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Key Publications

If you use LabKey Server for your research, please reference one of these publications about the platform:


Elizabeth Nelson
(206) 489-2564

All of Our Publications

If you need an article reprint, contact us.

Panorama: A Targeted Proteomics Knowledge Base
18 August 2014
High-throughput flow cytometry data normalization for clinical trials
1 March 2014
Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform
30 April 2013
Ancillary study management systems: a review of needs
7 January 2013
A cross-platform toolkit for mass spectrometry and proteomics
30 October 2012
Installation and Use of LabKey Server for Proteomics
1 December 2011
LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays
27 May 2011
LabKey Server: An open source platform for scientific data integration, analysis and collaboration
9 March 2011
The Best of Both Worlds: Integrating a Java Web Application with SAS® Using the SAS/SHARE® Driver for JDBC.
31 March 2010
Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials.
31 August 2008
Precursor-Ion Mass Re-Estimation Improves Peptide Identification on Hybrid Instruments
15 August 2008
A mouse model repository for cancer biomarker discovery
14 July 2008
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
6 October 2007
Installation and use of the Computational Proteomics Analysis System (CPAS)
1 June 2007
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.
27 July 2006
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.
8 June 2006
Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments.
4 April 2006
Our Posters
Performing quality control on targeted proteomics assays using Skyline and Panorama
2 June 2015
Sharing targeted proteomics assays using Skyline and Panorama
10 June 2013
LabKey Server: An Open Source Platform for Large-Scale, Translational Research
10 April 2013
Panorama: A private repository of targeted proteomics assays for Skyline
22 May 2012
Ancillary Study Management Systems: What Do We Need?
22 March 2012
Management and analysis of tandem mass spectrometry data using LabKey Server
17 July 2011
Accelerating AIDS Vaccine Discovery Through the Use of a Collaborative Web-based Information System
7 December 2009
Design for a High Performance, Configurable caGrid Data Services Platform
19 July 2009
Repository for Data and Analyses from Multiparameter Flow Cytometric Assays
9 December 2008
Adaptable Enterprise Pipeline for the Computational Proteomics Analysis System (CPAS)
27 August 2008
Adapting an Existing Data Service to be caBIG™ Silver-level Compliant
22 June 2008
A Clinical Proteomics Data Model for Managing Metadata of Mass Spectrometry Experiments
23 October 2007
An open-source framework for evaluating MS/MS score functions: "pluggable scoring" in X! Tandem
30 August 2006
A Platform for Comparative Mass Spectrometry Based Proteomics: Extending CPAS to support quantitation and ProteinProphet
29 August 2006
Our Case Studies
Harnessing the Web to Accelerate Clinical Research: How a LabKey Solution Helps Scientists Coordinate the Search for an HIV/AIDS Vaccine
23 May 2011
Papers and Posters by Other Authors

Cottingham K. Research Profile: CPAS: A proteomics data management system for the masses. Journal of Proteome Research. 2006;5(1):14.

McIntosh M. Comprehensive Analysis of Complex Proteins with High-Resolution LC-MS Instrumentation. J Biomol Tech. 2007;18(1):81-81.

Myers T, Law W, Eng JK, McIntosh M. Installation and Use of the Computational Proteomics Analysis System (CPAS). In: Baxevanis AD, Petsko GA, Stein LD, Stormo GD, eds. Current Protocols in Bioinformatics. Hoboken, NJ, USA: John Wiley & Sons, Inc.; 2007.

Nelson WD, Viele K, Lynn BC. Adapting Existing Proteomics Tools for Massively Parallel Peptide Discovery (MPPD).  RECOMB Satellite Conference on Computational Proteomics. San Diego, 2010.

Yang L, Chan D, Bhattaru R, Hu B, Schaefer C, Rudriguez H, Kinsinger C. P2-M CPAS-MART, a BioMart-Based Query Application for CPAS Proteomics Repository at NCI. J Biomol Tech. 2008 February; 19(1): 1–72, Sub-article 2.

