Bioinformatics for LC-MS/MS-Based Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 81

Table 4.9
Data exchange applications

Raw data converts and standards
mzXML http://tools.proteomecenter.org/wiki/index.php?
title = Formats:mzXML
Search result to pepXML and protXML converters
pepXML http://tools.proteomecenter.org/wiki/index.php?

title = Formats:pepXML

Scaffold ( 30 ) http://www.proteomesoftware.com /

Public data repositories
PeptideAtlas ( 75 )

http://www.peptideatlas.org /

Open
Proteomics
Database ( 131 )

http://apropos.icmb.utexas.edu/OPD/

Human
Proteinpedia
( 132 )

http://www.humanproteinpedia.org/index_html

Proteome com- https://proteomecommons.org/

mons

PRIDE ( 76 ) http://www.ebi.ac.uk/pride /

PRIDE
Converter

http://code.google.com/p/pride-converter/

so an additional tool (such as TPP's ProteinProphet) is needed
to infer the protein identities in the sample. ProtXML, again
only for MS/MS data, only includes the protein identifications
created from MS/MS-derived peptide sequence data. Most of
the major database search engines or reporting applications (e.g.,
Scaffold) can export to either pepXML or protXML directly or
there is a conversion program available that can perform the
transformation.

10.4.Repositories

With the development of data exchange formats and their adop-
tion by the proteomics community, it became possible to build
public repositories to hold LC-MS/MS data ( Table 4.9 ) . The
data repositories act as central locations to store and distribute
LC-MS/MS data and search results for inter-lab collaboration
and as supporting evidence for publication. The data repositories
are split between those that just accept raw MS data, a mixture of
data and identification information, and just identification infor-
mation. An example of a repository that is mainly used for raw
data is the ProteomeCommons Tranche data repository ( 74 ) .