email pappin@cshl.edu, phone (516) 367-6882, fax (516) 367-8873

My principal research interests have been related to methods development in proteomics, using chemical or computational approaches. Key areas include protein and peptide identification and quantitation using mass spectrometry (MS), especially when used in situations requiring high throughput. Huge strides have been made recently in both areas, but the ability to perform complex, multi-sample analyses is still difficult and time-consuming.

Global proteomic screens are now being increasingly accompanied with more specific, targeted measurements of specific proteins using techniques such as multiple reaction monitoring (MRM) and isotopically encoded peptide standards. Software tools that permit rapid, simplified access to the wealth of data in both types of experiment are essential, but only slowly evolving. One area of research in my laboratory concerns the development of such tools, particularly coupled to our ability to recognize, identify and quantify post-translationally modified peptides.

Lacking such powerful tools as hybridization and amplification with PCR, large-scale protein analysis is faced with the massive hurdle of reducing sample complexity as much as possible before introducing the sample stream into the mass spectrometer. This puts huge strains on our ability to separate very complex peptide mixtures, which often require multiple, successive levels of chromatography. Our approach to this problem is to attempt to reduce sample complexity by targeting specific classes of protein or peptide, rather than analyzing the entire unfractionated sample. Strategies are emerging that  could essentially be described as chemical sorting. This includes the use of chelation to enrich phosphopeptides from the total peptide pool, or the use of specific affinity-tagged small molecule inhibitors to pull down classes of kinases or phosphatases for more specific MS analysis.

Selected Publications