Reviews Covering LabKey Server

Andrews P, Falkner J. Open Access to Proteomics Data: A Valuable Resource for Biology and Medicine. Journal of Proteome Research. 2007;6(6):2047-2048.

Hamacher M, Stephan C, Meyer HE, Eisenacher M. Data handling and processing in proteomics. Expert Rev Proteomics. 2009;6(3):217-219.

Hanash S. Proteomics Technologies. In: Systems Biomedicine. Academic Press; 2009.

Johnson H, Gaskell SJ. Proteomics gets faster and smarter. Genome Biol. 2006;7(11):331.

Matthiesen R. Methods, algorithms and tools in computational proteomics: A practical point of view. Proteomics. 2007;7(16):2815-2832.

Piggee C. LIMS and the art of MS proteomics . Analytical Chemistry. 2008;80(13):4801-4806.

Schjellerup Philosof R. Computational Proteomics: Approaching Open Source Alternatives for MSE data. 2008.

Stephan C, Kohl M, Turewicz M, et al. Using Laboratory Information Management Systems as central part of a proteomics data workflow. Proteomics. 2010;10(6):1230-1249.

Pratt B. Collaborative Systems Biology: Open Source, Open Data, and Cloud Computing. In Collaborative Computational Technologies for Biomedical Research (eds S. Ekins, M. A. Z. Hupcey and A. J. Williams), 2011, John Wiley & Sons, Inc., Hoboken, NJ, USA.

Research Using LabKey Server


Cha S, Imielinski MB, Rejtar T, et al. In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection (LCM)-LC/MS: Annotation by protein set enrichment analysis (PSEA) and gene ontology (GO). Molecular & Cellular Proteomics. 2010.

Gano JJ, Simon JA. A Proteomic Investigation of Ligand-dependent HSP90 Complexes Reveals CHORDC1 as a Novel ADP-dependent HSP90-interacting Protein. Molecular & Cellular Proteomics. 2010;9(2):255-270.

Goodridge JP, Burian A, Lee N, Geraghty DE. HLA-F Complex without Peptide Binds to MHC Class I Protein in the Open Conformer Form. J Immunol. 2010;184(11):6199-6208.

Kullolli M, Hancock WS, Hincapie M. Automated Platform for Fractionation of Human Plasma Glycoproteome in Clinical Proteomics. Analytical Chemistry. 2010;82(1):115-120.

Li J, Hosseini Moghaddam SH, Chen X, Chen M, Zhong B. Shotgun strategy-based proteome profiling analysis on the head of silkworm Bombyx mori. Amino Acids. 2010;39(3):751-761.

Yu W, Taylor JA, Davis MT, et al. Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines. Proteomics. 2010;10(6):1172-1189.

Zeng Z, Hincapie M, Haab BB, et al. The development of an integrated platform to identify breast cancer glycoproteome changes in human serum . Journal of Chromatography A. 2010;1217(19):3307-3315.

Zornetzer GA, Frieman MB, Rosenzweig E, et al. Transcriptomic analysis reveals a mechanism for a pre-fibrotic phenotype in STAT1 knockout mice during SARS-Coronavirus infection. J Virol. 2010.


Fornek JL, Gillim-Ross L, Santos C, et al. A Single-Amino-Acid Substitution in a Polymerase Protein of an H5N1 Influenza Virus Is Associated with Systemic Infection and Impaired T-Cell Activation in Mice. J. Virol. 2009;83(21):11102-11115.

Katayama H, Paczesny S, Prentice R, et al. Application of serum proteomics to the Women’s Health Initiative conjugated equine estrogens trial reveals a multitude of effects relevant to clinical findings. Genome Med. 2009;1(4):47.

Kollmann TR, Crabtree J, Rein-Weston A, et al. Neonatal Innate TLR-Mediated Responses Are Distinct from Those of Adults. J Immunol. 2009;183(11):7150-7160.

