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Analysis of Mass Spectrometry Profiles of the Serum Proteome - Reply

Department of Biostatistics, and Applied Mathematics, University of Texas, M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Box 447, Houston, TX 77030, Fax 713-563-4242

^aE-mail kcoombes{at}mdanderson.org

To the Editor:

I am glad to see that Drs. Fung and Gavin find so much to agree with in my editorial (1). I would, however, like to briefly address their concerns. First, my claim that the Ciphergen software is "extremely conservative" about calling peaks is based on an analysis performed with 24 replicate spectra, which will be published elsewhere (2). We have made the raw spectra available at http://bioinformatics.mdanderson.org/Supplements/Datasets/KuererQC. I urge interested readers to download the data and test the conclusions for themselves. Second, my statement that their baseline correction introduces "substantial bias" should be clarified. Every baseline algorithm I have investigated (including the one we use in our own analyses) introduces substantial bias in peak heights in some portion of the spectrum. In my opinion, the difficulty arises because we do not have a good theoretical understanding of the processes that shape the baseline and must resort to ad hoc algorithms to remove it. One advance in the report by Malyarenko et al. (3) is an explanation of how the physics of the ion detector contributes to the baseline; this is an important first step toward better baseline correction.

References

1. Coombes KR. Analysis of mass spectrometry profiles of the serum proteome. [Editorial]Clin Chem 2005;51:1-2.[Free Full Text]
2. Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Hung MC, Kuerer HM. Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics;in press..
3. Malyarenko DI, Cooke WE, Adam BL, Malik G, Chen H, Tracy ER, et al. Enhancement of sensitivity and resolution of surface-enhanced laser desorption/ionization time-of-flight mass spectrometric records for serum peptides using time-series analysis techniques. Clin Chem 2005;51:65-74.[Abstract/Free Full Text]

This Article Extract Full Text (PDF) Submit an electronic Letter to the Editor about this paper Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Coombes, K. R. Search for Related Content PubMed Articles by Coombes, K. R. Related Collections Proteomics and Protein Markers