PubMed Reference and Associated DataSets
| Reference | Data | |
| Abelin, et al. Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity 2017, 46(2): 315-326. PubMed Link. | MassIVE | |
| Huang, et al.Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun 2017, 8:14864. PubMed Link. | CPTAC DCC | |
| Naba, et al. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression. Sci Rep 2017, 7:40495. PubMed Link. | MassIVE | |
| Ngo, et al. Aptamer-Based Proteomic Profiling Reveals Novel Candidate Biomarkers and Pathways in Cardiovascular Disease. Circulation 2016, 134(4):270-285. PubMed Link. | MassIVE | |
| Loh, et al. Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. Cell 2016, 166(5): 1295-1307. PubMed Link. | MassIVE | |
| Mertins, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 2016, 534(7605): 55-62. PubMed Link. | CPTAC DCC | |
| Bao, et al. Mitochondrial dysfunction remodels one-carbon metabolism in human cells. Elife 2016, 5. pii: e10575. PubMed Link. | MassIVE | |
| Abelin, et al. Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. Mol Cell Proteomics 2016, 15(5): 1622-1641. PubMed Link. | MassIVE | |
| Schneider, et al. Rps14 haploinsufficiency causes a block in erythroid differentiation mediated by S100A8 and S100A9. Nat Med 2016, 22(3): 288-297. PubMed Link. | MassIVE | |
| Fields, et al. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Mol Cell 2015, 60(5):816-27. PubMed Link. | MassIVE | |
| Surface, et al. H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs. Cell Rep 2016, pii: S2211-1247(15)01556-9. PubMed Link. | MassIVE | |
| Chen, et al. Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase. Proc Natl Acad Sci U S A 2015, 112(39):12093-8. PubMed Link. | MassIVE | |
| Svinkina, et al. Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow. Mol Cell Proteomics 2015, 14(9):2429-40. PubMed Link. | MassIVE | |
| Krönke, et al. Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS. Nature 2015, 523(7559):183-189. PubMed Link. | MassIVE | |
| Maier, et al. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol Cell Proteomics 2015, 14(6): 1435-1446. PubMed Link. | MassIVE | |
| Keshishian, et al. Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury. Mol Cell Proteomics 2015, pii: mcp.M114.046813. [Epub ahead of print] PubMed Link | MassIVE | |
| Jovanovic, et al. Dynamic profiling of the protein life cycle in response to pathogens. Science 2015, 347(6226): 1259038. PubMed Link | MassIVE | |
| Lu, et al. A Breast Cancer Stem Cell Niche Supported by Juxtacrine Signaling from Monocytes and Macrophages. Nature Cell Biol 2014, 16 (11) 1105-1117. PubMed Link. | MassIVE | |
| Naba, et al. Extracellular Matrix Signatures of Human Primary Metastatic Colon Cancers and their Metastases to Liver. BMC Cancer 2014, 14:518. PubMed Link. | MassIVE | |
| Undheim, et al. Clawing through evolution: Toxin diversification/convergence in the lineage Chilopoda (Centipedes). Mol Biol Evol, 2014, 31 (8): 2124-2148. PubMed Link. | MassIVE | |
| Krönke, et al. Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells. Science 2014, 343, 301-305. PubMed Link. | MassIVE | |
| Naba, et al. Extracellular Matrix Signatures of Human Mammary Carcinoma Identify Novel Metastasis Promoters. eLife, 2014, Mar 11;3:e01308. PubMed Link. | MassIVE | |
| Burgess, et al. Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry. Mol Cell Proteomics. 2014 Apr;13(4):1137-49. PubMed Link. | Broad FTP | |
| Mertins, et al. Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels. Mol Cell Proteomics. 2014 13: 1690-1704. PubMed Link. | CPTAC DCC | |
| Sancak, et al. EMRE is an Essential Component of the Mitochondrial Calcium Uniporter Complex. Science 2013. PubMed Link. | ||
| Chalkley , et al. iPRG 2012: A Study on Detecting Modified Peptides in a Complex Mixture. Mol Cell Proteomics 2014 13: 360-371. PubMed Link. | 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. | ||
| Rhee, et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. 2013 Mar;339(6125):1328-1331. PubMed Link. | ||
| Mertins, et al. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat Methods 2013, 10, 634-7. PubMed Link. | MassIVE | |
| 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 | |
| Wen, et al. Identification of regulators of polyploidization presents therapeutic targetsfor treatment of AMKL. Cell. 2012 150:575-89. PubMed Link. | MassIVE | |
| Raj, et al. Selective killing of cancer cells by a small molecule targeting the stress response to ROS. Nature. 2011 475:231-4. 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. | MassIVE | |
| 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. | ||
| 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. | MassIVE | |
| 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. | MassIVE | |
| Jaffe, et al. PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics. 2006 Oct;5(10):1927-41. PubMed Link. | Broad FTP |
