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Items: 39


Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database.

Dai Y, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM.

J Proteome Res. 2019 Oct 4;18(10):3671-3680. doi: 10.1021/acs.jproteome.9b00339. Epub 2019 Sep 18.


Differentiated fibrocytes assume a functional mesenchymal phenotype with regenerative potential.

Ling C, Nishimoto K, Rolfs Z, Smith LM, Frey BL, Welham NV.

Sci Adv. 2019 May 8;5(5):eaav7384. doi: 10.1126/sciadv.aav7384. eCollection 2019 May.


Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion.

Rolfs Z, Solntsev SK, Shortreed MR, Frey BL, Smith LM.

J Proteome Res. 2019 Jan 4;18(1):349-358. doi: 10.1021/acs.jproteome.8b00651. Epub 2018 Oct 31.


Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy.

Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, Smith LM.

J Proteome Res. 2018 Oct 5;17(10):3526-3536. doi: 10.1021/acs.jproteome.8b00469. Epub 2018 Sep 18.


Topology-Guided Stepwise Insertion of Three Secondary Linkers in Zirconium Metal-Organic Frameworks.

Zhang X, Frey BL, Chen YS, Zhang J.

J Am Chem Soc. 2018 Jun 20;140(24):7710-7715. doi: 10.1021/jacs.8b04277. Epub 2018 Jun 12.


Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers.

Cesnik AJ, Yang B, Truong A, Etheridge T, Spiniello M, Steinbrink MI, Shortreed MR, Frey BL, Jarrard DF, Smith LM.

Transl Oncol. 2018 Jun;11(3):808-814. doi: 10.1016/j.tranon.2018.04.002. Epub 2018 May 1.


Enhanced Global Post-translational Modification Discovery with MetaMorpheus.

Solntsev SK, Shortreed MR, Frey BL, Smith LM.

J Proteome Res. 2018 May 4;17(5):1844-1851. doi: 10.1021/acs.jproteome.7b00873. Epub 2018 Apr 2.


Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families.

Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM.

Anal Chem. 2018 Jan 16;90(2):1325-1333. doi: 10.1021/acs.analchem.7b04221. Epub 2017 Dec 22.


Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families.

Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM.

J Proteome Res. 2018 Jan 5;17(1):568-578. doi: 10.1021/acs.jproteome.7b00685. Epub 2017 Dec 15.


Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database.

Dai Y, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM.

J Proteome Res. 2017 Nov 3;16(11):4156-4165. doi: 10.1021/acs.jproteome.7b00516.


Fibrillin-2 and Tenascin-C bridge the age gap in lung epithelial regeneration.

Gilpin SE, Li Q, Evangelista-Leite D, Ren X, Reinhardt DP, Frey BL, Ott HC.

Biomaterials. 2017 Sep;140:212-219. doi: 10.1016/j.biomaterials.2017.06.027. Epub 2017 Jun 22.


Correction to "Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements".

Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM.

J Proteome Res. 2017 Jul 7;16(7):2660. doi: 10.1021/acs.jproteome.7b00333. Epub 2017 Jun 13. No abstract available.


Global Post-Translational Modification Discovery.

Li Q, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM.

J Proteome Res. 2017 Apr 7;16(4):1383-1390. doi: 10.1021/acs.jproteome.6b00034. Epub 2017 Mar 1.


Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements.

Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM.

J Proteome Res. 2016 Apr 1;15(4):1213-21. doi: 10.1021/acs.jproteome.5b01090. Epub 2016 Mar 16. Erratum in: J Proteome Res. 2017 Jul 7;16(7):2660.


Protein turnover during in vitro tissue engineering.

Li Q, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV.

Biomaterials. 2016 Mar;81:104-113. doi: 10.1016/j.biomaterials.2015.12.004. Epub 2015 Dec 14.


Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.

Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM.

J Proteome Res. 2016 Mar 4;15(3):800-8. doi: 10.1021/acs.jproteome.5b00817. Epub 2016 Jan 12.


Bioengineered vocal fold mucosa for voice restoration.

Ling C, Li Q, Brown ME, Kishimoto Y, Toya Y, Devine EE, Choi KO, Nishimoto K, Norman IG, Tsegyal T, Jiang JJ, Burlingham WJ, Gunasekaran S, Smith LM, Frey BL, Welham NV.

Sci Transl Med. 2015 Nov 18;7(314):314ra187. doi: 10.1126/scitranslmed.aab4014.


Proteomic analysis of naturally-sourced biological scaffolds.

Li Q, Uygun BE, Geerts S, Ozer S, Scalf M, Gilpin SE, Ott HC, Yarmush ML, Smith LM, Welham NV, Frey BL.

Biomaterials. 2016 Jan;75:37-46. doi: 10.1016/j.biomaterials.2015.10.011. Epub 2015 Oct 8.


Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.

Shortreed MR, Wenger CD, Frey BL, Sheynkman GM, Scalf M, Keller MP, Attie AD, Smith LM.

J Proteome Res. 2015 Nov 6;14(11):4714-20. doi: 10.1021/acs.jproteome.5b00599. Epub 2015 Sep 29.


