Proteomics2012-06-11T15:53:52+00:00/groups/10202015-11-27T12:15:14+00:00Yassene shared protein_network_2urn:uuid:b87a2e32-5bc0-4c74-8cb7-2f2d7ce88ec4Yassene2015-11-16T13:40:48+00:00Magnus Palmblad shared Get ENSEMBL cross-references for UniProt IDsThis small workflow uses the PICR ( http://www.ebi.ac.uk/Tools/picr/ ) WDSL Web Service to look up ENSEMBL (ENSP) cross-references for UniProt IDs. The input is a list of UniProt IDs and the output a corresponding list of ENSEMBL IDs. This instance of the workflow specifically uses the ENSEMBL_HUMAN database and taxonID 9606 (Homo sapiens).urn:uuid:a698609d-fe9a-4971-b12e-09df7b9ed178Magnus Palmblad2014-04-16T14:55:56+00:00Magnus Palmblad shared Tutorial_1_solutionFetch and combine transcriptomics and proteomics data from NSC11 cells in GEO and PRIDE respectively. Apply spectral counting on the proteomics data. The workflow demonstrates how to combine data from different domains (here microarray- based transcriptomics and mass spectrometry-based proteomics) and do something useful with the data. The workflow also demonstrates spreadsheet import and XPath parsing of XML data. This workflow is for tutorial/educational use only. The cells were not grown under the same conditions, nor should raw spectral counts be used for protein quantitation.urn:uuid:46718331-f5c6-4540-88aa-d9eba752f643Magnus Palmblad2014-04-16T14:54:09+00:00Magnus Palmblad shared Tutorial_1_startThis partial workflow is the starting point for Taverna tutorial held at the Leiden University Medical Center on April 17, 2014.urn:uuid:0c2dc8be-6abe-4bd2-86ca-0cfca281990bMagnus Palmblad2013-03-27T10:04:23+00:00Kate Mostovenko shared Comparison of Peptide and Protein Fractionation MethodsThis workflow was used to analyze the data in a manuscript by Mostovenko et al. (2013, submitted), comparing peptide and protein fractionation methods. The workflow identifies proteins by X!Tandem database search and validates the results using PeptideProphet. Additional information such as pI and fraction number is extracted and plotted for IEF and SCX data. For each protein identified in SDS-PAGE derived data sequences are downloaded from UniProt and plotted against the fraction number. Rshell script produces the figures essentially as they appear in the manuscript. Executing the workflow requires Rserve running and the Trans-Proteomic Pipeline ( http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP ) installed with default settings and in the default location. The Rshell scri …urn:uuid:2037c0b7-c28d-4c0d-99de-2babe46077f9Kate Mostovenko2012-08-01T08:50:28+00:00Magnus Palmblad shared de Bruin et al. Workflow 1This is "Workflow 1" from de Bruin et al., Mol. Cell. Proteomics 2012.urn:uuid:0ddc53ce-e517-451f-b727-07b63472abf5Magnus Palmblad2012-08-01T07:16:35+00:00Kate Mostovenko joined the Proteomics groupurn:uuid:60a70890-c0b5-4d9a-a64b-9fed8c2ee38fKate Mostovenko2012-07-31T16:04:55+00:00Magnus Palmblad shared Plasma Precipitation AnalysisABOUT THE WORKFLOW This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2012, submitted), comparing proteins in the precipitate with those left in solution after organic solvent precipitation. However, the workflow is generally applicable in comparisons of any binary fractionation method in proteomics, where the fractions are analyzed by liquid chromatography-tandem mass spectrometry. The workflow identifies proteins by SpectraST spectral library search and X!Tandem database search, validates the results using PeptideProphet and combines them with InterProphet. The proteins are quantified by spectral counting and the fractions compared with respect to protein molecular weight, isoelectric point and GRAVY hydrophobicity score. In the end, an Rshell script produces …urn:uuid:c60d7f11-d20a-444d-8a9e-1dd29f4e2183Magnus Palmblad2012-06-11T16:14:15+00:00Magnus Palmblad joined the Proteomics groupurn:uuid:28c2461f-97c3-4785-88ae-263a761571e2Magnus Palmblad2012-06-11T15:53:52+00:00Yassene created the Proteomics groupurn:uuid:3edf840a-a7f4-49fa-a552-17f844a5a85bYassene