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In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - iPRG 2008 Swiss-Prot 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: PXD003953 | Pride | 2016-08-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

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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1 - 5 of 31

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 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 analysis

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PIA - iPRG2008 Benchmark Dataset

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

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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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The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data.

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In-depth Analysis of Protein Inference Algorithms using a Workflow Framework and Well-Defined Metrics - PXD000603 Swiss-Prot analysis

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