Biomedical subjects

Gun Wook Park

Publications and source records attributed to Gun Wook Park.

4 recordsLinked to original sources

PubMed2006

Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis.

In shotgun proteomics, proteins can be fractionated by 1-D gel electrophoresis and digested into peptides, followed by liquid chromatography to separate the peptide mixture. Mass spectrometry generates hundreds of thousands of tandem mass spectra from these fractions, and proteins are identified by database searching. However, the search scores are usually not sufficient to distinguish the correct peptides. In this study, we propose a confident protein identification method for high-throughput analysis of human proteome. To build a filtering protocol in database search, we chose Pseudomonas putida KT2440 as a reference because this bacterial proteome contains fewer modifications and is simpler than the human proteome. First, the P. putida KT2440 proteome was filtered by reversed sequence database search and correlated by the molecular weight in 1-D-gel band positions. The characterization protocol was then applied to determine the criteria for clustering of the human plasma proteome into three different groups. This protein filtering method, based on bacterial proteome data analysis, represents a rapid way to generate higher confidence protein list of the human proteome, which includes some of heavily modified and cleaved proteins.

Blood Proteins↗

PubMed2006

Profiling human brain proteome by multi-dimensional separations coupled with MS.

In our initial attempt to analyze the human brain proteome, we applied multi-dimensional protein separation and identification techniques using a combination of sample fractionation, 1-D SDS-PAGE, and MS analysis. The complexity of human brain proteome requires multiple fractionation strategies to extend the range and total number of proteins identified. According to the method of Klose (Methods Mol. Biol. 1999, 112, 67), proteins of the temporal lobe of human brain were fractionated into (i) cytoplasmic and nucleoplasmic, (ii) membrane and other structural, and (iii) DNA-binding proteins. Each fraction was then separated by SDS-PAGE, and the resulting gel line was cut into approximately 50 bands. After trypsin digestion, the resulting peptides from each band were analyzed by RP-LC/ESI-MS/MS using an LTQ spectrometer. The SEQUEST search program, which searched against the IPI database, was used for peptide sequence identification, and peptide sequences were validated by reversed sequence database search and filtered by the Protein Hit Score. Ultimately, 1533 proteins could be detected from the human brain. We classified the identified proteins according to their distribution on cellular components. Among these proteins, 24% were membrane proteins. Our results show that the multiple separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures.

Brain↗

PubMed2005

Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis.

The proteome of a HUPO human serum reference sample was analyzed using multidimensional separation techniques at both the protein and the peptide levels. To eliminate false-positive identifications from the search results, we employed a data filtering method using molecular weight (MW) correlations derived from denaturing 1-DE. First, the six most abundant serum proteins were removed from the sample using immunoaffinity chromatography. 1-DE was then used to fractionate the remaining serum proteins according to the MW. Gel bands were isolated and in-gel digested with trypsin, and the resulting peptides were analyzed by 2-D LC/ESI-MS/MS. A SEQUEST search using the MS/MS results identified 494 proteins. Of these, 202 were excluded formally using protein data filtering as they were single-assignment proteins and their theoretical and electrophoretically-derived MWs did not correlate at high confidence. To evaluate this method, the results were compared with those of 1-D LC/MALDI-TOF/TOF and HUPO Plasma Proteome Project analyses. Our data filtering approach proved valuable in analysis of complex, large-scale proteomes such as human serum.

Amino Acid Sequence↗

PubMed2003

Pain and its treatment in patients with cancer in Korea.

Substantial pain is experienced by a lot of patients with cancer, and undertreated pain significantly undermines their quality of life. Despite international and national guidelines on cancer pain management, the practical effectiveness of management is still problematic. We did a prospective cross-sectional survey on pain prevalence, pain intensity, its impact on daily activity, and adequacy of pain management in 823 patients treated by medical oncologists and radiologic oncologists. At the time of the survey, 29.7% of the patients had pain that was moderate or severe. Performance status and tumor extent were significant predictors of pain presence and its intensity. Pain severity and the proportion of the patients whose function is impaired are highly associated. Among the patients with pain, only 37% rated pain relief as satisfactory. Forty-one percent of the patients with pain received inadequate pain management. Physicians did not adjust the analgesic prescription in about 53% of the patients who reported severe pain. These results demonstrate the alarming degree of undertreatment of pain in patients with cancer in Korea, and indicate the need to improve the management of cancer-related pain. Future research should elucidate the factors that impede adequate pain management in order to overcome obstacles to adequate treatment.

Adult↗