Spectrometry, protein structure analysis using

Soderblom, E.J. Goshe, M.B. Collision-induced dissociative chemical cross-linking reagents and methodology applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 2006, 78, 8059-8068. 

Sharma, S., Zheng, H., Huang, Y.J., et al. (2009) Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry. Proteins, 76 (4), 882-894. 

The techniques described thus far cope well with samples up to 10 kDa. Molecular mass determinations on peptides can be used to identify modifications occurring after the protein has been assembled according to its DNA code (post-translation), to map a protein structure, or simply to confirm the composition of a peptide. For samples with molecular masses in excess of 10 kDa, the sensitivity of FAB is quite low, and such analyses are far from routine. Two new developments have extended the scope of mass spectrometry even further to the analysis of peptides and proteins of high mass. 

Koing, S. 2005. Functional protein analysis using mass spectrometry. Current Organic Chemistry 9(9), 875-887. Osguthorpe, D. 2000. Ab initio protein folding. Current Opinion in Structural Biology 10(2), 146-152. 

The marriage of HPLC to mass spectrometry (MS), now developed into a mature instrumentation, continues to greatly impact many of the separation sciences, especially in pharmaceutical analysis where it has been used in new drug discovery [23,24] and in drug metabolite identification [25-27]. HPLC-MS has also made an impact on lipid research, providing a convenient approach to the analysis of phospholipids and fatty acids [28,29]. It has also greatly benefited the field of proteomics [30-34], especially analysis of protein structure and function. 

The complexity of quality control for proteins, as compared to small molecules, is most evident in the requirements for proof of structure. Many small molecules can be fully characterized using a few spectroscopic techniques (e.g., NMR, IR, mass spectrometry, and UV) in conjunction with an elemental analysis. However, proving the proper structure for a protein is much more complex because 1) the aforementioned spectroscopic techniques do not provide definitive structural data for proteins, and 2) protein structure includes not only molecular composition (primary structure) but additionally, secondary, tertiary, and, in some cases, quaternary features. Clearly, no single analytical test will address all of these structural aspects hence a large battery of tests is required. 

Finally, using PNA as an affinity capture reagent recently was extended to probing RNA-protein complexes (RNPs) in cells (33). In this application, the PNA is functionalized with a peptide that allows uptake into cells and is complementary to an RNA component of an RNP. The PNA also bears two affinity tags, the first of which is a benzophenone-modifled phenylalanine residue that can photocross-link the PNA to a protein present in the RNP. The second tag is a biotin group, which allows the purification of the cross-linked PNA-protein. Subsequent analysis by mass spectrometry identifies both the protein and its cross-linking site. As is the case for PNA used to deliver a fluorophore to a specific site in an RNA, this method requires that the PNA not disrupt the structure being probed. 

The study of protein structure, function, quantity, and interactions during maturation and progression of disease is referred to as proteomics. Analytical approaches that use a combination of two-dimensional (2-D) gel electrophoresis for protein separation and MS analysis for protein identification followed by database searches is a widely practiced proteomics strategy.The tryptic peptides extracted from gels are analyzed by MALDI-TOF MS and microcolunm or capillary LC tandem mass spectrometry (MS/MS) techniques. Typically, the MALDI-TOF MS techniques are used to quickly identify peptide fragments and confirm the presence of known proteins. Nano-scale capillary LC/MS/MS techniques (using 50-100 pm diameter columns, operating at flow rates of 20-500 nL/min) are... 

The successful candidate will perfom structural analysis on a wide variety of proteins using state of the art Edman sequencing and mass spectrometry instruments. The candidate will also be involved in development of new techniques to aid in protein characterization. 

Edman degradation was originally developed for determination of the primary structure (i.e., amino acid sequence) of peptides and proteins. Sequence analysis is not regularly performed for quality control in routine peptide synthesis but is more often employed for problem solving. As described earlier in this chapter, efficient characterization of synthetic peptides can be readily obtained by a combination of RP-EDPLC and mass spectrometry. Amino acid analysis is also valuable if MS is not available. If an incorrect mass or a discrepancy in the amino acid composition is found, one obvious alternative is to resynthesize the peptide. But, in order to deduce the cause of a failed synthesis, additional analyses must be performed. Both Edman degradation and tandem MS can be used to obtain sequence information... 

---