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From Mass Spectrometry-Based Proteomics to System Biology

Martin Damsbo, Jacob Poder, Erik Nielsen, Christian Ravnsborg, Alexandre Podtelejnikov
Thermo Fisher Scientific, Odense, Denmark

Poster: From Mass Spectrometry-Based Proteomics to System Biology, ASMS 2011 (1.0 MB)

Express Biological Pathway Analysis of Mass Spectrometry-Based Proteomics Datasets

Martin Damsbo1, Christian Ravnsborg1 and Amy Zumwalt2
1Thermo Fisher Scientific, Odense, Denmark, 2Thermo Fisher Scientific, San Jose, CA

Poster: Express Biological Pathway Analysis of MS-Based Proteomics Datasets, US HUPO 2011 (175.7 kB)

Integration of a Central Protein Repository into a Standard Data Processing Application for Mining Proteomics Data

Kai Fritzemeier1, Bernard Delanghe1 and Christian Ravnsborg2
1Thermo Fisher Scientific, San Jose, CA, USA; 2Thermo Fisher Scientific, Odense, Denmark

Poster: Integration of a Central Protein Repository into a Standard Data Processing Application, US HUPO 2011 (407.4 kB)

Comprehensive Bioinformatic Analysis of the Yeast Proteome.

Martin Damsbo, Christian Ravnsborg Ingrell, Jacob Kristensen, Michael Barrett Andersen, Alexandre Podtelejnikov
Thermo Fisher Scientific, Odense, Denmark.

Poster: Comprehensive bioinformatic analysis of yeast proteome, ASMS 2011 (301.6 kB)

Express Bioinformatic Analysis of Sialic Acid-containing Glycopeptides
from Early-onset Diabetes Type 1 Patients

Keld Poulsen1,3; Lene A. Jakobsen1; Christian Ravnsborg Ingrell4; Flemming Pociot2, Niels H.H. Heegaard3 and Martin R. Larsen1

1Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark,  
2Steno Diabetes Center, Gentofte, Denmark,

3
Department of Autoimmunology, Statens Serum Institut, Denmark,
4
Proxeon A/S, Staermosegaardsvej 6, Odense Denmark.

Poster: Express bioinformatic analysis (270.0 kB)

Global Bioinformatical Analysis of Human Liver Proteome

M. Bern, C. R. Ingrell, A. Podtelejnikov, O. Vorm

Proxeon A/S, Odense, Denmark.

Poster: Global bioinformatic analysis

(197.1 kB)

Statistical analysis of proteomics datasets with reference databases

John Chakel, Christian Ingrell, Martin Damsbo, Morten Bern

Proxeon A/S, Odense, Denmark.

 

Poster: Statistical analysis of proteomics (254.3 kB)

Express bioinformatic comparative analysis of E. coli samples

J. Chakel1, P.A. Haynes2, M. Damsbo2, M. Bern1, J. Chick2, K. Neilson2  

1 Proxeon A/S, Odense, Denmark,
2
Australien Proteome Analysis Facility, Sydney, Australia.

Poster: Express bioinformatic comparative (902.0 kB)

Evaluation of Efficiency of Cross-Species Comparisons Using
ProteinCenter

D. Potter, H. Jespersen, A. Podtelejnikov, M. Bern  

Proxeon A/S, Odense, Denmark.

 

Poster: Evaluation of efficiency

(430.8 kB)

The Search for Post-translational Modified Biomarkers for Diabetes Type 1
in Microparticles from Interleukin 1beta Stimulated Beta Cells

"ProteinCenter provided with me with a biological overview of my identified proteins in minutes without the hassle of gathering biological annotation from many different sources"

Søren Skov Jensen Ph.D. student

Protein Research Group, University of Southern Denmark.

Application note:  Search for post-translational (152.3 kB)

Optimization of phosphoproteomics for quantitative determination
of cellular signalling pathways using low amounts of sample material

"ProteinCenter enabled me to quickly statistically compare two lists of proteins according to GO"

Kasper E. Keller Ph.d. Student

Protein Research Group, University of Southern Denmark.

Application note: Optimization of phosphoproteomics (56.2 kB)

Phosphoproteome analysis of human stem cell plasma
membranes using TiO2 columns and mass spectrometry.

"ProteinCenter showed that 64% of the identified proteins were membrane proteins and ~75% were functionally related to membranes."

Tine E. Thingholm Ph.D. student

Protein Research Group, University of Southern Denmark.

Application note: Phosphoproteome analyis (227.6 kB)

Global phosphoproteome database:
phosphorylation sites prediction vs. experimental data

 "ProteinCenter enabled straightforward statistical and bioinformatics analysis of phosphoproteome datasets. Using the current collection of phosphorylation sites as the training set will make it possible to improve the neural network prediction and also opens the possibility to discover new kinase motifs."

Alexandre Podtelejnikov 1, Morten Bern 1, Hans Jespersen 1 ,Søren Schandorff 2, Ole Vorm 1

1 Proxeon, Odense, Denmark,
2
University of Southern Denmark

Poster: Global phosphoproteome database (299.0 kB)

Large-scale and high-confidence proteomic analysis of human seminal Plasma

 "Body fluids are targets of proteomic analysis because of their potential for biomarker
discovery. ProteinCenter was used to interpret the complex data obtained from proteomic analysis of bodily fluids."

Bartosz Pilch 1,2 and Matthias Mann 1,2 

1 Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern      Denmark, Denmark,
2 Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Germany

Application note: Large scale, high confidence proteomic (271.2 kB)