Dataset Information

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

ABSTRACT: 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. +1 301-451-4394 Fax: +1 301-480-5170 E-mail: nitalazarau@niaid.nih.gov 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)

REANALYSED by: PAe005207

OTHER RELATED OMICS DATASETS IN: PAe005207PRJNA347645

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Aleksandra Nita-Lazar

PROVIDER: PXD000471 | Pride | 2014-07-22

REPOSITORIES: Pride

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

An Eunkyung E Narayanan Manikandan M Manes Nathan P NP Nita-Lazar Aleksandra A

Molecular & cellular proteomics : MCP 20140720 10

In addition to forming macrophages and dendritic cells, monocytes in adult peripheral blood retain the ability to develop into osteoclasts, mature bone-resorbing cells. The extensive morphological and functional transformations that occur during osteoclast differentiation require substantial reprogramming of gene and protein expression. Here we employ -omic-scale technologies to examine in detail the molecular changes at discrete developmental stages in this process (precursor cells, intermediat ...[more]

PMID: 25044017

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Project description:We used phosphoproteomics to compare the responses of the ERK1/2 inhibitors, SCH772984 and GDC0994, and the MKK1/2 inhibitor, trametinib. These are compared with responses to the MKK1/2 inhibitor, selumetinib (AZD6244), previously measured by our lab in the same metastatic melanoma cell line. In three replicate experiments, we quantified a total of 12,805 class I phosphosites on 3,819 proteins in the trametinib-SCH772984-DMSO experiment, and 7,074 class I phosphosites on 2,453 in the GDC0994-SCH772984-DMSO experiment. This included 466 phosphosites that reproducibly decreased in response to at least one inhibitor in the trametinib-SCH772984-DMSO experiment and 414 phosphosites in the GDC0994-SCH772984-DMSO experiment. The results demonstrate linearity in signaling through the MAP kinase pathway. By comparing multiple inhibitors targeted to multiple tiers of protein kinases in the MAPK pathway, we gain insight into regulation and new targets of the oncogenic BRAF driver pathway in cancer cells, and a useful approach for evaluating the specificity of drugs and drug candidates. SILAC Experimental Design Experiment 1 Replicate 1: Heavy – DMSO, Medium – SCH772984, Light – Trametinib Replicate 2: Heavy – SCH772984, Medium – Trametinib, Light – DMSO Replicate 3: Heavy – Trametinib, Medium – DMSO, Light – SCH772984 SILAC Experimental Design Experiment 2 Replicate 1: Heavy – DMSO, Medium – SCH772984, Light – GDC0994 Replicate 2: Heavy – SCH772984, Medium – GDC0994, Light – DMSO Replicate 3: Heavy – GDC0994, Medium – DMSO, Light – SCH772984 File List 1. Zipped MaxQuant search results folder containing index and output folders for each raw file, ‘combined’ output folder, and mqpar.xml MaxQuant search parameters file 2. Individual raw files of phosphopeptide-enriched ERLIC fractions and total protein fractions 3. Zipped MaxQuant version used for analysis 4. FASTA file containing Uniprot human identifications 5. Instructions for viewing annotated spectra

			Action	DRS
	011811_MOUSE_uniprot_sprot.fasta	Fasta
	021411_E26.raw	Raw
	021411_E27.raw	Raw
	021411_E33.raw	Raw
	021411_E34.raw	Raw