nita-Lazar* *corresponding author: Cellular Networks Proteomics Unit Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda, Maryland, 20892, USA Tel. [phone] Fax: [phone] E-mail: [e-mail] This dataset includes: 1. Raw LC-MS(/MS) spectra (*.raw), and 2. The output from data analyses using IP2 (Intergrated Proteomics Application, San Diego, CA) searched against the UniProt_mouse_01-18-2011 set of protein sequences (normal + reversed). Note that the version of IP2 that was used could only analyze two SILAC channels at a time, so two analyses were performed (light-medium, light-heavy) (the current version can analyze 3-plex SILAC all together in one analysis). Also, IP2 was run using two criteria (1 or 2 peptides per protein). Lanes D and E were lanes of an SDS-PAGE gel, and each was 3-plex SILAC: Lane D: Light (Osteoclast Precursor), Medium (Mature Osteoclast), Heavy (Intermediate Osteoclast) Lane E: Light (Osteoclast Precursor), Medium (Intermediate Osteoclast), Heavy (Mature Osteoclast)