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A

Guillen-Ahlers H, Rao P.K, Perumalla D.S, Montoya M.J, Jadhav A.YL, Shortreed M.R, Smith L.M, Olivier M. 2018. Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells. Journal of Visualized Experiments. (136)

Connell C., Fung S., Heiner C., Bridgham J., Chakerian V., Heron E., Jones B., Menchen S., Mordan W., Raff M. et al.. 1987. Automated DNA-Sequence Analysis. BioTechniques. 5:342-&.

Buxton E.C, Westphall M., Jacobson W., Tong X.C, Smith L.M. 1996. Automation in large-scale DNA sequencing. Laboratory Robotics and Automation. 8:339-349.

B

Donnelly D.P, Rawlins C.M, DeHart C.J, Fornelli L, Schachner L.F, Lin Z, Lippens J.L, Aluri K.C, Sarin R, Chen B et al.. 2019. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature methods. 16(7)

Donnelly D.P, Rawlins C.M, DeHart C.J, Fornelli L, Schachner L.F, Lin Z, Lippens J.L, Aluri K.C, Sarin R, Chen B et al.. 2019. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature methods. 16(7)

Ling C.Y, Li Q.Y, Brown M.E, Kishimoto Y., Toya Y., Devine E.E, Choi K.O, Nishimoto K., Norman I.G, Tsegyal T. et al.. 2015. Bioengineered vocal fold mucosa for voice restoration. Science Translational Medicine. 7

C

Jorabchi K., Westphall M.S, Smith L.M. 2008. Charge assisted laser desorption/ionization mass spectrometry of droplets. Journal of the American Society for Mass Spectrometry. 19:833-840.

Frey B.L, Ladror D.T, Sondalle S.B, Krusemark C.J, Jue A.L, Coon J.J, Smith L.M. 2013. Chemical Derivatization of Peptide Carboxyl Groups for Highly Efficient Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 24:1710-1721.

D

Jarecki JL, Frey BL, Smith L.M, Stretton AO. 2011. Discovery of Neuropeptides in the Nematode Ascaris suum by Database Mining and Tandem Mass Spectrometry. Journal of Proteome Research. 10:3098-3106.

E

Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al.. 2022. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23

Miller R.M, Jordan B., Mehlferber M.M, Jeffery E.D, Chatzipantsiou C., Kaur S., Millikin R.J, Dai Y.X, Tiberi S., Castaldi P.J et al.. 2022. Enhanced protein isoform characterization through long-read proteogenomics. Genome Biology. 23

F

Jagtap P.D, Johnson J.E, Onsongo G., Sadler F.W, Murray K., Wang Y.B, Shenykrnan G.M, Bandhakavi S., Smith L.M, Griffin T.J. 2014. Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework. Journal of Proteome Research. 13:5898-5908.

Jagtap P.D, Johnson J.E, Onsongo G., Sadler F.W, Murray K., Wang Y.B, Shenykrnan G.M, Bandhakavi S., Smith L.M, Griffin T.J. 2014. Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework. Journal of Proteome Research. 13:5898-5908.

Jia W.Y, Kim S.H, Scalf M.A, Tonzi P., Millikin R.J, Guns W.M, Liu L., Mastrocola A.S, Smith L.M, Huang T.T et al.. 2021. Fused in sarcoma regulates DNA replication timing and kinetics. Journal of Biological Chemistry. 297

H

Mayer K.S, Chen X., Sanders D., Chen J., Jiang J., N P., Scalf M., Smith L.M, Zhong X.. 2019. HDA9-PWR-HOS15 is a core histone deacetylase complex regulating transcription and development. Plant Physiology. 180(1):342-355.

Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al.. 2018. How many human proteoforms are there? Nature Chemical Biology. 14:206-214.

Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al.. 2018. How many human proteoforms are there? Nature Chemical Biology. 14:206-214.

Guillen-Ahlers H., Rao P.K, Levenstein M.E, Kennedy-Darling J., Perumalla D.S, Jadhav A.Y, Glenn J.P, Ludwig-Kubinski A., Drigalenko E., Montoya M.J et al.. 2016. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.

Spiniello M., Knoener R.A, Steinbrink M.I, Yang B., Cesnik A.J, Buxton K.E, Scalf M., Jarrard D.F, Smith L.M. 2018. HyPR-MS for multiplexed discovery of MALAT1, NEAT1, and NORAD lncRNA protein interactomes. Journal of Proteome Research. 17(9):3022-3038.

I

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. 2018. Identification and quantification of murine mitochondrial proteoforms using an integrated top-down and intact-mass strategy. Journal of Proteome Research. 17(10):3526-3536.

Thiel A.J, Frutos A.G, Jordan C.E, Corn R.M, Smith L.M. 1997. In situ surface plasmon resonance imaging detection of DNA hybridization to oligonucleotide arrays on gold surfaces. Analytical Chemistry. 69:4948-4956.

J. Mellors S, Jorabchi K, Smith L.M, J. Ramsey M. 2010. Integrated Microfluidic Device for Automated Single Cell Analysis Using Electrophoretic Separation and Electrospray Ionization Mass Spectrometry. Analytical Chemistry. 82:967-973.

L

Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.L, Frey B.L, Jarrard D.F, Smith L.M. 2018. Long noncoding RNAs AC009014. 3 and newly discovered XPLAID differentiate aggressive and indolent prostate cancers. Translational Oncology. 11(3):808-814.

Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.R, Frey B.L, Jarrard D.F, Smith L.M. 2018. Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 11:808-814.

M

Chen D.H, Johnson A.F, Severin J.M, Rank D.R, Smith L.M, Guilfoyle R.A. 1996. M13-102: A vector for facilitating construction and improving quality of M13 shotgun libraries. Gene. 172:53-57.

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