PhD research in proteomics related bioinformatics with CSC scholarship in the
Netherlands (prerequisite: master student)

I’m looking for highly motivated students applying for China Scholarship Coun
cil PhD scholarships, who would like to prepare a PhD in proteomics related bi
oinformatics in the Netherlands. The PhD research involve the development of b
ioinformatics platform to identify and quantify glycopeptides from liquid chro
matography coupled to tandem mass spectrometry data acquired with electron tra
nsfer (ETD) and collision induced dissociation (CID) fragmentation methods. Th
is platform includes development of large spectral archives1 using SpectraST2
tool and glycopeptide identification workflow to annotate consensus spectra of
spectral archives using both ETD and CID MS/MS spectra of the glycopeptides.
The spectral archives based glycopeptide identification workflow will be integ
rated with msComapre3 quantitative and other time alignment modules and will p
rovide a comprehensive bioinformatics platform for discovery of glycopeptides
pattern changes in complex biological samples.

This research require motivated candidate with strong mathematical, statistica
l background and programming skills in R and/or Matlab and in c++ and/or java.
This project will be performed in collaboration with the research group of Dr
Henry Lam working at the Hong Kong University of Science and Technology and w
ith other bioinformatics and proteomics laboratories located in the Netherland
s.

Interested candidates should send their CV and motivation letter to Peter Horv
atovich (p.l.horvatovich@rug.nl).

References
1.Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA,
Smith RD, Pevzner PA., Spectral archives: extending spectral libraries to anal
yze both identified and unidentified spectra, Nat Methods, 2011, 8(7):587-91.
PMID: 21572408
2.Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R., Building consen
sus spectral libraries for peptide identification in proteomics, Nat Methods,
2008, 5(10):873-5. PMID: 18806791
3.Hoekman B, Breitling R, Suits F, Bischoff R, Horvatovich P., msCompare: a fr
amework for quantitative analysis of label-free LC-MS data for comparative bio
marker studies, Mol Cell Proteomics, 2012 in April issue. PMID: 22318370