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Items: 19

1.

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry.

Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP.

Anal Chem. 2019 Mar 19;91(6):4010-4016. doi: 10.1021/acs.analchem.8b05399. Epub 2019 Feb 26.

PMID:
30672687
2.

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer.

Hebert AS, Prasad S, Belford MW, Bailey DJ, McAlister GC, Abbatiello SE, Huguet R, Wouters ER, Dunyach JJ, Brademan DR, Westphall MS, Coon JJ.

Anal Chem. 2018 Aug 7;90(15):9529-9537. doi: 10.1021/acs.analchem.8b02233. Epub 2018 Jul 18.

3.

Nonlinear Regression Improves Accuracy of Characterization of Multiplexed Mass Spectrometric Assays.

Galitzine C, Egertson JD, Abbatiello S, Henderson CM, Pino LK, MacCoss M, Hoofnagle AN, Vitek O.

Mol Cell Proteomics. 2018 May;17(5):913-924. doi: 10.1074/mcp.RA117.000322. Epub 2018 Feb 9.

4.

MSstatsQC: Longitudinal System Suitability Monitoring and Quality Control for Targeted Proteomic Experiments.

Dogu E, Mohammad-Taheri S, Abbatiello SE, Bereman MS, MacLean B, Schilling B, Vitek O.

Mol Cell Proteomics. 2017 Jul;16(7):1335-1347. doi: 10.1074/mcp.M116.064774. Epub 2017 May 8.

5.

New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins.

Abbatiello S, Ackermann BL, Borchers C, Bradshaw RA, Carr SA, Chalkley R, Choi M, Deutsch E, Domon B, Hoofnagle AN, Keshishian H, Kuhn E, Liebler DC, MacCoss M, MacLean B, Mani DR, Neubert H, Smith D, Vitek O, Zimmerman L.

Mol Cell Proteomics. 2017 Mar;16(3):327-328. doi: 10.1074/mcp.E117.067801. Epub 2017 Feb 9. No abstract available.

6.

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes.

Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder E, Carr SA, Jaffe JD.

Mol Cell Proteomics. 2016 May;15(5):1622-41. doi: 10.1074/mcp.M116.058354. Epub 2016 Feb 24.

7.

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.

Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA.

Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18.

8.

A framework for installable external tools in Skyline.

Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B.

Bioinformatics. 2014 Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.

9.

Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S.

Mol Cell Proteomics. 2014 Mar;13(3):907-17. doi: 10.1074/mcp.M113.036095. Epub 2014 Jan 17.

10.

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.

Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG.

Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8.

11.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA.

Mol Cell Proteomics. 2013 Sep;12(9):2623-39. doi: 10.1074/mcp.M112.027078. Epub 2013 May 20.

12.

Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.

Mani DR, Abbatiello SE, Carr SA.

BMC Bioinformatics. 2012;13 Suppl 16:S9. doi: 10.1186/1471-2105-13-S16-S9. Epub 2012 Nov 5.

13.

Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry.

Whiteaker JR, Zhao L, Abbatiello SE, Burgess M, Kuhn E, Lin C, Pope ME, Razavi M, Anderson NL, Pearson TW, Carr SA, Paulovich AG.

Mol Cell Proteomics. 2011 Apr;10(4):M110.005645. doi: 10.1074/mcp.M110.005645. Epub 2011 Jan 18.

14.

Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry.

Maclean B, Tomazela DM, Abbatiello SE, Zhang S, Whiteaker JR, Paulovich AG, Carr SA, Maccoss MJ.

Anal Chem. 2010 Dec 15;82(24):10116-24. doi: 10.1021/ac102179j. Epub 2010 Nov 19.

15.

Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry.

Abbatiello SE, Mani DR, Keshishian H, Carr SA.

Clin Chem. 2010 Feb;56(2):291-305. doi: 10.1373/clinchem.2009.138420. Epub 2009 Dec 18.

16.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.

Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA.

Nat Biotechnol. 2009 Jul;27(7):633-41. doi: 10.1038/nbt.1546. Epub 2009 Jun 28. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.

17.

Mass spectrometric quantification of asparagine synthetase in circulating leukemia cells from acute lymphoblastic leukemia patients.

Abbatiello SE, Pan YX, Zhou M, Wayne AS, Veenstra TD, Hunger SP, Kilberg MS, Eyler JR, Richards NG, Conrads TP.

J Proteomics. 2008 Apr 30;71(1):61-70. doi: 10.1016/j.jprot.2007.11.009. Epub 2007 Dec 5.

PMID:
18541474
18.

Efficient expression, purification, and characterization of C-terminally tagged, recombinant human asparagine synthetase.

Ciustea M, Gutierrez JA, Abbatiello SE, Eyler JR, Richards NG.

Arch Biochem Biophys. 2005 Aug 1;440(1):18-27.

PMID:
16023613
19.

Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor.

Koide A, Abbatiello S, Rothgery L, Koide S.

Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1253-8. Epub 2002 Jan 29.

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