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Experimental Errors in QSAR Modeling Sets: What We Can Do and What We Cannot Do.

Zhao L, Wang W, Sedykh A, Zhu H.

ACS Omega. 2017 Jun 30;2(6):2805-2812. doi: 10.1021/acsomega.7b00274. Epub 2017 Jun 19.


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.


Enhanced Detection of Low-Abundance Human Plasma Proteins by Integrating Polyethylene Glycol Fractionation and Immunoaffinity Depletion.

Liu Z, Fan S, Liu H, Yu J, Qiao R, Zhou M, Yang Y, Zhou J, Xie P.

PLoS One. 2016 Nov 10;11(11):e0166306. doi: 10.1371/journal.pone.0166306. eCollection 2016.


A Proteogenomic Approach to Understanding MYC Function in Metastatic Medulloblastoma Tumors.

Staal JA, Pei Y, Rood BR.

Int J Mol Sci. 2016 Oct 19;17(10). pii: E1744. Review.


A multicenter study benchmarks software tools for label-free proteome quantification.

Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S.

Nat Biotechnol. 2016 Nov;34(11):1130-1136. doi: 10.1038/nbt.3685. Epub 2016 Oct 3.


Quantifying differences in cell line population dynamics using CellPD.

Juarez EF, Lau R, Friedman SH, Ghaffarizadeh A, Jonckheere E, Agus DB, Mumenthaler SM, Macklin P.

BMC Syst Biol. 2016 Sep 21;10(1):92.


Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.

Kosti I, Jain N, Aran D, Butte AJ, Sirota M.

Sci Rep. 2016 May 4;6:24799. doi: 10.1038/srep24799.


Publishing confirming and non-confirming data.

Alberts B, Kamb A.

F1000Res. 2016 Feb 4;5:135. doi: 10.12688/f1000research.7847.1. eCollection 2016.


Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts.

Tabb DL, Wang X, Carr SA, Clauser KR, Mertins P, Chambers MC, Holman JD, Wang J, Zhang B, Zimmerman LJ, Chen X, Gunawardena HP, Davies SR, Ellis MJ, Li S, Townsend RR, Boja ES, Ketchum KA, Kinsinger CR, Mesri M, Rodriguez H, Liu T, Kim S, McDermott JE, Payne SH, Petyuk VA, Rodland KD, Smith RD, Yang F, Chan DW, Zhang B, Zhang H, Zhang Z, Zhou JY, Liebler DC.

J Proteome Res. 2016 Mar 4;15(3):691-706. doi: 10.1021/acs.jproteome.5b00859. Epub 2015 Dec 22.


Advances in Proteomic Technologies and Its Contribution to the Field of Cancer.

Mesri M.

Adv Med. 2014;2014:238045. doi: 10.1155/2014/238045. Epub 2014 Sep 7. Review.


The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.

Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL.

Mol Cell Proteomics. 2015 Dec;14(12):3299-309. doi: 10.1074/mcp.O115.051888. Epub 2015 Oct 4.


Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.

Terfve CD, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J.

Nat Commun. 2015 Sep 10;6:8033. doi: 10.1038/ncomms9033.


Compartmentalization of membrane trafficking, glucose transport, glycolysis, actin, tubulin and the proteasome in the cytoplasmic droplet/Hermes body of epididymal sperm.

Au CE, Hermo L, Byrne E, Smirle J, Fazel A, Kearney RE, Smith CE, Vali H, Fernandez-Rodriguez J, Simon PH, Mandato C, Nilsson T, Bergeron JJ.

Open Biol. 2015 Aug;5(8). pii: 150080. doi: 10.1098/rsob.150080.


Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis.

Lin LL, Hsu CL, Hu CW, Ko SY, Hsieh HL, Huang HC, Juan HF.

BMC Genomics. 2015 Jul 18;16:533. doi: 10.1186/s12864-015-1753-4.


MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.

Rardin MJ, Schilling B, Cheng LY, MacLean BX, Sorensen DJ, Sahu AK, MacCoss MJ, Vitek O, Gibson BW.

Mol Cell Proteomics. 2015 Sep;14(9):2405-19. doi: 10.1074/mcp.O115.048181. Epub 2015 May 17.


A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R.

Sci Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. eCollection 2014.


Expression, sorting, and segregation of Golgi proteins during germ cell differentiation in the testis.

Au CE, Hermo L, Byrne E, Smirle J, Fazel A, Simon PH, Kearney RE, Cameron PH, Smith CE, Vali H, Fernandez-Rodriguez J, Ma K, Nilsson T, Bergeron JJ.

Mol Biol Cell. 2015 Nov 5;26(22):4015-32. doi: 10.1091/mbc.E14-12-1632. Epub 2015 Mar 25.


Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC.

Nat Neurosci. 2014 Nov;17(11):1491-9. doi: 10.1038/nn.3829. Epub 2014 Oct 28. Review.


Toward better benchmarking: challenge-based methods assessment in cancer genomics.

Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G.

Genome Biol. 2014 Sep 17;15(9):462. doi: 10.1186/s13059-014-0462-7.

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