Samuel H Payne
Current Research:
My current research, generously funded by the NSF IGERT for plant systems biology, focuses on developing both computational and biological aspects of Mass Spectrometry. One aspect of my plant biology research is the re-annotation of the Arabidopsis proteome. Using peptides identified by mass spectrometry we validate, correct and expand the current protein predictions. Our results find over 800 novel genes in arabidopsis, and extensions or corrections to an additional 800 loci. My two advisors for these projects are Steve Briggs and Vineet Bafna.
I just finished the development of phosphorylation specific scoring functions for the lab’s InsPecT software. Finding phospho-peptides is an important part of understanding the dynamic proteome. Current MS/MS programs are both too slow and inaccurate in their annotation of phospho-peptide spectra. I have trained a Bayesian network to recognize the fragmentation probabilities of phospho-peptides, and incorporated that into the scoring function of InsPecT. Using InsPecT’s tag filter make the program over 10-100 times faster than X!Tandem and SEQUEST respectively. Now that the scoring function is trained to discern true phospho-peptide fragmentation, it is also 10-40% more sensitive as well, recovering more spectral annotations at a given false-discovery rate. This a collaboration with Huilin Zhou.
Fun past projects include work on unrestrictive modifications searches to formulate an effective false-positive calculation (Tanner 2008); metabolic capabilities of eukaryotes using a comparative genomic approach (Payne 2006 and Payne 2005); human genetics and SNP correlation with high blood pressure (Rana 2007); transcriptional control of the growth/differentiation switch in Dictyostelium (Hirose 2006)
Publications:
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Proteogenomic discovery,
correction and confirmation of Arabidopsis gene models. In review.
Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. Phosphorylation specific MS/MS scoring for rapid and accurate phospho-proteome analysis. In press, J Proteome Res
Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. High-coverage phosphoproteome analysis using HILIC based mult-dimensional chromatography. in press Mol Cell Proteomics
Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth P, David L, Loomis WF, Briggs SP, Bafna V. Accurate Annotation of Peptide Modifications through Unrestrictive Database Search. Journal of Proteome Research 2008, 7:170-181 PubMed
Rana BK, Insel PA, Payne SH, Abel K, Beutler E, Ziegler MG, Schork NJ, O'Connor DT. Population-based sample reveals gene-gender interactions in blood pressure in White Americans. Hypertension. 2007 Jan;49(1):96-106. PubMed
Payne SH and Loomis WF (2006) Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences.
Hirose S, Payne SH, Loomis WF (2006) cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum. Eukaryot Cell. 2006 Jul;5(7):1104-10. PubMed
Payne SH (2005) Metabolic pathways, p. 41-57. In W. F. Loomis and A. Kuspa (ed.), Dictyostelium genomics. Horizon Press, Far Hills, N.J.
Publications that impressed me:
The following publications were superb. Although not in my particular field, I loved reading them and am grateful for such fine work.
The Kellis yeast genome alignment:
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. PubMed
Designing a Protein/DNA interaction:
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 2006 Jun 1;441(7093):656-9 PubMed
College: Brigham Young
B.S. Computer Science
Graduate School: University of California San Diego
Ph.D. Bioinformatics
Research: Proteomics, Mass Spectrometry
Unrestrictive searches, Proteogenomics,
Root-knot nematode,
Phosphate specific scoring.
Journals: Nature, PNAS, Mol Cell Proteomics
I am a Bioinformatics PhD student in the Vineet Banfa Lab at the University of California at San Diego (UCSD), working computational mass spectrometry. Prior to mass spectrometry, I pursued research in human disease genetics, systems biology, and transcriptional control. As an undergraduate student in computer science at BYU, I researched image processing and pattern recognition with Bryan Morse. I also did a research internship at the NIH/NIAMS Lab of Structural Biology with Bernard Heymann.
