Cluster analysis of chromatographic profiles of urine proteins

Preparation of urine samples for proteomic analysis

Reproducible procedures for the preparation of protein samples isolated from human urine are essential for meaningful proteomic analyses. Key applications are the discovery of novel proteins or their modifications in the human urine as well as protein biomarker discovery for diseases and drug treatments. The methodology presented here features experimental steps aimed at limiting protein losses because of organic solvent precipitation, effective separation of proteins from other compounds in the human urine and molecular weight-based enrichment of proteins in two distinct fractions. Urinary proteins are separated from cellular debris in the urine via centrifugation, concentrated with 5-kDa-cutoff membrane concentration devices and separated via size exclusion chromatography into fractions with a higher and a lower molecular weight than 30 kDa, respectively. A successive optional affinity removal step for highly abundant plasma proteins is described. Finally, buffer exchange steps useful for specific downstream proteomic analysis experiments of urinary proteins are presented, such as 2-dimensional gel electrophoresis, differential protein or peptide labeling and digestion with trypsin for LC-MS/MS analysis.

Electrophoresis and chromatography of wheat proteins: available methods, and procedures for statistical evaluation of the data

Analysis of gluten proteins from the wheat grain endosperm has long challenged the analytical chemist. Several hundred unique polypeptides are present, many in large polymers. This complexity, plus useful relationships of composition to genotype and quality, encouraged development and application of electrophoresis and chromatography for gluten analysis. We review the methods of polyacrylamide gel electrophoresis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, isoelectric focusing and high-performance liquid chromatography available for study of wheat proteins. Singly and in combination, they provide rapid, reproducible, high-resolution separations based on size, charge, or surface hydrophobicity. As challenging and important as the analyses themselves, however, is interpretation of data. Subjective evaluation is sometimes possible, but statistical methods such as similarity scores, clustering, principal components, multiple linear regression, and partial least squares now are increasingly used for data analysis. We review the use of these procedures, and precautions necessary to avoid misinterpretation of data. Optimal evaluation of protein analytical data will enhance the value of such analyses in wheat breeding, marketing, and processing.

A study of the mechanisms of proteinuria in nephritis and chronic renal failure

This study was carried out on 50 patients suffering from renal disorders; 30 nephritis patients and 20 chronic renal failure patients. Twenty-four healthy persons were used as a control group. In order to cast some light on the degree of the impaired glomerular permeability with respect to the blood proteins, selectivity of proteinuria was assessed by means of the clearance of albumin, ceruloplasmin, transferrin, and haptoglobin. Disturbances in the metabolism of these proteins were observed and discussed in light of the proteinuria selectivity index. The demonstration of the selective proteinuria in the presence of haptoglobin was concluded to be indicative of the degree of impaired glomerular permeability in nephritis and chronic renal failure.

The determination of peaks in biological waveforms

A method to determine the primary peaks of a waveform, in the presence of noise and a drifting baseline, is proposed. The method is based on a definition of a peak in terms of its height relative to adjacent valleys. Two algorithms to determine the set of primary peaks are presented. Some theoretical results, which ensure the stability of the algorithms, are given. The approach is illustrated by the analysis of chromatogram peaks.