Sample Clean-Up Ways to Overcome the Bottleneck in Proteome Analysis

Sample Clean-Up Ways to Overcome the Bottleneck in Proteome Analysis 

A proteomic analysis of a sample usually consists of four steps. These are extraction of the proteins from the sample, their separation, detection, and finally identification/analysis of the individual separated proteins. Major attention must be paid to the sample processing, sample handling, and the sample clean-up since any error or sample loss during this stage influences the final result. 

Most biofluids contain large amoimts of well-known proteins such as albumin and IgGs, which overwhelm the separation system and make the detection of low-abundance proteins and peptides very difficult. It is thus advantageous to remove these proteins prior to digestion and separation. Besides the already 

Approaches using affinity peptide capture and RP-HPLC separations have been applied with varying degrees of success. Overall, MD affinity chromatography is likely to play an increasingly important role in the context of sample clean-up, and identification and characterization of specific classes of peptides and proteins in the proteome. 

As many reports have shown, there remains a tremendous amount of information in the low-MW fraction of biological samples such as serum or urine. Serum or plasma may be divided into a high-MW and a low-MW fraction by ultrafiltration or SEC. Nevertheless, even ultrafiltration at a cut-off of 10 kDa still leaves a considerable amount of albumin in urine or in ultrafiltered serum, since the MW cut-off is not sharp as may be related to the distribution of the pore sizes. 

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