Dataset Information

Hs_Retinal_stem_cell_iTRAQ_1

ABSTRACT: Human Retinal_stem_cell, iTRAQ, Cellzome, sample 1

REANALYSIS of: PXD000865

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Others

SUBMITTER: Wilhelm et al.

PROVIDER: PAe004981 | PeptideAtlas | 2014-12-31

REPOSITORIES: PeptideAtlas

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Publications

Mass-spectrometry-based draft of the human proteome.

Wilhelm Mathias M Schlegl Judith J Hahne Hannes H Gholami Amin Moghaddas AM Lieberenz Marcus M Savitski Mikhail M MM Ziegler Emanuel E Butzmann Lars L Gessulat Siegfried S Marx Harald H Mathieson Toby T Lemeer Simone S Schnatbaum Karsten K Reimer Ulf U Wenschuh Holger H Mollenhauer Martin M Slotta-Huspenina Julia J Boese Joos-Hendrik JH Bantscheff Marcus M Gerstmair Anja A Faerber Franz F Kuster Bernhard B

Nature 20140501 7502

Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data, called ProteomicsDB. The information assembled from human tissues, cell lines ...[more]

PMID: 24870543

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Project description:The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of transcript and protein levels of tissue regulated genes. Until now, such studies of have only included microarray or short length sequence tags for transcript profiling. Furthermore, most comparisons of transcript and protein levels have been based on absolute expression values from within the same tissue and not relative expression values based on tissue ratios. Presented here is a novel study of two porcine tissues based on integrative analysis of data from expression profiling of identical samples using cDNA microarray, 454-sequencing and iTRAQ-based proteomics. Sequence homology identified 2.541 unique transcripts that are detectable by both microarray hybridizations and 454-sequencing of 1.2 million cDNA tags. Both transcript-based technologies showed high reproducibility between sample replicates of the same tissue, but the correlation across these two technologies was modest. Thousands of genes being differentially expressed were identified with microarray. Out of the 306 differentially expressed genes, identified by 454-sequencing, 198 (65 %) were also found by microarray. The relationship between the regulation of transcript and protein levels was analyzed by integrating iTRAQ-based proteomics data. Protein expression ratios were determined for 354 genes, of which 148 could be mapped to both microarray and 454-sequencing data. A comparison of the expression ratios from the three technologies revealed that differences in transcript and protein levels across heart and muscle tissues are positively correlated. We show that the reproducibility within cDNA microarray and 454-sequencing is high, but that the agreement across these two technologies is modest. We demonstrate that the regulation of transcript and protein levels across identical tissue samples is positively correlated when the tissue expression ratios are used for comparison. The results presented are of interest in systems biology research in terms of integration and analysis of high-throughput expression data from mammalian tissues. Keywords: tissue comparison, platform comparison Tissue samples of heart (HEA) and Longissimus dorsi (LDO) were prepared by pooling from five healthy Hampshire gilts at age four to six months and division into six sub-samples, three for each tissue named HEA1, HEA2, HEA3, LDO1, LDO2 and LDO3. The exact same six tissue samples were used for subsequent expression profiling with cDNA microarray, 454-sequencing and iTRAQ-based proteomics. A reference sample for the cDNA microarray experiment and iTRAQ-based proteomics was constructed by combining the six samples. In the microarray experiment, three cDNA microarray slides were used per sample.

Dataset Information

Hs_Retinal_stem_cell_iTRAQ_1

Publications

Mass-spectrometry-based draft of the human proteome.

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