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Protocols

IPI specifications

Information


Unique identifier OMICS_15166
Name IPI
Alternative name International Protein Index
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/International_Protein_Index

Maintainer


  • person_outline Paul Kersey

Publication for International Protein Index

IPI citations

 (289)
library_books

The Rab11 binding protein RELCH/KIAA1468 controls intracellular cholesterol distribution

2018
PMCID: 5940305
PMID: 29514919
DOI: 10.1083/jcb.201709123

[…] University Center for Medical Research and Education. The database search was conducted using ProteinLynx Global Server (v.2.4; Waters Corp.) or MASCOT Server (v.2.3; Matrix Science) software and the International Protein Index database (mouse; v.3.77 or 3.87; EMBL-EBI). […]

library_books

Identification of serum proteins AHSG, FGA and APOA I as diagnostic biomarkers for gastric cancer

2018
PMCID: 5925839
PMID: 29719494
DOI: 10.1186/s12014-018-9194-0

[…] activated using 25% normalized collision energy at the default activation q of 0.25. All MS/MS spectra were profiled with SEQUEST [v.28 (revision 12), Thermo Electron Corp.] which searched the human International Protein index (IPI) database (IPI human v3.64 fasta with 71,983 entries) and the UniprotKB (http://www.uniprot.org) for peptide-to-spectral matching. To minimize false positives, a decoy […]

call_split

Secretome analysis of rat osteoblasts during icariin treatment induced osteogenesis

2018
PMCID: 5928639
PMID: 29532868
DOI: 10.3892/mmr.2018.8715
call_split See protocol

[…] MS peptide mass fingerprinting (PMF) data was obtained using Mascot Distiller software (v.2.3.2; Matrix Science Ltd., London, UK) (), and searches of PMF peptide sequences were performed based on the international protein index (IPI) rat FASTA database (v3.31; 41,251 sequences; 21,545,744 residues; ftp://ftp.ebi.ac.uk/pub/databases/IPI). Sequence alignments were generated using the CLC Free Workbe […]

library_books

Kinome and phosphoproteome of high grade meningiomas reveal AKAP12 as a central regulator of aggressiveness and its possible role in progression

2018
Sci Rep
PMCID: 5794791
PMID: 29391485
DOI: 10.1038/s41598-018-19308-y

[…] ing 4800 Plus MALDI TOF/TOF TM (AB SCIEX, Framingham, MA) with mass range of 800–3500 m/z and S/N > 50. MS/MS spectral data were analyzed using ProteinPilot 4.0 (AB SCIEX, Framingham, MA) referencing International Protein Index (IPI) and UniProtKB/Swiss-Prot database using Proteome Discoverer 1.3 (Thermo Scientific, Pittsburgh, PA) with the following parameters: MMTS for cysteine alkylation, up to […]

library_books

Non canonical Wnt signaling regulates neural stem cell quiescence during homeostasis and after demyelination

2018
Nat Commun
PMCID: 5750230
PMID: 29296000
DOI: 10.1038/s41467-017-02440-0

[…] n a manually validated data set to remove the low-quality MS/MS spectra. The resulting spectra were analyzed against a mouse protein FASTA sequence database EBI-IPI (European Bioinformatics Institute–International Protein Index) , and a decoy database with reversed sequences was used to calculate the confidence levels and the false positive rates. The spectra were further validated by DTAselect. F […]

library_books

FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell Derived Cardiac Progenitors

2017
Stem Cell Reports
PMCID: 5768897
PMID: 29249665
DOI: 10.1016/j.stemcr.2017.11.008

[…] ized collision energy was set to 35%, and one microscan was acquired for each spectrum. Singly charged ions were excluded from triggering ms2 scans.All acquired mass spectra were searched against the International Protein Index database (Version 3.26) using the SEQUEST algorithm (). The SEQUEST database search criteria included: 0.2 Da mass tolerance for the precursor ion, 0.5 Da mass tolerance fo […]

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IPI institution(s)
EMBL Outstation, The European Bioinformatics Institute, Hinxton, UK
IPI funding source(s)
This work has in part been funded by EU grant number QLRI-CT-2001-00015 under the RTD program “Quality of Life and Management of Living Resources”.

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