Skip to main content

Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.

Publication ,  Journal Article
Lin, SM; Haney, RP; Campa, MJ; Fitzgerald, MC; Patz, EF
Published in: Cancer Inform
2005

The use of MALDI-TOF mass spectrometry as a means of analyzing the proteome has been evaluated extensively in recent years. One of the limitations of this technique that has impeded the development of robust data analysis algorithms is the variability in the location of protein ion signals along the x-axis. We studied technical variations of MALDI-TOF measurements in the context of proteomics profiling. By acquiring a benchmark data set with five replicates, we estimated 76% to 85% of the total variance is due to phase variation. We devised a lobster plot, so named because of the resemblance to a lobster claw, to help detect the phase variation in replicates. We also investigated a peak alignment algorithm to remove the phase variation. This operation is analogous to the normalization step in microarray data analysis. Only after this critical step can features of biological interest be clearly revealed. With the help of principal component analysis, we demonstrated that after peak alignment, the differences among replicates are reduced. We compared this approach to peak alignment with a model-based calibration approach in which there was known information about peaks in common among all spectra. Finally, we examined the potential value at each point in an analysis pipeline of having a set of methods available that includes parametric, semiparametric and nonparametric methods; among such methods are those that benefit from the use of prior information.

Duke Scholars

Published In

Cancer Inform

EISSN

1176-9351

Publication Date

2005

Volume

1

Issue

1

Start / End Page

32 / 40

Location

United States

Related Subject Headings

  • Bioinformatics
  • 4003 Biomedical engineering
  • 3211 Oncology and carcinogenesis
  • 1112 Oncology and Carcinogenesis
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Lin, S. M., Haney, R. P., Campa, M. J., Fitzgerald, M. C., & Patz, E. F. (2005). Characterising phase variations in MALDI-TOF data and correcting them by peak alignment. Cancer Inform, 1(1), 32–40.
Lin, Simon M., Richard P. Haney, Michael J. Campa, Michael C. Fitzgerald, and Edward F. Patz. “Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.Cancer Inform 1, no. 1 (2005): 32–40.
Lin SM, Haney RP, Campa MJ, Fitzgerald MC, Patz EF. Characterising phase variations in MALDI-TOF data and correcting them by peak alignment. Cancer Inform. 2005;1(1):32–40.
Lin, Simon M., et al. “Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.Cancer Inform, vol. 1, no. 1, 2005, pp. 32–40.
Lin SM, Haney RP, Campa MJ, Fitzgerald MC, Patz EF. Characterising phase variations in MALDI-TOF data and correcting them by peak alignment. Cancer Inform. 2005;1(1):32–40.

Published In

Cancer Inform

EISSN

1176-9351

Publication Date

2005

Volume

1

Issue

1

Start / End Page

32 / 40

Location

United States

Related Subject Headings

  • Bioinformatics
  • 4003 Biomedical engineering
  • 3211 Oncology and carcinogenesis
  • 1112 Oncology and Carcinogenesis