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| Projects | Publications | Members | Collaborators | Go to CPAS |
Wang P, Tang H, Zhang H, Whiteaker J, Paulovich AG, McIntosh M. Normalization regarding non-random missing values in high-throughput mass spectrometry data. Proceedings of the Pacific Symposium on Biocomputing 2006;11:315-326.
Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, MacLean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh M. Computational Proteomics Analysis System (CPAS): An Extensible, Open-source Analytic System for Evaluating and Publishing Proteomic Data and High throughput Biological Experiments. J Proteome Res 2006;5(1):112-121.
Bellew M, Coram M, Fitzgibbon M, Igra M, Randolph T, Wang P, May D, Eng J, Fang R, Lin CW, Chen J, Goodlet D, Whiteaker J, Paulovich A, McIntosh M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006; Advance Access published June 9, 2006. Supplementary material
MacLean B, Eng JK, Beavis RC, McIntosh M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 2006; Advance Access published July 28, 2006. Supplementary material
Wang P, Coram M, Tang H, Fitzgibbon M, Zhang H, Yi E, Aebersold R, McIntosh M. A statistical method for chromatographic alignment of LC-MS data. Biostatistics 2006; Advance Access published August 2, 2006.
May D, Fitzgibbon M, Liu Y, Holzman T, Eng J, Whiteaker J, Paulovich A, McIntosh M. A Platform for Accurate Mass and Time Analyses of Mass Spectrometry Data. Journal of Proteome Research 2007; Advance Access published June 9, 2007.
Matt Fitzgibbon, Qunhua Li, and Martin McIntosh, Modes of Inference for Evaluating the Confidence of Peptide Identifications, Journal of Proteome Research, Web Release Date: 08-Dec-2007.
Loch CM, Ramirez AB, Liu Y, Sather CL, Delrow JJ, Scholler N, Garvik BM, Urban ND, McIntosh MW, Lampe PD (Dec 2007) Use of High Density Antibody Arrays to Validate and Discover Cancer Serum Biomarkers, Molecular Oncology, 1 (3), 313-20
Sato AH, Anderson GL, Urban N, McIntosh MW. Comparing adaptive and non-adaptive algorithms for cancer early detection with novel biomarkers. Cancer Biomarkers. 2006; 2 (3-4):151-162.
Wang P, Tang H, Zhang H, Whiteaker J, Paulovich AG, McIntosh M. Normalization regarding non-random missing values in high-throughput mass spectrometry data. Proceedings of the Pacific Symposium on Biocomputing. 2006; 11: 315-326.
Bogusky M, McIntosh MW. Biomedical informatics for proteomics. Nature. 2003 Mar 13; 422(6928):233-237.
McIntosh MW, Urban N. A parametric empirical Bayes method for cancer screening using longitudinal observations of a biomarker. Biostatistics. 2003 Jan; 4(1):27-40.
Daniel B. Martin, Ted Holzman, Damon May, Amelia Peterson, Ashley Eastham, Jimmy Eng, Martin McIntosh, MRMer: An interactive open-source and cross-platform system for data extraction and visualization of Multiple Reaction Monitoring experiments, (under review)
Matthew Fitzgibbon, Wendy Law, Damon May, Andrea Detter, and Martin McIntosh. Open-source platform for the analysis of liquid chromatography-mass spectrometry (LC-MS) data. Chapter in Clinical Proteomics in the Methods in Molecular Biology series, Humana Press, 2007, Edited by Antonia Vlahou.
Myers T, Law W, Detter A, Eckels J, Eng J, MacLean B, Rauch A, Snelling G, and McIntosh M. Installation and use of the Computational Proteomics Analysis System (CPAS). Chapter in Current Protocols in Bioinformatics, 2007, John Wiley & Sons, Inc. Edited by John Yates.
McIntosh MW, Pepe MS. Combining several screening tests: optimality of the risk score. Biometrics. 2002 Sep; 58(3):657-664.
Whiteaker, J. R.; Zhang, H.; Zhao, L.; Wang, P.; Kelly-Spratt, K. S.; Ivey, R. G.; Piening, B. D.; Feng, L.; Kasarda, E.; Gurley, K. E.; Eng, J. K.; Chodosh, L. A.; Kemp, C. J.; McIntosh, M. W.; Paulovich, A. G, Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer, J. Proteome Res.; (Article); 2007; 6(10); 3962-3975
Faca, V.; Pitteri, S. J.; Newcomb, L.; Glukhova, V.; Phanstiel, D.; Krasnoselsky, A.; Zhang, Q.; Struthers, J.; Wang, H.; Eng, J.; Fitzgibbon, M.; McIntosh, M.; Hanash, S., Contribution of Protein Fractionation to Depth of Analysis of the Serum and Plasma Proteomes, J. Proteome Res.; (Article); 2007; 6(9); 3558-3565
Whiteaker JR, Zhang H, Eng JK, Fang R, Piening BD, Feng LC, Lorentzen TD, Schoenherr RM, Keane JF, Holzman T, Fitzgibbon M, Lin C, Zhang H, Cooke K, Liu T, Camp DG 2nd, Anderson L, Watts J, Smith RD, McIntosh MW, Paulovich AG. Head-to-head comparison of serum fractionation techniques. Journal of Proteome Research. 2007 Feb; 6(2):828-836. doi: 10.1021/pr0604920.
