%0 Journal Article %J Journal of Proteome Research %D 2022 %T Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 br %A Miller, R. M. %A Knoener, R. A. %A Benner, B. E. %A Frey, B. L. %A Scalf, M. %A Shortreed, M. R. %A Sherer, N. M. %A Smith, L. M. %B Journal of Proteome Research %V 21 %P 993-1001 %8 Apr %@ 1535-3893 %G eng %M WOS:000784194300013 %R 10.1021/acs.jproteome.1c00867 %0 Journal Article %J Genome Biology %D 2022 %T Enhanced protein isoform characterization through long-read proteogenomics %A Miller, R. M. %A Jordan, B. %A Mehlferber, M. M. %A Jeffery, E. D. %A Chatzipantsiou, C. %A Kaur, S. %A Millikin, R. J. %A Dai, Y. X. %A Tiberi, S. %A Castaldi, P. J. %A Shortreed, M. R. %A Luckey, C. J. %A Conesa, A. %A Smith, L. M. %A Mays, A. D. %A Sheynkman, G. M. %B Genome Biology %V 23 %8 Mar %@ 1474-760X %G eng %M WOS:000764049100002 %] 69 %R 10.1186/s13059-022-02624-y %0 Journal Article %J Analyst %D 2022 %T Overview and considerations in bottom-up proteomics %A Miller, R. M. %A Smith, L. M. %B Analyst %@ 0003-2654 %G eng %M WOS:000885653200001 %R 10.1039/d2an01246d %0 Journal Article %J Journal of Proteome Research %D 2021 %T Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus %A Shortreed, M. R. %A Millikin, R. J. %A Liu, L. %A Rolfs, Z. %A Miller, R. M. %A Schaffer, L. V. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1997-2004 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900021 %R 10.1021/acs.jproteome.0c00838 %0 Journal Article %J Journal of Proteome Research %D 2021 %T Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data %A Schaffer, L. V. %A Anderson, L. C. %A Butcher, D. S. %A Shortreed, M. R. %A Miller, R. M. %A Pavelec, C. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 317-325 %8 Jan %@ 1535-3893 %G eng %M WOS:000605145400028 %R 10.1021/acs.jproteome.0c00403 %0 Journal Article %J Journal of Proteome Research %D 2021 %T ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics %A Miller, R. M. %A Ibrahim, K. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1936-1942 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900014 %R 10.1021/acs.jproteome.0c00954 %0 Journal Article %J Journal of Proteome Research %D 2021 %T Spritz: A Proteogenomic Database Engine %A Cesnik, A. J. %A Miller, R. M. %A Ibrahim, K. %A Lu, L. %A Millikin, R. J. %A Shortreed, M. R. %A Frey, B. L. %A Smith, L. M. %B Journal of Proteome Research %V 20 %P 1826-1834 %8 Apr %@ 1535-3893 %G eng %M WOS:000637005900003 %R 10.1021/acs.jproteome.0c00407