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Protocols

Integr8 specifications

Information


Unique identifier OMICS_21084
Name Integr8
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publication for Integr8

Integr8 citations

 (31)
call_split

Scalable, cGMP compatible purification of extracellular vesicles carrying bioactive human heterodimeric IL 15/lactadherin complexes

2018
J Extracell Vesicles
PMCID: 5844027
PMID: 29535850
DOI: 10.1080/20013078.2018.1442088
call_split See protocol

[…] on the mass spectrometer during the MS2 data acquisition. Spectra were searched against the human UniProt database downloaded from the European Bioinformatics Institute website (http://www.ebi.ac.uk/integr8), January 2017, utilizing Proteome Discoverer 1.4 (Thermo Scientific). Up to two missed tryptic cleavage sites were allowed during the database search, while the oxidation (+15.9949 Da) of met […]

call_split

Using structural knowledge in the protein data bank to inform the search for potential host microbe protein interactions in sequence space: application to Mycobacterium tuberculosis

2017
BMC Bioinformatics
PMCID: 5379762
PMID: 28376709
DOI: 10.1186/s12859-017-1550-y
call_split See protocol

[…] n domain) and 1 (identical domain composition). Besides the RBH approach, we separately obtained the above statistics for the predicted orthologs of MTB proteins retrieved from three other databases: Integr8 [], eggNOG [] and KEGG Orthology []. […]

library_books

The endoplasmic reticulum and casein containing vesicles contribute to milk fat globule membrane

2016
Mol Biol Cell
PMCID: 5042581
PMID: 27535430
DOI: 10.1091/mbc.E16-06-0364

[…] ic peptides and possible N-ter protein acetylation were searched. Several databases were used: the Uniprot KB Mus musculus, C57BL6 database (49,728 entries, version March 2011 from EBI [www.ebi.ac.uk/integr8]) and the contaminant database (trypsin, keratins, etc.). The identified proteins were filtered according to the following restrictions: 1) a minimum of two different peptides was required wit […]

library_books

The MarR like protein PchR (YvmB) regulates expression of genes involved in pulcherriminic acid biosynthesis and in the initiation of sporulation in Bacillus subtilis

2016
BMC Microbiol
PMCID: 4992311
PMID: 27542896
DOI: 10.1186/s12866-016-0807-3

[…] cation was performed with X!Tandem software (X! Tandem Sledgehammer 2013.09.01.1; http://www.thegpm.org) against a protein database of B. subtilis 168 (downloaded to ftp://ftp.ebi.ac.uk/pub/databases/integr8/last_release/fasta/proteomes contain 4253 proteins associated to a classical proteomic contaminant database). The X!Tandem search parameters were as follows: trypsin specificity with two misse […]

library_books

Threonine 89 Is an Important Residue of Profilin 1 That Is Phosphorylatable by Protein Kinase A

2016
PLoS One
PMCID: 4882052
PMID: 27228149
DOI: 10.1371/journal.pone.0156313

[…] verer™ software (v. 1.4.0, ThermoFisher Scientific, Waltham, MA, USA) against a UniProt human proteome database (January 2013 release) from the European Bioinformatics Institute (http://www.ebi.ac.uk/integr8). The following modifications were used: static modification of cysteine (carboxyamidomethylation, +57.05 Da), variable modification of methionine (oxidation, +15.99Da) and variable modificati […]

call_split

Comparative Proteomics Reveals Important Viral Host Interactions in HCV Infected Human Liver Cells

2016
PLoS One
PMCID: 4726516
PMID: 26808496
DOI: 10.1371/journal.pone.0147991
call_split See protocol

[…] of peptides previously selected for CID. Tandem mass spectra were searched against a combined UniProt human protein database (03/2011) from the European Bioinformatics Institute (http://www.ebi.ac.uk/integr8) and the Hepatitis C virus genotype 2a (isolate JFH-1) protein sequence (UniProt Accession Q99IB8) using SEQUEST (ThermoFisher Scientific). For a fully tryptic peptide to be considered legitim […]

Citations

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Integr8 institution(s)
The EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; RZPD Deutsches Ressourcenzentrum fur Genomforschung GmbH, Berlin, Germany; Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558 Université Lyon 1, Lyon, France; BIOBASE GmbH, Wolfenbuttel, Germany
Integr8 funding source(s)
Supported by the award of grant number QLRICT-2001000015 from the European Union under the RTD program ‘Quality of Life and Management of Living Resources’.

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