Mannova P, Fang R, Wang H, Deng B, McIntosh MW, Hanash SM, Beretta L. Modification of host lipid raft proteome upon hepatitis C virus replication. Molecular and Cellular Proteomics. 2006 Dec; 5(12):2319-2325.
Abdi F, Quinn JF, Jankovic J, McIntosh M, Leverenz JB, Peskind E, Nixon R, Nutt J, Chung K, Zabetian C, Samii A, Lin M, Hattan S, Pan C, Wang Y, Jin J, Zhu D, Li GJ, Liu Y, Waichunas D, Montine TJ, Zhang J. Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders, Journal of Alzheimer's Disease. 2006 Aug; 9(3):293-348.
Piening BD, Wang P, Bangur CS, Whiteaker J, Zhang H, Feng L-C, Keane JF, Eng JK, Tang H, Prakash A, McIntosh MW, Paulovich A. Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles. Journal of Proteome Research. 2006; 5(7):1527-1534.
Faca V, Coram M, Phanstiel D, Glukhova V, Zhang Q, Fitzgibbon M, McIntosh M, and Hanash S. Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS. Journal of Proteome Reseach. 2006 Aug; 5(8):2009-2018.
Sharon J. Pitteri, Vitor M. Faca, Karen S. Kelly-Spratt, A. Erik Kasarda, Hong Wang, Qing Zhang, Lisa Newcomb, Alexei Krasnoselesky, Sophie Paczesny, Gina Choi, Matthew Fitzgibbon, Martin W. McIntosh, Christopher J. Kemp, Samir M. Hanash, Plasma Proteome Profiling of a Mouse Model of Breast Cancer Identifies a Set of Up-Regulated Proteins In Common with Human Breast Cancer Cells, (in-press Journal of Proteome Research)
Jason D. Thorpe, Xiaobo Duan, Robin Forrest, Kimberly Lowe, Lauren Brown, Elliot Segal, Brad Nelson, Garnet L. Anderson, Martin McIntosh, Nicole Urban, Effects of Blood Collection Conditions on Ovarian Cancer Serum Markers, PlosONE, December 2007/
McIntosh MW, Liu Y, Drescher C, Urban N, Diamandis EP. Validation and characterization of human kallikrein 11 as a serum marker for diagnosis of ovarian carcinoma. Clinical Cancer Research. 2007 Aug 1;13(15 Pt 1):4422-4428. doi: 10.1158/1078-0432.CCR-06-2224.
Simon I, Liu Y, Krall KL, Urban N, Wolfert RL, Kim NW, McIntosh MW. Evaluation of the novel serum markers B7-H4, Spondin 2, and DcR3 for diagnosis and early detection of ovarian cancer. Gynecologic Oncology. 2007 Jul; 106(1):112-118. doi:10.1016/j.ygyno.2007.03.007.
Yaziji H, Battifora H, Barry TS, Hwang HC, Bacchi CE, McIntosh MW, Kussick SJ, Gown AM. Evaluation of 13 Antibodies in the Distinction Between Epitheloid Mesothelinoma and Adenocarcinoma; identification of a Three-Antibody Immunohistochemical Panel with High Sensitivity and Specificity, Modern Pathology. 2006; 19:514- 523.
Fang R, Elias DA, Monroe ME, Shen Y, Mcintosh M, Wang P, Goddard CD, Callister SJ, Moore RJ, Gorby YA, Fredrickson JK, Lipton MS, and Smith RD. Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach. Molecular and Cellular Proteomics. 2006 Apr; 5(4):714-725.
Goodell, V. Salazar LG, Urban N, Drescher CW, Gray H, Swensen RE, McIntosh MW, Disis ML. Antibody Immunity to the p53 Oncogenic Protein Is a Prognostic Indicator in Ovarian Cancer. Journal of Clinical Oncology. 2006 Jan 10; 24(5): 762-8.
Feng Q, Balasubramanian A, Hawes SE, Toure P, Sow PS, Dem A, Dembele B, Critchlow CW, Xi L, Lu H, McIntosh MW, Young AM, Kiviat NB. Detection of Hypermethylated Genes in Biopsies and Exfoliated Cell Samples in Women with and without Cervical Neoplasia and Cervical Cancer, Journal of the National Cancer Institute. 2005 Feb 16; 97(4):273-282.
