Data Sets

PubMed Reference and Associated DataSets

Reference   Data
Sancak, et al. EMRE is an Essential Component of the Mitochondrial Calcium Uniporter Complex. Science 2013. PubMed Link. Broad FTP
Chalkley , et al. iPRG 2012: A Study on Detecting Modified Peptides in a Complex Mixture. Mol Cell Proteomics 2013 [Epub Oct 31] MassIVE
Guthals, et al. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. J Proteome Res. 2013, 12(6), 2846-57. PubMed Link. MassIVE
Udeshi, et al. Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments. Mol Cell Proteomics. 2013 Mar;12(3):825-31. PubMed Link. Broad FTP
Rhee, et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. 2013 Mar;339(6125):1328-1331. PubMed Link. Broad FTP
Guthals, et al. Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics. 2012 Oct;11(10):1084-96. PubMed Link. MassIVE
Ku, et al. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol. 2012 Oct 3;13(10):R85. PubMed Link.                 Broad FTP
Kuhn, et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics. 2012 Jun;11(6):M111.013854. PubMed Link. Broad FTP
Mertins, et al. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics. 2012 Jun;11(6):M111.014423. PubMed Link. MassIVE
Naba, et al. The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics. 2012 Apr;11(4):M111.014647. PubMed Link. MassIVE
Udeshi, et al. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol Cell Proteomics. 2012 May;11(5):148-59. PubMed Link. MassIVE
Addona, et al. A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. 2011 Jun 19;29(7):635-43. PubMed Link. Broad FTP
Burgener, et al. Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers. J Proteome Res. 2011 Nov 4;10(11):5139-49. PubMed Link. Broad FTP
Chevrier, et all. Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits. Cell, 2011, 147(4) 853-867. doi: 10.1016/j.cell.2011.10.022. PubMed Link. MassIVE
Guan, et al. Cdk5 is required for memory function and hippocampal plasticity via the cAMP signaling pathway. PLoS One. 2011;6(9):e25735. PubMed Link. MassIVE
iPRG-2011: Study Materials & Additional Data for Identification of Electron Transfer Dissociation (ETD) Mass Spectra Broad FTP
Berven, et al. Optimizing performance of glycopeptide capture for plasma proteomics. J Proteome Res. 2010 Apr 5;9(4):1706-15. PubMed Link. MassIVE
iPRG-2010: Study Materials & Additional Data for Phosphopeptide Identification Broad FTP
Paulovich,et al. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. 2010 Mol Cell Proteomics 9:242-254. PubMed Link. CPTAC DCC
Rudnick, et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. 2010 Mol Cell Proteomics 9:225-241. PubMed Link. CPTAC DCC
Tabb, et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. 2010 J Proteome Res 9(2):761-76. PubMed Link. CPTAC DCC
Addona, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009 Jul;27(7):633-41. PubMed Link. MassIVE
Burkard, et al. Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells. PLoS Biol. 2009 May 5;7(5):e1000111. PubMed Link. MassIVE
Du, et al. Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy. Nat Biotech, 2009, 27, 77-83. PubMed Link. MassIVE
Fusaro, et al. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009 Feb;27(2):190-8. PubMed Link. Broad FTP
Hahn, et al. Proteomic and genetic approaches identify Syk as an AML target. Cancer Cell. 2009 Oct 6;16(4):281-94. PubMed Link. MassIVE
Kuhn, et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem. 2009 Jun;55(6):1108-17. PubMed Link. Broad FTP
Rudomin, et al. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). J Proteome Res. 2009 Jun;8(6):3154-60. PubMed Link. MassIVE
Jaffe, et al. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol Cell Proteomics. 2008 Oct;7(10):1952-62. PubMed Link. MassIVE
Pagliarini, et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell. 2008 Jul 11;134(1):112-23. PubMed Link. Broad FTP
Bandeira, et al. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics. 2007 Jul;6(7):1123-34. PubMed Link. Broad FTP
Keshishian, et al. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics. 2007 Dec;6(12):2212-29. PubMed Link. MassIVE
Lowery, et al. Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate. EMBO J. 2007 May 2;26(9):2262-73. PubMed Link. MassIVE
Gillette_NCI_2006. Mouse Models Dataset: Tyler Jacks Lab, BDI. Broad FTP
Jaffe, et al. PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics. 2006 Oct;5(10):1927-41. PubMed Link. Broad FTP