Protein Separation and Characterization by np-RP−HPLC Followed by Intact MALDI-TOF Mass Spectrometry and Peptide Mass Mapping Analyses

Abstract

Due to their complexity, the separation of intact proteins from complex mixtures is an important step to comparative proteomics and the identification and characterization of the proteins by mass spectrometry (MS). In the study reported, we evaluated the use of non-porous-reversed-phase (np-RP) HPLC for intact protein separation prior to MS analyses. The separation system was characterized and compared to 1D-SDS-PAGE electrophoresis in terms of resolution and sensitivity. We demonstrate that np-RP HPLC protein separation is highly reproducible and provides intact protein fractions which can be directly analyzed by MALDI-TOF MS for intact molecular weight determination. An in-well digestion protocol was developed, allowing for rapid protein identification by peptide mass fingerprinting (PMF) and resulted in comparable or improved peptide recovery compared with in-gel digestion. The np-RP sensitivity of detection by UV absorbance at 214 nm for intact proteins was at the low ng level and the sensitivity of peptide analysis by MALDI-TOF MS was in the 10-50 pg level. A membrane protein fraction was characterized to demonstrate application of this methodology. Among the identified proteins, multiple forms of vimentin were observed. Overall we demonstrate that np-RP HPLC followed by MALDI-TOF MS allows for rapid, sensitive and reproducible protein fractionation and very specific protein characterization by integration of PMF analysis with MS intact molecular weight information. Keywordsnon-porous reversed phase HPLC; protein liquid chromatography; peptide mass fingerprint; intact protein mass spectrometry

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