Robert Moritz, PhD


Send Email

(206) 732-1244


Dr. Robert Moritz, a native of Australia, joined the ISB faculty in mid 2008 as Associate Professor and Director of Proteomics. Dr. Moritz began his work in 1983 in the Joint Protein Structure laboratory of Prof. Richard J. Simpson (JPSL-Ludwig Institute for Cancer Research, and The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia). During his 25 years at JPSL, Dr. Moritz designed and implemented a number of technologies currently used in many proteomics laboratories across the globe. Examples include technologies such as the development of micro-chromatography for proteomics from the late 1980’s to its current day implementation, a micro-fractionation technique widely used by many laboratories worldwide. His collaborative research into cytokine biochemistry, protein-receptor chemistry and cellular biochemistry culminated in the novel identification of a number of proteins (e.g., IL-6, IL-9 A33 ligand, DIABLO, as well as several others), their interacting partners, and 3-dimensional structures of their cell surface receptors important in human health concerns such as cancer and inflammation. During his time at JPSL, Dr. Moritz progressed through the ranks whilst obtaining his Bachelor’s degree in Biochemistry with first-class Honors, and his Ph.D., from the University of Melbourne.

Dr. Moritz has brought wide-ranging skills and expertise to ISB, much of it drawn from his Australian experience. There, in 2005, he conceptualized a shared proteomics high-performance computing system, organized a consortia of proteomic scientists from all states in Australia, and proposed a computational system specifically for proteomics data analysis for all Australian researchers to access. For this work, in 2006, he was awarded an enabling grant from the Australian National Health and Medical Research Council worth AUS$2M. With that award, he established a bioinformatics center in Australia that enabled proteomic researchers anywhere in the country to analyze mass spectrometry data. It was the first effort on a national scale to bring proteomic data analysis and algorithms to any researcher in the whole country without the need for them to build their own bioinformatics group. In late 2006, the Australian Proteomics Computational Facility (APCF, was inaugurated, and Dr. Moritz remains as Director of the APCF. The dedicated proteomics data analysis facility is equipped with a 1000 CPU high-performance computing cluster, and full-time software engineers for the continued development of proteomics algorithms and data validation. This facility serves all researchers in Australia and others regardless of their global geographical location. He is continuing that work at ISB by expanding the ISB proteomics centre into a national facility with online tools for data analysis.

PhD, University of Melbourne, Australia

Proteomics, protein chemistry, technology development


Keller A, Bader S.L, Shteynberg D, Hood L, Moritz RL.  2015.  Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data Independent Acquisition MS using SWATHProphet. Molecular & cellular proteomics : MCP.

Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.  2015.  Kojak: Efficient analysis of chemically cross-linked protein complexes.. J Proteome Res.

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.  2015.  Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics. Clinical applications.


Vialas V., Sun Z, Y. Loureiro PCV, Carrascal M., Abian J., Monteoliva L., Deutsch EW, Aebersold R, Moritz RL, Gil C..  2014.  A Candida albicans PeptideAtlas. Journal of proteomics. 97:62-8.

Muller EEL, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA,Roume H, Lin J, May P, Hicks ND et al..  2014.  Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.. Nat Commun. 5:5603.

Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L,Bernhardt J, Salazar MG, Sun Z, Shteynberg D et al..  2014.  Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells.. Front Microbiol. 5:392.

Lindner SE, Sartain MJ, Hayes K, Harupa A, Moritz RL, Kappe SHI, Vaughan AM.  2014.  Enzymes involved in plastid-targeted phosphatidic acid synthesis are essential for Plasmodium yoelii liver-stage development.. Mol Microbiol. 91(4):679-93.

Bundgaard L, Jacobsen S, Sørensen MAamand, Sun Z, Deutsch EW, Moritz RL,Bendixen E.  2014.  The Equine PeptideAtlas–a resource for developing proteomics‐based veterinary research. Proteomics.

Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR,Yates JR, MacCoss MJ, Moritz RL et al..  2014.  Kinetochore Biorientation in Saccharomyces cerevisiae Requires a Tightly Folded Conformation of the Ndc80 Complex..Genetics.

Kusebauch U, Ortega C., Ollodart A., Rogers RS, Sherman DR, Moritz RL,Grundner C..  2014.  Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proceedings of the National Academy of Sciences of the United States of America.

Carpp L.N, Rogers RS, Moritz RL, Aitchison JD.  2014.  Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection. Molecular & cellular proteomics : MCP.

Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND.  2014.  Quantitative Proteomic Analysis Reveals Effects of Epidermal Growth Factor Receptor (EGFR) on Invasion-promoting Proteins Secreted by Glioblastoma Cells.. Mol Cell Proteomics. 13(10):2618-31.

Rosenberger G, Koh CChiek, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M,Liu Y, Caron E, Vichalkovski A et al..  2014.  A repository of assays to quantify 10,000 human proteins by SWATH-MS. SCIENTIFIC DATA. 1

Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL.  2014.  Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis … [et al.]. 46:13251-132528.


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.


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.


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.


Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon P, Shteynberg D,Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA et al..  2010.  Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics. 9:2076-88.


Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL et al..  2008.  Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 26:164-7.


Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H,Apweiler R, Haab BB, Simpson RJ, Eddes JS et al..  2005.  Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5:3226-45.