Quantifying peptide signal in MALDI-TOF mass spectrometry data

Molecular and Cellular Proteomics

Volumn 4, Issue 12, 2005, Pages 1990-1999

  Randolph, Timothy W ^a   Mitchell, Bree L ^a   McLerran, Dale F ^b   Lampe, Paul D ^a,b   Feng, Ziding ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE;

ADULT; AGED; ARTICLE; CALIBRATION; CONTROLLED STUDY; DILUTION; FEMALE; HUMAN; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; SERUM; SIGNAL NOISE RATIO; SIGNAL TRANSDUCTION; STATISTICAL MODEL;

ANIMALS; BIOLOGICAL MARKERS; BLOOD PROTEINS; CATTLE; COMPUTER SIMULATION; FEMALE; HUMANS; INSULIN; MALE; PEPTIDES; REFERENCE VALUES; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SPECTROPHOTOMETRY;

EID: 29244440404     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M500130-MCP200     Document Type: Article

References (14)

1. Baggerly, K. A., Morris, J. S., Edmonson, S. R., and Coombes, K. R. (2005) Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J. Natl. Cancer Inst. 97, 307-309
2. Diamandis, E. P. (2004) Analysis of serum proteomic patterns for early cancer diagnosis: Drawing attention to potential problems. J. Natl. Cancer Inst. 96, 353-356
3. Ransohoff, D. F. (2005) Lessons from controversy: ovarian cancer screening and serum proteomics. J. Natl. Cancer Inst. 97, 315-319
4. Morris, J. S., Coombes, K. R., Koomen, J., Baggerly, K. A., and Kobayashi, R. (2005) Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum. Bioinformatics 21, 1764-1775
5. Coombes, K. R., Fritsche, H. A., Clarke, C., Chen, J. N., Baggerly, K.A., Morris, J. S., Xiao, L. C., Hung, M. C., and Kuerer, H. M. (2003) Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin. Chem. 49, 1615-1623
6. Tibshirani, R., Hastie, T., Narasimhan, B., Soltys, S., Shi, G., Koong, A., and Le, Q.-T. (2004) Sample classification from protein mass spectrometry by 'peak probability contrasts'. Bioinformatics 20, 3034-3044
7. Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K., and Zhao, H. (2003) Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 19, 1636-1643
8. Yasui, Y., McLerran, D., Adam, B. L., Winget, M., Thomquist, M., and Feng, Z. (2003) An automated peak identification/calibration procedure for high-dimensional protein measures from mass spectrometers. J. Biomed. Biotechnol. 2003, 242-248
9. Baggerly, K. A., Morris, J. S., Wang, J., Gold, D., Xiao, L. C., and Goombes, K. R. (2005) A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples. Proteomics 3, 1667-1672
10. Coombes, K. R. (2005) Analysis of mass spectrometry profiles of the serum proteome. Clin. Chem. 51, 1-2
11. Mitchell, B. L., Yasui, Y., Lampe, J. W., Gafken, P. R., and Lampe, P. D. (2005) Evaluation of MALDI-TOF MS proteomic profiling: identification of α2-hs glycoprotein b-chain as a biomarker of diet. Proteomics 5, 2238-2246
12. Percival, D. B., and Walden, A. T. (2000) Wavelet Methods for Time Series Analysis, Cambridge University Press, Cambridge, UK
13. Randolph, T. W., and Yasui, Y. (2005) Multiscale processing of mass spectrometry data. Biometrics, in press
14. Schell, M. J., and Singh, F. (1997) The reduced monotonic regression method. J. Am. Stat. Assoc. 92, 128-135