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In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 UniProt proteome analysis

ABSTRACT: This dataset is no actual new study but the results of the benchmark of the iPRG2008 benchmark dataset used in the manuscript "In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics".

INSTRUMENT(S): Q TRAP

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Julian Uszkoreit

LAB HEAD: Katrin Marcus

PROVIDER: PXD003954 | Pride | 2016-08-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	PT_model.txt	Txt
	iPRG2008_combined_faked_rt.mgf	Mgf
	mascot-iPRG2008_combined_faked_rt.idXML	Other
	merge1-mascot-fdr_filtered-iPRG2008_combined_faked_rt.idXML	Other
	merge1-mascot-iPRG2008_combined_faked_rt.pepXML	Pepxml

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Publications

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain Enrique E Uszkoreit Julian J Sachsenberg Timo T Pfeuffer Julianus J Liang Xiao X Hermjakob Henning H Sanchez Aniel A Eisenacher Martin M Reinert Knut K Tabb David L DL Kohlbacher Oliver O Perez-Riverol Yasset Y

Journal of proteomics 20160804

In mass spectrometry-based shotgun proteomics, protein identifications are usually the desired result. However, most of the analytical methods are based on the identification of reliable peptides and not the direct identification of intact proteins. Thus, assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Currently, different protein inference algorithms and tools are available for the prot ...[more]

PMID: 27498275

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In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 Swiss-Prot analysis

Project description:This dataset is no actual new study but the results of the benchmark of the iPRG2008 benchmark dataset used in the manuscript "In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics".

2016-08-10 | PXD003953 | Pride

In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 provided DB analysis

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In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 UniProt proteome with isoforms analysis

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PIA - iPRG2008 Benchmark Dataset

Project description:This dataset is no actual new study but the iPRG2008 benchmark dataset used in the PIA manuscript.

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FeatureFinderIdentification (OpenMS) analysis of the iPRG-2015 dataset

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2017-07-07 | PXD006336 | Pride

Integrative analysis of histone ChIP-seq and gene expression microarray data using Bayesian mixture models

Project description:Histone modifications are a key epigenetic mechanism to activate or repress the expression of genes. Data sets of matched microarray expression data and histone modification data measured by ChIP-seq exist, but methods for integrative analysis of both data types are still rare. Here, we present a novel bioinformatic approach to detect genes that are differentially expressed between two conditions putatively caused by alterations in histone modification. We introduce a correlation measure for integrative analysis of ChIP-seq and gene expression data and demonstrate that a proper normalization of the ChIP-seq data is crucial. We suggest applying Bayesian mixture models of different distributions to further study the distribution of the correlation measure. The implicit classification of the mixture models is used to detect genes with differences between two conditions in both gene expression and histone modification. The method is applied to different data sets and its superiority to a naive separate analysis of both data types is demonstrated. This GEO series contains the expression data of the Cebpa example data set. This data set was derived from sorted Cebpafl/fl and Cebpafl/fl;Mx1Cre murine hematopoietic LSKCD150- 18 post pIpC injections (conditional deletion of Cebpa). The specimens from three Cebpafl/fl and three Cebpafl/fl;Mx1Cre mice were hybridized separately on six Affymetrix Mouse Gene 1.0 ST arrays. Associated histone modification ChIP-seq data is provided by series GSE43007.

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Pre-leukemic Cebpa mutant myeloid progenitors

Project description:In this study, we use pre-malignant cells from different Cebpa mutant acute myeloid leukemia (AML) models. We have used conditional KO models (CreLoxP) and isolated hematopoietic cells shortly after induction of recombination, in order to look at pre-leukemic cells, which have acquired the first hit, but not yet undergone full malignant transformation. We have sorted granulocyte-macrophage progenitors (GMPs) and the more immature population pre-granulocyte-macrophages (preGMs) from pre-leukemic mice. We analyzed gene-expression profiles in order to find deregulated genes, which make the cells more prone to undergo transformation.

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Development of MLL-rearranged leukemia is dependent on a transcriptional program orchestradt by C/EBPα

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2013-12-10 | E-GEOD-46534 | biostudies-arrayexpress

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture.

Project description:The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of researchers and their results were collectively analyzed. The results from the twenty-four participants, who represented a broad spectrum of experience levels with this type of data analysis, produced several important observations. First, there is significantly more variability in the ability to assess whether a results is significant than there is to determine the correct answer. Second, labile post-translational modifications, particularly tyrosine sulfation, present a challenge for most researchers. Finally, for modification site localization there are many tools being employed, but researchers are currently unsure of the reliability of the results these programs are producing.

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