Dataset Information

Drosophila melanogaster exp 135

ABSTRACT: PeptideRank is an approach that uses a rank-based algorithm for peptide detectability prediction from shotgun proteomics data. The best performance is achieved when it is trained on organism-specific shotgun proteomics datasets. The Drosophila shotgun proteomics data presented here have been used amongst others to train and validate PeptideRank.

INSTRUMENT(S): LTQ

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Sandra Goetze

LAB HEAD: Erich Brunner

PROVIDER: PXD000726 | Pride | 2019-06-04

REPOSITORIES: Pride

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Publications

Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.

Qeli Ermir E Omasits Ulrich U Goetze Sandra S Stekhoven Daniel J DJ Frey Juerg E JE Basler Konrad K Wollscheid Bernd B Brunner Erich E Ahrens Christian H CH

Journal of proteomics 20140527

The in silico prediction of the best-observable "proteotypic" peptides in mass spectrometry-based workflows is a challenging problem. Being able to accurately predict such peptides would enable the informed selection of proteotypic peptides for targeted quantification of previously observed and non-observed proteins for any organism, with a significant impact for clinical proteomics and systems biology studies. Current prediction algorithms rely on physicochemical parameters in combination with ...[more]

PMID: 24878426

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Project description:The local protein composition of chromatin is important for the regulation of transcription and other functions. By integrative analysis of genome-wide binding maps of 53 broadly selected chromatin components in Drosophila cells, we show that the genome is segmented into five principal chromatin types that are defined by unique, yet overlapping combinations of proteins, and form domains that can extend over >100 kb. We identify a novel repressive chromatin type that covers about half of the genome and lacks classic heterochromatin markers. Furthermore, transcriptionally active euchromatin consists of two distinct types that differ in molecular organization and H3K36 methylation, and regulate distinct classes of genes. Finally, we provide evidence that the different chromatin types act as guides that help to target DNA-binding factors to specific subsets of their recognition motifs. These results uncover basic principles of chromatin organization in a higher eukaryote. For this study, we generated whole-genome DamID binding profiles of 45 chromatin proteins in Drosophila Kc167 cells. Additionally, we perused published binding data of 8 chromatin proteins and generated a binding profile of one exogenous (yeast) DNA binding factor in Kc167 cells. On the same array platform, we obtained ChIP-on-chip profiles of histone H3, H1, H3K9me2, H3K27me3, H3K4me2, and H3K79me3. See supplementary files below. Gene expression was measured by RNA tag profiling. See GeneCounts supplementary file below. [1] RNA tag sequences were optained on an Illumina GAII with the digital gene expression (DGE) module from duplicate RNA samples. [2] All DamID and ChIP experiments were done in Drosophila Kc167 cells in duplicate. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation, where Dam-fusion material was hybridized over Dam-only material. For ChIP, immunoprecipitated material was hybridized over ChIP input material. 18 previously-submitted Samples were included in this study. 10 of 18 Samples have been renormalized for the GSE22069 study: GSM509087, GSM509088, GSM509089, GSM509090, GSM509091, GSM509092, GSM509093, GSM509094, GSM509095, GSM509096 New GSM accession numbers have been issued for these 10 samples. 8 of 18 Samples are identical in the original studies and in GSE22069: GSM423290, GSM423291, GSM423298, GSM423299, GSM493592, GSM493593, GSM509085, GSM509086 [3] The genomic locations in files GSE22069_norm_aggregated_discretized_tiling_arrays.txt and GSE22069_norm_aggregated_tiling_arrays.txt are relative to FlyBase release 5 (BDGP R5/dm3).

Dataset Information

Drosophila melanogaster exp 135

Publications

Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.

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