McIntosh MW, Drescher C, Urban N, Hellstrom KE, Hellstrom I. Combining CA125 and SMR serum markers for diagnosis and early detection of ovarian carcinoma, Gynecologic Oncology. 2004 Oct; 95(1):9-15.
Hellstrom I, Raycraft J, Ledbetter M, Ledbetter J, Schummer M, McIntosh MW, Drescher C, Urban N, Hellstrom KE. The HE4 (WFDC2) protein is a biomarker for ovarian carcinoma. Cancer Research. 2003 Jul 1; 63(13):3695-3700.
DuBois ML, Haimberger ZW, McIntosh MW, Gottschling DE. A quantitative assay for telomere protection in Saccharomyces cerevisiae. Genetics. 2002 Jul; 161(3):995-1013.
Tinker LF, Perri MG, Patterson RE, Bowen DJ, McIntosh M, Parker LM, Sevick MA, Wodarski LA. The effects of physical and emotional status on adherence to a low-fat dietary pattern in the Women's Health Initiative. Journal of the American Dietetic Association. 2002 Jun; 102(6):789-800, 888.
Andersen MR, Peacock S, Nelson J, Wilson S, McIntosh M, Drescher C, Urban N. Worry about ovarian cancer risk and use of ovarian cancer screening by women at risk for ovarian cancer. Gynecologic Oncology. 2002 Apr; 85(1):3-8.
McIntosh MW, Urban N, Karlan B. Generating longitudinal screening algorithms using novel biomarkers for disease. Cancer Epidemiology, Biomarkers and Prevention. 2002 Feb; 11(2):159-166.
Pauler DK, Menon U, McIntosh MW, Symecko HL, Skates SJ, Jacobs IJ. Factors influencing serum CA125II levels in healthy postmenopausal women. Cancer Epidemiology, Biomarkers and Prevention. 2001 May; 10(5):489-493.
Crump KC, McIntosh MW, Urban N, Anderson G, Karlan BY. Ovarian cancer tumor marker behavior in asymptomatic healthy women: implications for screening. Cancer Epidemiology, Biomarkers and Prevention. 2000 Oct; 9(10):1107-1111.
Rauch A, Bellew M, Igra M, MacLean B, Hussey P, Holzman T, Fitzgibbon M, Eng J, Shulman N, DeRosa S, McIntosh M. Introducing the Computational Proteomics Analysis System (CPAS). Presented at the HUPO 4th Annual World Congress, Munich, Germany. Aug 28-Sep 1, 2005.
Bellew M, Coram M, Fitzgibbon M, Igra M, May D, Wang P, Eng J, Fang R, Whiteaker J, Zhang H, Paulovich A, McIntosh M. msInspect: An Informatics Tool for Integrated Analysis of LC-MS and LC-MS/MS Data Generated from Complex Protein Mixtures. Presented at the U.S. HUPO 2nd Annual Conference, Boston, MA. Mar 12-15, 2006.
Fang R, Wang P, Eng J, Mannova P, Beretta L, McIntosh M. A Procedure for Measuring Retention Time Deviations and Improving the Accuracy of Peptide Identifications for LC-MS/MS. Presented at the U.S. HUPO 2nd Annual Conference, Boston, MA. Mar 12-15, 2006.
Fang R, Fitzgibbon M, May D, Mannova P, Wang H, Eng J, Goodlet D, Hanash S, Beretta L, McIntosh M. Analysis Platform for Differential Quantitative Proteomics Analysis. Presented at the 54th ASMS Conference on Mass Spectrometry, Seattle, WA. May 28-Jun 1, 2006.
Igra M, MacLean B, Eckels J, Rauch A, Hussey P, Faca V, Hanash S, McIntosh M. A Platform for Comparative Mass Spectrometry Based Proteomics: Extending CPAS to support quantitation and ProteinProphet. Presented at the 54th ASMS Conference on Mass Spectrometry, Seattle, WA. May 28-Jun 1, 2006.
MacLean B, Eng J, Beavis R, McIntosh M. An open-source framework for evaluating MS/MS score functions: "pluggable scoring" in X! TANDEM. Presented at the 54th ASMS Conference on Mass Spectrometry, Seattle, WA. May 28-Jun 1, 2006.
May D, Fitzgibbon F, McIntosh M. Post-Acquisition Mass Calibration and Filtering of High-Resolution Mass Spectrometry Data. Presented at USHUPO, Seattle, WA, 2007.
Law W, May D, McIntosh M. Quantitative Accurate Mass Methods for Mass Spectrometry Signal Processing Analysis Integrated into an Open-Source Platform. Presented at Canary Fund's EDI Symposium, Palo Alto, CA, 2007.