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Statistical analysis of multiple iTRAQ/TMT experiments labeled with variable reporter ion tags using ProteoIQ

Ningombam Sanjib Meitei, Arun Apte, Arijit Biswas, Mark Pitman, Parimal Samir and Andrew J. Link; ABRF 2015 Annual Meeting, US

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Extracellular vesicle-mediated reversal of the prostate cancer phenotype Panagopoulos, K et al (2014); The Journal of Cancer Research, October 1, 2014 74; 2497, doi: 10.1158/1538-7445.AM2014-2497
Proteomic investigation of human α7-nicotinic acetylcholine receptor interacting proteins Matthew, M et al (2014);
The Journal of the Federation of American Societies for Experimental Biology, vol. 28 no. 1 Supplement 1147.5
Interleukin-1-induced changes in the glioblastoma secretome suggest its role in tumor progression Tarassishin, L et al (2014); Journal of Proteomics, Volume 99, 17 March 2014, Pages 152–168

Accurate Identification of Deamidated Peptides in Global Proteomics Using a Quadrupole Orbitrap Mass Spectrometer

Nepomuceno AI1, Gibson RJ, Randall SM, Muddiman DC
J Proteome Res. 2014 Feb 7;13(2):777-85. doi: 10.1021/pr400848n. Epub 2013 Dec 12


Reversal of chemosensitivity and induction of cell malignancy of a non-malignant prostate cancer cell line upon extracellular vesicle exposure

Kiriaki Panagopoulos, Sam Cross-Knorr, Christen Dillard, Dionysios Pantazatos, Michael Del Tatto, David Mills, Lisa Goldstein, Joseph Renzulli, Peter Quesenberry, Devasis Chatterjee
Mol Cancer. 2013; 12: 118. Published online Oct 8, 2013. doi: 10.1186/1476-4598-12-118


Insights into pediatric diffuse intrinsic pontine glioma through proteomic analysis of cerebrospinal fluid

Amanda M. Saratsis, Sridevi Yadavilli, Suresh Magge, Brian R. Rood, Jennifer Perez, D. Ashley Hill, Eugene Hwang, Lindsay Kilburn, Roger J. Packer, and Javad Nazarian
Neuro Oncol. May 2012; 14(5): 547–560. Published online Apr 5, 2012. doi: 10.1093/neuonc/nos067


Stable isotope labeling by amino acids in cell culture (SILAC) - an introduction for biologist

L.J. Graham, Robert; J. Sweredoski, Michael; Hess, Sonja
Current Proteomics. Volume 8, Number 1, April 2011 , pp. 2-16(15). doi: http://dx.doi.org/10.2174/157016411794697354


Identification of contractile vacuole proteins in Trypanosoma cruzi

Paul N. Ulrich, Veronica Jimenez equal contributor, Miyoung Park, Vicente P. Martins, James Atwood III, Kristen Moles, Dalis Collins, Peter Rohloff, Rick Tarleton, Silvia N. J. Moreno, Ron Orlando, Roberto Docampo
PLOS One. Published: March 18, 2011 DOI: 10.1371/journal.pone.0018013


Protein profile of exosomes from trabecular meshwork cells

WD Stamer, EA Hoffman, JM Luther, DL Hachey, KL Schey
J Proteomics. Author manuscript; available in PMC May 16, 2012.
Published in final edited form as: J Proteomics. May 16, 2011; 74(6): 796–804. Published online Mar 8, 2011. doi: 10.1016/j.jprot.2011.02.024


Differential proteomics of plant development

Takáč T1, Pechan T, Samaj J
J Proteomics. 2011 May 1;74(5):577-88. doi: 10.1016/j.jprot.2011.02.002. Epub 2011 Feb 18


Improving proteome coverage on a LTQ-Orbitrap using design of experiments

Genna L. Andrews, Ralph A. Dean, Adam M. Hawkridge, David C. Muddiman
J Am Soc Mass Spectrom. Author manuscript; available in PMC Apr 1, 2012.
Published in final edited form as: J Am Soc Mass Spectrom. Apr 2011; 22(4): 773–783. Published online Feb 15, 2011. doi: 10.1007/s13361-011-0075-2


Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS

Emine Gokce, Genna L. Andrews, Ralph A. Dean, David C. Muddiman
J Chromatogr B Analyt Technol Biomed Life Sci. Author manuscript; available in PMC Jul 8, 2013.
Published in final edited form as: J Chromatogr B Analyt Technol Biomed Life Sci. Mar 15, 2011; 879(0): 610–614. Published online Feb 4, 2011. doi: 10.1016/j.jchromb.2011.01.032


Differential epithelial and stromal protein profiles in keratoconus and normal corneas

Joseph R, Srivastava OP, Pfister RR
Exp Eye Res. 2011 Apr;92(4):282-98. doi: 10.1016/j.exer.2011.01.008. Epub 2011 Jan 31


Less label, more free: Approaches in label-free quantitative mass spectrometry

Neilson KA1, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, van Sluyter SC, Haynes PA
Proteomics. 2011 Feb;11(4):535-53. doi: 10.1002/pmic.201000553. Epub 2011 Jan 17


Direct comparison of stable isotope labeling by amino acids in cell culture and spectral counting for quantitative proteomics

Collier TS, Sarkar P, Franck WL, Rao BM, Dean RA, Muddiman DC
Anal Chem. 2010 Oct 15;82(20):8696-702. doi: 10.1021/ac101978b


A Comprehensive Qualitative and Quantitative Suite for Proteomics

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