Biomedical subjects

Han Roelofsen

Publications and source records attributed to Han Roelofsen.

4 recordsLinked to original sources

PubMed2007

Proteomics profiling of urine with surface enhanced laser desorption/ionization time of flight mass spectrometry.

BACKGROUND: Urine consists of a complex mixture of peptides and proteins and therefore is an interesting source of biomarkers. Because of its high throughput capacity SELDI-TOF-MS is a proteomics technology frequently used in biomarker studies. We compared the performance of seven SELDI protein chip types for profiling of urine using standard chip protocols. RESULTS: Performance was assessed by determining the number of detectable peaks and spot to spot variation for the seven array types and two different matrices: SPA and CHCA. A urine sample taken from one healthy volunteer was applied in eight-fold for each chip type/matrix combination. Data were analyzed for total number of detected peaks (S/N > 5). Spot to spot variation was determined by calculating the average CV of peak intensities. In addition, an inventory was made of detectable peaks with each chip and matrix type. Also the redundancy in peaks detected with the different chip/matrix combinations was determined. A total of 425 peaks (136 non-redundant peaks) could be detected when combining the data from the seven chip types and the two matrices. Most peaks were detected with the CM10 chip with CHCA (57 peaks). The Q10 with CHCA (51 peaks), SEND (48 peaks) and CM10 with SPA (48 peaks) also performed well. The CM10 chip with CHCA also has the best reproducibility with an average CV for peak intensity of 13%. CONCLUSION: The combination of SEND, CM10 with CHCA, CM10 with SPA, IMAC-Cu with SPA and H50 with CHCA provides the optimal information from the urine sample with good reproducibility. With this combination a total of 217 peaks (71 non-redundant peaks) can be detected with CV's ranging from 13 to 26%, depending on the chip and matrix type. Overall, CM10 with CHCA is the best performing chip type.

Journal Article↗

PubMed2006

Peak quantification in surface-enhanced laser desorption/ionization by using mixture models.

Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks corresponding to proteins in the sample. The peak areas are proportional to the measured concentrations of the corresponding proteins. Quantifying peak areas is difficult for existing methods because peak shapes are not constant across a spectrum and because peaks often overlap. We present a new method for quantifying peak areas. Our method decomposes a spectrum into peaks and a baseline using so-called statistical finite mixture models. We illustrate our method in detail on 8 samples from culture media of adipose tissue and globally on 64 samples from serum to compare our method to the standard Ciphergen method. Both methods give similar estimates for singleton peaks, but not for overlapping peaks. The Ciphergen method overestimates the heights of such peaks while our method still gives appropriate estimates. Peak quantification is an important step in pre-processing SELDI-TOF data and improvements therein will pay off in the later biomarker discovery phase.

Adipose Tissue↗

PubMed2005

In vitro sampling and storage of proteins with an ultrafiltration collection device (UCD) and analysis with absorbance spectrometry and SELDI-TOF-MS.

Frequent in vivo sampling of blood proteins is often stressful, making it difficult to obtain more than a few samples. As a result, only limited time-profiles can be made. We have developed an ultrafiltration collection device (UCD) for continuous sampling. The UCD consists of a hollow fiber, a coil and a flow creator. Hollow fiber membranes are often hydrophobic and this can result in adsorption of protein and/or peptides, leading to clogged membranes. Adsorption was tested with a hydrophobic and hydrophilic peptide and two biocompatible hollow fibers made from different materials. The hollow fiber made from poly(ethylene) coated with ethylenevinyl alcohol gave near 100% recovery for both peptides. This was in contrast to the poly(sulfone) hollow fiber when sampling the hydrophobic peptide. Filling the coil with various peptide concentrations gave good recovery and insignificant diffusion even after storage for 6 d at 37 degrees C. Continuous pulse-free sampling was tested by vacuum. An average flow rate of 423 +/- 50 nl min(-1) over a period of 4 d was created using S-Monovette. The flow rate gradually declined during this period by <5% every consecutive day. In addition, we also examined a complex sample-serum in the poly(ethylene) hollow fiber. Serum and ultrafiltrate were spotted onto a protein chip and analyzed by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Six proteins out of 64 were found to be significantly different between serum and the ultrafiltrate (p < 0.05). The UCD has the potential to be used for in vivo real-time monitoring.

Blood Proteins↗

PubMed2004

Proteomic analyzes of copper metabolism in an in vitro model of Wilson disease using surface enhanced laser desorption/ionization-time of flight-mass spectrometry.

In Wilson disease, mutations in the ATP7B-gene lead to hepatic accumulation of copper that becomes toxic when the hepatic binding capacity is exceeded, leading to oxidative stress and acute liver failure. Several proteins are probably involved in dealing with the excess copper and oxidative stress. As a first step towards biomarker discovery and analyzes of copper metabolism in Wilson disease patients we characterized copper-induced changes in protein expression in cell lysates and culture media from an in vitro copper-overload model using surface enhanced laser desorption/ionization (SELDI) proteomics technology. HepG2 cells were cultured for 48 h with a physiological (0.5 microM) or a pathological (100 microM) copper concentration. Samples were applied to weak cation exchange (WCX) proteinchip arrays and chips were analyzed by time of flight (TOF)-mass spectrometry. Copper-coated IMAC chips were used to detect copper-binding proteins in cell lysate of copper depleted cells using buffers with increasing imidazole concentrations. Data from the 2 to 50 kDa range indicate that high extra-cellular copper substantially altered both intra-cellular protein expression as well as the composition of the secretome. In the lysate 15 proteins were found up-regulated, while 6 proteins were down-regulated. In culture media 21 proteins were increased while 4 proteins were decreased in abundance. Copper-coated protein chips revealed the presence of 18 high-affinity copper-binding proteins. Further identification is necessary to determine the exact cellular roles of the discovered proteins.

Carcinoma, Hepatocellular↗