Lazarev AV, Rejtar T, Dai S, Karger BL. Centrifugal methods and devices for rapid in-gel digestion of proteins. Electrophoresis. 2009;30(6):966-973.

Li J, Chen X, Fan W, et al. Proteomic and Bioinformatic Analysis on Endocrine Organs of Domesticated Silkworm, Bombyx mori L. for a Comprehensive Understanding of Their Roles and Relations. Journal of Proteome Research. 2009;8(6):2620-2632.

Pitteri SJ, Hanash SM, Aragaki A, et al. Postmenopausal estrogen and progestin effects on the serum proteome. Genome Med. 1(12):121-121. 2009.

Wang H, Wong C, Chin A, et al. Quantitative Serum Proteomics Using Dual Stable Isotope Coding and nano LC-MS/MSMS. Journal of Proteome Research. 2009;8(12):5412-5422.


Alldridge L, Metodieva G, Greenwood C, et al. Proteome Profiling of Breast Tumors by Gel Electrophoresis and Nanoscale Electrospray Ionization Mass Spectrometry. Journal of Proteome Research. 2008;7(4):1458-1469.

Faça VM, Ventura AP, Fitzgibbon MP, et al. Proteomic Analysis of Ovarian Cancer Cells Reveals Dynamic Processes of Protein Secretion and Shedding of Extra-Cellular Domains. PLoS ONE. 3(6).

Faca VM, Song KS, Wang H, et al. A Mouse to Human Search for Plasma Proteome Changes Associated with Pancreatic Tumor Development. PLoS Med. 2008;5(6):e123.

Fang Q, Strand A, Law W, et al. Brain-specific Proteins Decline in the Cerebrospinal Fluid of Humans with Huntington's Disease. Molecular & Cellular Proteomics. 2009;8(3):451 -466.

Jansen K, Blimkie D, Furlong J, et al. Polychromatic flow cytometric high-throughput assay to analyze the innate immune response to Toll-like receptor stimulation. Journal of Immunological Methods. 2008;336(2):183-192.

Krasnoselsky AL, Faca VM, Pitteri SJ, Zhang Q, Hanash SM. Isoform Analysis of LC−MS/MS Data from Multidimensional Fractionation of the Serum Proteome. Journal of Proteome Research. 2008;7(6):2546-2552.

McElrath MJ, De Rosa SC, Moodie Z, et al. HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case–cohort analysis. The Lancet. 2008;372(9653):1894-1905.

Nelson WD, Viele K, Lynn BC. An integrated approach for automating validation of extracted ion chromatographic peaks. Bioinformatics. 2008;24(18):2103 -2104.

Ramos-Fernández A, Paradela A, Navajas R, Albar JP. Generalized Method for Probability-based Peptide and Protein Identification from Tandem Mass Spectrometry Data and Sequence Database Searching. 2008;7(9):1748-1754.

Zhang Q, Menon R, Deutsch EW, et al. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol. 2008;9(6):R93.


Mato JM, He F, Beretta L. The 2006 Human Liver Proteome Project (HLPP) Workshops . Prot. Clin. Appl. 2007;1(5):442-445.

May D, Fitzgibbon M, Liu Y, et al. A Platform for Accurate Mass and Time Analyses of Mass Spectrometry Data. 2007;6(7):2685-2694.

Pereira-Faca SR, Kuick R, Puravs E, et al. Identification of 14-3-3(theta)as an Antigen that Induces a Humoral Response in Lung Cancer. Cancer Research. 2007;67(24):12000 -12006.

Whiteaker JR, Zhang H, Zhao L, et al. Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer. Journal of Proteome Research. 2007;6(10):3962-3975.


Cottingham K. Proteomics Projects: HUPO HLPP takes on a herculean task. Journal of Proteome Research. 2006;5(9):2077.

Faca V, Coram M, Phanstiel D, et al. Quantitative Analysis of Acrylamide Labeled Serum Proteins by LC−MS/MS. Journal of Proteome Research. 2006;5(8):2009-2018.