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PIPE specifications


Unique identifier OMICS_30010
Alternative names Protein Information and Property Explorer, PIPE2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Maintained No


No version available


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Publications for Protein Information and Property Explorer

PIPE citations


Making proteomics data accessible and reusable: Current state of proteomics databases and repositories

PMCID: 4409848
PMID: 25158685
DOI: 10.1002/pmic.201400302

[…] e, and validate an MRM assay. ATAQS uses FireGoose [] to connect to various web services, such as PeptideAtlas (used to select spectra), TIQAM (to generate in silico peptides for a given protein []), PIPE2 (to generate a list of proteins, to design an MRM assay, and for other various analysis tasks), and PABST (peptide atlas best SRM transition, used to generate optimal transitions). […]


Quantitative Mass Spectrometry Analysis Using PAcIFIC for the Identification of Plasma Diagnostic Biomarkers for Abdominal Aortic Aneurysm

PLoS One
PMCID: 3233585
PMID: 22163325
DOI: 10.1371/journal.pone.0028698
call_split See protocol

[…] Gene Ontology (GO) annotations of significant differentially abundant proteins were automatically assigned with the freely available internet tool Protein Information and Property Explorer . Assignments were manually filtered according to the biological implications in the pathology, and validated using the GO Consortium tool AmiGO Version 1.7 a […]


A Statistics based Platform for Quantitative N terminome Analysis and Identification of Protease Cleavage Products*

PMCID: 2871423
PMID: 20305283
DOI: 10.1074/mcp.M000032-MCP201

[…] r spectrum merging and weighted averaging, and for peptide isoform assignments and positional annotation, we used in-house Perl scripts using appropriate BioPerl packages. For identifier mapping, the Protein Information and Property Explorer system () was used. For active site mapping, amino acid occurrences were calculated as described previously (), and heat maps generated using TM4:MeV. Protein […]


Multiplex N terminome Analysis of MMP 2 and MMP 9 Substrate Degradomes by iTRAQ TAILS Quantitative Proteomics*

PMCID: 2871422
PMID: 20305284
DOI: 10.1074/mcp.M000050-MCP201

[…] cripts using appropriate BioPerl packages (). Peptide positions within protein sequences represent amino acid numbering in the mature fully processed form of each protein. For identifier mapping, the Protein Information and Property Explorer system () was used. For active site mapping, amino acid occurrences were calculated as described previously (), and heat maps were generated using TM4:MeV. Pr […]


Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses

PMCID: 2816815
PMID: 20157357
DOI: 10.1007/s12177-009-9042-6
call_split See protocol

[…] The Protein Information and Property Explorer (PIPE) [] was used to add functional annotations to the protein results from the human and mouse lenses. Annotations were not available for bovine or chicken […]


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PIPE institution(s)
Institute for Systems Biology, Seattle, WA, USA; Institute of Molecular Systems Biology, and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
PIPE funding source(s)
Supported by the National Heart, Lung and Blood Institute, NIH, under contract N01-HV-28179 and the Duchy of Luxembourg.

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