Publications

Found 44 results
Filters: Author is Moritz, R. L.  [Clear All Filters]
2013
Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.  2013.  Combining results of multiple search engines in proteomics. Mol Cell Proteomics. 12:2383-93.
Picotti P, Clement-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Rost H, Sun Z, Rinner O, Reiter L et al..  2013.  A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature.
Hoopmann MR, Moritz RL.  2013.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol. 24:31-8.
Sun B, Utleg AG, Hu Z, Qin S, Keller A, Lorang C, Gray L, Brightman A, Lee D, Alexander V et al..  2013.  Glycocapture-Assisted Global Quantitative Proteomics (gagQP) Reveals Multiorgan Responses in Serum Toxicoproteome. Journal of proteome research.
Moruz L., Hoopmann MR, Rosenlund M., Granholm V., Moritz RL, Kall L..  2013.  Mass fingerprinting of complex mixtures: protein inference from high-resolution Peptide masses and predicted retention times. J Proteome Res. 12:5730-41.
Huttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J et al..  2013.  N-Glycoprotein SRMAtlas: a resource of mass-spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Molecular & cellular proteomics : MCP.
Tauro B.J, Mathias RA, Greening D.W, Gopal S.K, Ji H, Kapp EA, Coleman B.M, Hill A.F, Kusebauch U, Hallows JL et al..  2013.  Oncogenic H-Ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition. Mol Cell Proteomics.
Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL.  2013.  The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res. 12:162-71.
Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie T.J, Slagel J, Moritz RL, Hackett M et al..  2013.  A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res. 23:1839-51.
Lindner SE, Swearingen KE, Harupa A, Vaughan AM, Sinnis P, Moritz RL, Kappe SH.  2013.  Total and putative surface proteomics of malaria parasite salivary gland sporozoites. Molecular & cellular proteomics : MCP.
2012
Brusniak MY, Chu CS, Kusebauch U, Sartain MJ, Watts JD, Moritz RL.  2012.  An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology. Proteomics. 12:1176-84.
Gold ES, Ramsey SA, Sartain MJ, Selinummi J, Podolsky I, Rodriguez DJ, Moritz RL, Aderem A.  2012.  ATF3 protects against atherosclerosis by suppressing 25-hydroxycholesterol-induced lipid body formation. The Journal of experimental medicine. 209:807-17.
Bislev SL, Deutsch EW, Sun Z, Farrah T, Aebersold R, Moritz RL, Bendixen E, Codrea MC.  2012.  A Bovine PeptideAtlas of milk and mammary gland proteomes. Proteomics.
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J et al..  2012.  A cross-platform toolkit for mass spectrometry and proteomics. Nature biotechnology. 30:918-20.
Hoopmann MR, Moritz RL.  2012.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Current opinion in biotechnology.
Swearingen KE, Moritz RL.  2012.  High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics. Expert review of proteomics. 9:505-17.
Vidal M, Chan DW, Gerstein M, Mann M, Omenn GS, Tagle D, Sechi S, Apweiler R, Bader J, Barnes S et al..  2012.  The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clinical proteomics. 9:6.
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.  2012.  Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC bioinformatics. 13:324.
Hoopmann MR, MacCoss MJ, Moritz RL.  2012.  Identification of Peptide features in precursor spectra using hardklor and kronik. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 13:Unit1318.
Hood LE, Omenn GS, Moritz RL, Aebersold R, K YR, Amos M, Hunter-Cevera J, Locascio L.  2012.  New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences. Proteomics.
Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Huttenhain R, Schiess R et al..  2012.  PASSEL: The PeptideAtlas SRM Experiment Library. Proteomics.
Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Rontved CM, Aebersold R, Moritz RL, Bendixen E.  2012.  Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus uberis. Journal of proteome research. 11:1832-43.
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B et al..  2012.  Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). Journal of proteome research. 11:1412-1419.
Huttenhain R, Soste M, Selevsek N, Rost H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL et al..  2012.  Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science translational medicine. 4:142ra94.
Qin S, Zhou Y, Lok AS, Tsodikov A, Yan X, Gray L, Yuan M, Moritz RL, Galas D, Omenn GS et al..  2012.  SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients. Proteomics. 12:1244-52.
Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL.  2012.  The State of the Human Proteome in 2012 as Viewed through PeptideAtlas. Journal of proteome research.
Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K et al..  2012.  TraML--A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists. Molecular & cellular proteomics : MCP. 11:R111015040.
2011
Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, Krijgsveld J, Lane WS, Lilley KS, MacCoss MJ, Moritz RL et al..  2011.  The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics. 11:1371-81.
Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J et al..  2011.  ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics. 12:78.
Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Turecek F.  2011.  Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics. J Am Soc Mass Spectrom. 22:13-30.
Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmstrom J, Ossola R et al..  2011.  A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & cellular proteomics : MCP.
Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.  2011.  iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & cellular proteomics : MCP.
Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L.  2011.  jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions. Journal of proteome research.
Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.  2011.  Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Molecular & cellular proteomics : MCP.
Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL et al..  2011.  Parallel evolution of transcriptome architecture during genome reorganization. Genome research. 21:1892-904.
Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R.  2011.  The Protein Information and Property Explorer 2: Gaggle-like exploration of biological proteomic data within one webpage. Proteomics. 11:154-8.
Mathias RA, Chen YS, Goode RJ, Kapp EA, Mathivanan S, Moritz RL, Zhu HJ, Simpson RJ.  2011.  Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: towards developing an MDCK protein database. Proteomics. 11:1238-53.