Molecular fingerprinting reflects different histotypes and brain region in low grade gliomas.

Background: Paediatric low-grade gliomas (LGGs) encompass a heterogeneous set of tumours of different histologies, site of lesion, age and gender distribution, growth potential, morphological features, tendency to progression and clinical course. Among LGGs, Pilocytic astrocytomas (PAs) are the most common central nervous system (CNS) tumours in children. They are typically well-circumscribed, classified as grade I by the World Health Organization (WHO), but recurrence or progressive disease occurs in about 10-20% of cases.

Shape-based feature matching improves protein identification via LC-MS and tandem MS.

The characterization of proteins via liquid chromatography-mass spectrometry (LC-MS) and tandem MS is a challenge due to the large dynamic range and the high complexity of the molecules of interest. In LC-MS experiments, the inconsistent variation in the travel time of analytes in the LC column results in nonlinear shifts in the LC retention time (RT). This variability must be corrected to accurately match corresponding peptide features across samples in LC-MS experiments.

Serum apolipoproteins C-I and C-III are reduced in stomach cancer patients: results from MALDI-based peptidome and immuno-based clinical assays.

Finding new peptide biomarkers for stomach cancer in human sera that can be implemented into a clinically practicable prediction method for monitoring of stomach cancer. We studied the serum peptidome from two different biorepositories. We first employed a C8-reverse phase liquid chromatography approach for sample purification, followed by mass-spectrometry analysis.

Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials.

Background: The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution.

Improved model-based, platform-independent feature extraction for mass spectrometry.

Motivation: Mass spectrometry (MS) is increasingly being used for biomedical research. The typical analysis of MS data consists of several steps. Feature extraction is a crucial step since subsequent analyses are performed only on the detected features.