Discovery of biomarkers is a fast developing field in proteomics research. Liquid chromatography coupled on line to mass spectrometry (LC-MS) has become a powerful method for the sensitive detection, quantification and identification of proteins and peptides in biological fluids like serum. However, the presence of highly abundant proteins often masks those of lower abundance and thus generally...

Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest i...

A data dependent peak model (DDPM) based spectrum deconvolution method was developed for analysis of high resolution LC-MS data. To construct the selected ion chromatogram (XIC), a clustering method, the density based spatial clustering of applications with noise (DBSCAN), is applied to all m/z values of an LC-MS data set to group the m/z values into each XIC. The DBSCAN constructs XICs without...

PURPOSE Human aqueous humor (hAH) provides nutrition and immunity within the anterior chamber of the eye. Characterization of the protein composition of hAH will identify molecules involved in maintaining a homeostatic environment for anterior segment tissues. The present study was conducted to analyze the proteome of hAH. METHODS hAH samples obtained during elective cataract surgery were div...

A viable, quick, and reliable method for determining urinary creatinine by liquid chromatography/tandem mass spectrometry (LC/MS/MS) was developed and used to evaluate spot urine samples collected for the Washington Environmental Biomonitoring Survey (WEBS): part of the Washington State Department of Health, Public Health Laboratories (PHL). 50 µL of urine was mixed with a 1 : 1 acetonitrile/wa...

A quantitative HPLC – fluorescence method for the simultaneous determination of sulfamerazine (SMR) and sulfamethoxazole (SMX) in honey has been developed. Sample pretreatment included acidic hydrolysis, followed by solid phase extraction (SPE) procedure. The liquid chromatography (LC) separation was carried out on RP C 18 column and sulfonamides were detected by fluorescence detector after pre...

Immune complexome analysis is a method for identifying and profiling of antigens in circulating immune complexes (CICs); it involves separation of immune complexes from serum, direct tryptic digestion of these complexes, and protein analysis via nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS). To improve this method, we initially investigated the effects of two factors-the g...

We examined the tear film proteome of patients with Sjögren's syndrome (SS) and dry eye syndrome (group A), patients with dry eye symptoms (group B) and normal volunteers (group C). Tear samples were pooled from 8 subjects from each group and were subjected to two-dimensional-nano-liquid chromatography coupled with tandem mass spectrometry (2D-nano-LC-MS/MS). The tear breakup time for group A w...