IPI - MSIPI

MSIPI is a database derived from IPI containing additional information about cSNPs and N-terminal peptides in a format suitable for easy use in mass spectrometry search engines. MSIPI is available in the directory ftp://ftp.ebi.ac.uk/pub/databases/IPI/msipi.

MSIPI is produced by the Max-Planck Institute for Biochemistry at Martinsried and the University of Southern Denmark, and distributed by the EBI.

Publication

A mass spectrometry–friendly database allows proteomic identification of cSNPs.

Schandorff, S; Olsen, JV, Bunkenborg, J; Blagoev,B; Zhang,Y; Andersen, JS & Mann, M

Nature Methods - 4: 465 - 466 (2007).

full-text PDF

Useful Links

Mascot (Matrix Science) help page to setup a MSIPI Sequence Database.

How to setup the MSIPI database in Mascot (Matrix Science)

msipi.fasta is setup in MASCOT like any other IPI database, but with a different parsing rule due to the new header start: >MSIPI:

Rule to parse accession string from FASTA file:

Rule XX: ">MSIPI:\(.*\)|"

Rule to parse description string from FASTA file:

Rule XX: ">*|\(.*\)"

See below for an illustration:

Change the Proteolytic enzymes and specific chemical cleavage agents which are defined in config/enzymes by adding:

*
Title: TrypsinMSIPI
Cleavage[0]:KR
Restrict[0]:P
Cterm[0]
Cleavage[1]:J
Cterm[1]
Cleavage[2]:J
Nterm[2]
*

No need to specify the mass value for J

The mass value for J is by default 0 in Mascot

Remember to specify this new reagent “TrypsinMSIPI” used for protein digestion.

How to identify the appended peptides

The appended peptides may be identified a number of different ways, but here is a simple example.

Use the length of the original proteins (which has been added to the header description) to look for peptide occurrences outside this range.