Formaldehyde crosslinking: a tool for the study of chromatin complexes.

Hoffman EA, Frey BL, Smith LM, Auble DT.

J Biol Chem. 2015 Oct 30;290(44):26404-11. doi: 10.1074/jbc.R115.651679. Epub 2015 Sep 9. Review.


Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM.

BMC Genomics. 2014 Aug 22;15:703. doi: 10.1186/1471-2164-15-703.


Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae.

Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM.

J Proteome Res. 2014 Aug 1;13(8):3810-25. doi: 10.1021/pr5004938. Epub 2014 Jul 17.


Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions.

Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM.

Biochem Biophys Res Commun. 2014 Mar 14;445(3):535-41. doi: 10.1016/j.bbrc.2014.01.040. Epub 2014 Jan 30.


Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.

Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM.

J Proteome Res. 2014 Jan 3;13(1):228-40. doi: 10.1021/pr4009207. Epub 2013 Nov 11.


Chemical derivatization of peptide carboxyl groups for highly efficient electron transfer dissociation.

Frey BL, Ladror DT, Sondalle SB, Krusemark CJ, Jue AL, Coon JJ, Smith LM.

J Am Soc Mass Spectrom. 2013 Nov;24(11):1710-21. doi: 10.1007/s13361-013-0701-2. Epub 2013 Aug 6.


Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.

Sheynkman GM, Shortreed MR, Frey BL, Smith LM.

Mol Cell Proteomics. 2013 Aug;12(8):2341-53. doi: 10.1074/mcp.O113.028142. Epub 2013 Apr 29.


Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry.

Welham NV, Chang Z, Smith LM, Frey BL.

Biomaterials. 2013 Jan;34(3):669-76. doi: 10.1016/j.biomaterials.2012.09.050. Epub 2012 Oct 25.


Sequence-specific capture of protein-DNA complexes for mass spectrometric protein identification.

Wu CH, Chen S, Shortreed MR, Kreitinger GM, Yuan Y, Frey BL, Zhang Y, Mirza S, Cirillo LA, Olivier M, Smith LM.

PLoS One. 2011;6(10):e26217. doi: 10.1371/journal.pone.0026217. Epub 2011 Oct 20.


Complete chemical modification of amine and acid functional groups of peptides and small proteins.

Krusemark CJ, Frey BL, Smith LM, Belshaw PJ.

Methods Mol Biol. 2011;753:77-91. doi: 10.1007/978-1-61779-148-2_6.


Discovery of neuropeptides in the nematode Ascaris suum by database mining and tandem mass spectrometry.

Jarecki JL, Frey BL, Smith LM, Stretton AO.

J Proteome Res. 2011 Jul 1;10(7):3098-106. doi: 10.1021/pr2001176. Epub 2011 May 27.


Alkylating tryptic peptides to enhance electrospray ionization mass spectrometry analysis.

Kulevich SE, Frey BL, Kreitinger G, Smith LM.

Anal Chem. 2010 Dec 15;82(24):10135-42. doi: 10.1021/ac1019792. Epub 2010 Nov 29.


Ion-Ion Reactions with Fixed-Charge Modified Proteins to Produce Ions in a Single, Very High Charge State.

Frey BL, Krusemark CJ, Ledvina AR, Coon JJ, Belshaw PJ, Smith LM.

Int J Mass Spectrom. 2008 Oct 1;276(2-3):136-143.


Modifying the charge state distribution of proteins in electrospray ionization mass spectrometry by chemical derivatization.

Krusemark CJ, Frey BL, Belshaw PJ, Smith LM.

J Am Soc Mass Spectrom. 2009 Sep;20(9):1617-25. doi: 10.1016/j.jasms.2009.04.017. Epub 2009 May 4.


Relative quantification of carboxylic acid metabolites by liquid chromatography-mass spectrometry using isotopic variants of cholamine.

Lamos SM, Shortreed MR, Frey BL, Belshaw PJ, Smith LM.

Anal Chem. 2007 Jul 15;79(14):5143-9. Epub 2007 Jun 12.


Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry.

Shortreed MR, Lamos SM, Frey BL, Phillips MF, Patel M, Belshaw PJ, Smith LM.

Anal Chem. 2006 Sep 15;78(18):6398-403.


Controlling gas-phase reactions for efficient charge reduction electrospray mass spectrometry of intact proteins.

Frey BL, Lin Y, Westphall MS, Smith LM.

J Am Soc Mass Spectrom. 2005 Nov;16(11):1876-87. Epub 2005 Sep 28.


Alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice.

Rabaglia ME, Gray-Keller MP, Frey BL, Shortreed MR, Smith LM, Attie AD.

Am J Physiol Endocrinol Metab. 2005 Aug;289(2):E218-24. Epub 2005 Mar 1.


Aberrant S(RN)1 Reaction of 4-Aminophenol with alpha,p-Dinitrocumene: EPR Observation of Intermediates.

Scamehorn RG, Mahnke LA, Krause RD, Frey BL, Hendriksen DL, Jahn KS, Kultgen SG, Walton JC.

Org Lett. 2000 Mar 23;2(6):827-829.


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