Intact‐protein based sample preparation strategies for proteome analysis in combination with mass spectrometry

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Abstract
The complexity of tissue and cell proteomes and the vast dynamic range of protein abundance present a formidable challenge for analysis that no one analytical technique can overcome. As a result, there is a need to integrate technologies to achieve the high‐resolution and high‐sensitivity analysis of complex biological samples. The combined technologies of separation science and biological mass spectrometry (Bio‐MS) are the current workhorse in proteomics, and are continuing to evolve to meet the needs for high sensitivity and high throughput. They are relied upon for protein quantification, identification, and analysis of post‐translational modifications (PTMs). The standard technique of two dimensional poly‐acrylamide gel electrophoresis (2D PAGE) offers relatively limited resolution and sensitivity for the simultaneous analysis of all cellular proteins, with only the most highly abundant proteins detectable in whole cell or tissue‐derived samples. Hence, many alternative strategies are being explored. Numerous sample preparation procedures are currently available to reduce sample complexity and to increase the detectability of low‐abundance proteins. Maintaining proteins intact during sample preparation has important advantages compared with strategies that digest proteins at an early step. These strategies include the ability to quantitate and recover proteins, and the assessment of PTMs. A review of current intact protein‐based strategies for protein sample preparation prior to mass spectrometry (MS) is presented in the context of biomedically driven applications. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:413–426, 2005