Proteome-Wide Quantitation by SILAC - LC-MS/MS in Proteomics: Methods and Applications - page 200

user to define a number of critical parameters in an easily
operationally display. MSQuant performs automated quan-
titation of complete proteome-wide SILAC data sets and
provide the user an optimal display of the raw data for man-
ual validation. Furthermore, MSQuant contain a number
of additional functionalities for assigning and scoring phos-
phorylation sites or analyzing data from protein correla-
tion profiling-SILAC (PCP-SILAC, see Chapter 15 in this
book ), as well as several add-on scripts for different types of
proteomics data processing. The MaxQuant software ( 22 )
performs SILAC quantitation in a highly automated fash-
ion and provides high identification rates. To increase the
identification rates, MaxQuant uses elaborate algorithms
taking into account the intensity of precursor peaks, chro-
matographic elution time, and accurate mass measurements
from high resolution instruments. In contrast to the two
software solutions described above which uses Mascot as a
search engine, the Census software ( 29 ) relies on Sequest.
In addition, Census is flexible in terms of instrument speci-
ficity as it uses files in the generalized mzXML format as
input.

Acknowledgements

We would like to thank all members of the Center for Experi-
mental BioInformatics (CEBI) for useful discussions, especially
Dr. Irina Kratchmarova for the critical reading of the chap-
ter. The research leading to these results has received funding
from the European Commission's 7th Framework Programme
(grant agreement HEALTH-F4-2008-201648/PROSPECTS),
the Danish Natural Science Research Council and the Lundbeck
Foundation.

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