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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.


A five-level classification system for proteoform identifications.

Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolić L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, Kelleher NL.

Nat Methods. 2019 Oct;16(10):939-940. doi: 10.1038/s41592-019-0573-x. No abstract available.


Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands".

Rolfs Z, Müller M, Shortreed MR, Smith LM, Bassani-Sternberg M.

Sci Immunol. 2019 Aug 16;4(38). pii: eaaw1622. doi: 10.1126/sciimmunol.aaw1622.


Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms.

Schaffer LV, Tucholski T, Shortreed MR, Ge Y, Smith LM.

Anal Chem. 2019 Sep 3;91(17):10937-10942. doi: 10.1021/acs.analchem.9b02343. Epub 2019 Aug 14.


Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data.

Miller RM, Millikin RJ, Hoffmann CV, Solntsev SK, Sheynkman GM, Shortreed MR, Smith LM.

J Proteome Res. 2019 Sep 6;18(9):3429-3438. doi: 10.1021/acs.jproteome.9b00330. Epub 2019 Aug 23.


Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS.

Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM.

RNA. 2019 Oct;25(10):1337-1352. doi: 10.1261/rna.072157.119. Epub 2019 Jul 11.


Identification and Quantification of Proteoforms by Mass Spectrometry.

Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM.

Proteomics. 2019 May;19(10):e1800361. doi: 10.1002/pmic.201800361. Review.


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.


Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells.

Guillen-Ahlers H, Rao PK, Perumalla DS, Montoya MJ, Jadhav AYL, Shortreed MR, Smith LM, Olivier M.

J Vis Exp. 2018 Jun 1;(136). doi: 10.3791/57140.


Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus.

Lu L, Millikin RJ, Solntsev SK, Rolfs Z, Scalf M, Shortreed MR, Smith LM.

J Proteome Res. 2018 Jul 6;17(7):2370-2376. doi: 10.1021/acs.jproteome.8b00141. Epub 2018 Jun 11.


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.


ProForma: A Standard Proteoform Notation.

LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO.

J Proteome Res. 2018 Mar 2;17(3):1321-1325. doi: 10.1021/acs.jproteome.7b00851. Epub 2018 Feb 14.


Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance.

Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R.

Stem Cell Reports. 2018 Feb 13;10(2):627-641. doi: 10.1016/j.stemcr.2017.12.016.


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.


Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys.

Proffitt JM, Glenn J, Cesnik AJ, Jadhav A, Shortreed MR, Smith LM, Kavanagh K, Cox LA, Olivier M.

BMC Genomics. 2017 Nov 13;18(1):877. doi: 10.1186/s12864-017-4279-0.


Ultrafast Peptide Label-Free Quantification with FlashLFQ.

Millikin RJ, Solntsev SK, Shortreed MR, Smith LM.

J Proteome Res. 2018 Jan 5;17(1):386-391. doi: 10.1021/acs.jproteome.7b00608. Epub 2017 Nov 8.


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.


Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry.

Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM.

J Proteome Res. 2017 Sep 1;16(9):3433-3442. doi: 10.1021/acs.jproteome.7b00448. Epub 2017 Aug 4.


Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins.

Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM.

Anal Chem. 2017 Aug 1;89(15):7841-7846. doi: 10.1021/acs.analchem.7b01784. Epub 2017 Jul 11.


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.


HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae.

Guillen-Ahlers H, Rao PK, Levenstein ME, Kennedy-Darling J, Perumalla DS, Jadhav AY, Glenn JP, Ludwig-Kubinski A, Drigalenko E, Montoya MJ, Göring HH, Anderson CD, Scalf M, Gildersleeve HI, Cole R, Greene AM, Oduro AK, Lazarova K, Cesnik AJ, Barfknecht J, Cirillo LA, Gasch AP, Shortreed MR, Smith LM, Olivier M.

Genomics. 2016 Jun;107(6):267-73. doi: 10.1016/j.ygeno.2016.05.002. Epub 2016 May 13.


Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.

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

Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):521-45. doi: 10.1146/annurev-anchem-071015-041722. Epub 2016 Mar 30. Review.


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.


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.


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.


Multiplexed programmable release of captured DNA.

Kennedy-Darling J, Holden MT, Shortreed MR, Smith LM.

Chembiochem. 2014 Nov 3;15(16):2353-6. doi: 10.1002/cbic.201402343. Epub 2014 Aug 26.


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.


Advanced methods for the analysis of chromatin-associated proteins.

Guillen-Ahlers H, Shortreed MR, Smith LM, Olivier M.

Physiol Genomics. 2014 Jul 1;46(13):441-7. doi: 10.1152/physiolgenomics.00041.2014. Epub 2014 May 6. Review.


Multiplexed analysis of cage and cage free chicken egg fatty acids using stable isotope labeling and mass spectrometry.

Torde RG, Therrien AJ, Shortreed MR, Smith LM, Lamos SM.

Molecules. 2013 Dec 5;18(12):14977-88. doi: 10.3390/molecules181214977.


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.


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.


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.


To understand the whole, you must know the parts: unraveling the roles of protein-DNA interactions in genome regulation.

Smith LM, Shortreed MR, Olivier M.

Analyst. 2011 Aug 7;136(15):3060-5. doi: 10.1039/c1an15037e. Epub 2011 Jun 1. Review.


Parallel detection of intrinsic fluorescence from peptides and proteins for quantification during mass spectrometric analysis.

Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon JJ, Smith LM.

Anal Chem. 2011 Mar 15;83(6):2187-93. doi: 10.1021/ac103023q. Epub 2011 Feb 11.


Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction.

Hallows WC, Yu W, Smith BC, Devries MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith LM, Zhao S, Guan KL, Denu JM.

Mol Cell. 2011 Jan 21;41(2):139-49. doi: 10.1016/j.molcel.2011.01.002. Erratum in: Mol Cell. 2011 Feb 18;41(4):493. Devires, Mark K [corrected to Devries, Mark K].


Aldehyde-terminated amorphous carbon substrates for the fabrication of biomolecule arrays.

Lockett MR, Shortreed MR, Smith LM.

Langmuir. 2008 Sep 2;24(17):9198-203. doi: 10.1021/la800991t. Epub 2008 Aug 2.


Revealing the role of phosphatidylserine in shear stress-mediated protection in endothelial cells.

Freed JK, Shortreed MR, Kleefisch CJ, Smith LM, Greene AS.

Endothelium. 2008 Jul-Aug;15(4):225-30. doi: 10.1080/10623320802228849.


Carbon-on-metal films for surface plasmon resonance detection of DNA arrays.

Lockett MR, Weibel SC, Phillips MF, Shortreed MR, Sun B, Corn RM, Hamers RJ, Cerrina F, Smith LM.

J Am Chem Soc. 2008 Jul 9;130(27):8611-3. doi: 10.1021/ja802454c.


In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication.

Phillips MF, Lockett MR, Rodesch MJ, Shortreed MR, Cerrina F, Smith LM.

Nucleic Acids Res. 2008 Jan;36(1):e7. Epub 2007 Dec 15.


Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions.

Lockett MR, Shortreed MR, Smith LM.

Anal Chem. 2007 Aug 1;79(15):6031-6. Epub 2007 Jun 27.


Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays.

Chen S, Zheng T, Shortreed MR, Alexander C, Smith LM.

Anal Chem. 2007 Aug 1;79(15):5698-702. Epub 2007 Jun 20.


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.


Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films.

Peelen D, Kodoyianni V, Lee J, Zheng T, Shortreed MR, Smith LM.

J Proteome Res. 2006 Jul;5(7):1580-5.

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