References Associated with Literature Topic: Other large-scale proteomic analysis Help

Ai HW  (2012) Biochemical analysis with the expanded genetic lexicon. Anal Bioanal Chem 403(8):2089-102
Chan CT, et al.  (2012) Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 3():937
Chen L, et al.  (2012) Analysis of metabolic pathway using hybrid properties. Protein Pept Lett 19(1):99-107
Dos Santos SC, et al.  (2012) Quantitative- and phospho-proteomic analysis of the yeast response to the tyrosine kinase inhibitor imatinib to pharmacoproteomics-guided drug line extension. OMICS 16(10):537-51
Fomenko DE and Gladyshev VN  (2012) Comparative genomics of thiol oxidoreductases reveals widespread and essential functions of thiol-based redox control of cellular processes. Antioxid Redox Signal 16(3):193-201
Homma K, et al.  (2012) Intrinsically disordered regions have specific functions in mitochondrial and nuclear proteins. Mol Biosyst 8(1):247-55
Peterson AC, et al.  (2012) Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol Cell Proteomics 11(11):1475-88
Poulsen JW, et al.  (2012) Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. J Proteomics 75(13):3886-97
Swearingen KE, et al.  (2012) Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Mol Cell Proteomics 11(4):M111.014985
Yang J, et al.  (2012) Integrated phospholipidomics and transcriptomics analysis of Saccharomyces cerevisiae with enhanced tolerance to a mixture of acetic acid, furfural, and phenol. OMICS 16(7-8):374-86
Zhong F, et al.  (2012) Regular Patterns for Proteome-Wide Distribution of Protein Abundance across Species. PLoS One 7(3):e32423
Canelas AB, et al.  (2011) An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab Eng 13(3):294-306
Dearmond PD, et al.  (2011) Thermodynamic analysis of protein-ligand interactions in complex biological mixtures using a shotgun proteomics approach. J Proteome Res 10(11):4948-58
Del Alamo M, et al.  (2011) Defining the Specificity of Cotranslationally Acting Chaperones by Systematic Analysis of mRNAs Associated with Ribosome-Nascent Chain Complexes. PLoS Biol 9(7):e1001100
Drew K, et al.  (2011) The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res 21(11):1981-94
Ellis JJ and Kobe B  (2011) Predicting Protein Kinase Specificity: Predikin Update and Performance in the DREAM4 Challenge. PLoS One 6(7):e21169
Eyers CE, et al.  (2011) CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. Mol Cell Proteomics 10(11):M110.003384
Helsens K, et al.  (2011) Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. J Proteome Res 10(8):3578-89
Kubota T, et al.  (2011) Quantitative proteomic analysis of chromatin reveals that Ctf18 acts in the DNA replication checkpoint. Mol Cell Proteomics 10(7):M110.005561
Lee MV, et al.  (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol 7():514
Tran BQ, et al.  (2011) Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides. J Proteome Res 10(2):800-11
Valentine SJ, et al.  (2011) Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters. J Proteome Res 10(5):2318-29
Wong JW, et al.  (2011) Disulfide Bond Acquisition through Eukaryotic Protein Evolution. Mol Biol Evol 28(1):327-34
Xu Y, et al.  (2011) Mass spectrometry- and lysine amidination-based protocol for thermodynamic analysis of protein folding and ligand binding interactions. Anal Chem 83(9):3555-62
de Brevern AG, et al.  (2011) Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet. J Theor Biol 276(1):209-17
Breitkreutz A, et al.  (2010) A global protein kinase and phosphatase interaction network in yeast. Science 328(5981):1043-6
Fendt SM and Sauer U  (2010) Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates. BMC Syst Biol 4():12
Ghosh K and Dill K  (2010) Cellular proteomes have broad distributions of protein stability. Biophys J 99(12):3996-4002
Helbig AO, et al.  (2010) Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Mol Cell Proteomics 9(5):928-39
Levy ED  (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 403(4):660-70