III. Proteoform family identification, quantification, and visualization

Proteoform families

I created software named Proteoform Suite, along with other members of Prof. Smith’s research group, that automated the identification, quantification, and visualization of proteoform families, i.e. the diverse forms of a protein from the same gene. This software uses only the intact masses of these proteoforms to perform this analysis, whereas most proteoform studies use fragmentation to reveal more sequence information. We also contributed the valuable concept of the “proteoform family,” which clarifies the important relationships between proteoforms. I used this software tool to identify thousands of yeast proteoforms and quantify the abundance changes in these proteoforms in response to salt stress. This revealed expected significant changes in acetylation and phosphorylation states of the SBH1 proteoform family and many new significant changes.

Beyond my study of yeast proteoforms, Proteoform Suite has been used to show we can expand identifications with top-down mass spectrometry by around 50% in both yeast and mouse and perform label-free proteoform quantification (Schaffer, et al.). It has also been used to reveal proteoforms in Escherichia coli (Dai, et al.). These tools continue to be applied for proteoform analysis by others, including for human samples.

Research Papers

(1) Cesnik, A. J.; Shortreed, M. R.; Schaffer, L. V.; Knoener, R. A.; Frey, B. L.; Scalf, M.; Solntsev, S. K.; Dai, Y. Gasch, A. P.; Smith, L. M. “Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.” Journal of Proteome Research 2018 17, 568–578.

(2) Schaffer, L. V.; Shortreed, M. R.; Cesnik, A. J.; Frey, B. L.; Scalf, M.; Solntsev, S. K.; Dai, Y.; Gasch, A. P.; Smith, L. M. “Expanding Proteoform Identifications in Top-­Down Proteomic Analyses by Constructing Proteoform Families.” Analytical Chemistry 2018, 90, 2, 1325–1333.

(3) Schaffer, L. V.; Rensvold, J. W..; Shortreed, M. R.; Cesnik, A. J.; Jochem, A.; Scalf, M.; Frey, B. L; Pagliarini, D. J.; Smith, L. M. “Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top­Down and Intact­-Mass Strategy.” Journal of Proteome Research 2018, 17, 10, 3526–3536.

(4) Dai, Y.; Shortreed, M. R.; Scalf, M.; Frey, B. L.; Cesnik, A. J.; Solntsev, S. K.; Schaffer, L. V.; Smith, L. M. “Elucidating E. coli Proteoform Families Using Intact­-Mass Proteomics and a Global PTM Discovery Database.” Journal of Proteome Research 2017, 16, 11, 4156–4165.

(5) Shortreed, M. R.; Frey, B. L.; Scalf, M.; Knoener, R. A.; Cesnik, A. J.; Smith, L. M. “Elucidating Proteoform Families from Proteoform Intact Mass and Lysine Count Measurements.” Journal of Proteome Research 2016, 15, 4, 1213–1221.