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FHCRC MALDI Dilution Processed Data

Dataset Abstract:

These data come from a dilution experiment aimed at elucidating which features in MALDI-TOF mass spectrometry data are informative for quantifying peptide content. The details of the experiment are described in [1]. The primary dataset consists of 250 spectra collected from 5 different serum sources (5 people from a health study), each subject to 10 different concentrations of a peptide mixture that contained several known peptides. Each of the 50 prepared samples were spotted, randomly, 5 times each on a single plate producing a total of 5x10x5 = 250 spectra. An additional 30 spectra arise from: 2 replicate spectra from each of the 10 concentrations of the peptide mixture, plus 2 replicates of serum-only spectra from each of the 5 serum samples. NOTE: An error was made during the process of randomly spotting samples to the plate: one of the replicates from concentration 6 was spotted on top of a serum-only sample. The result is that two spectra from this design are missing: serum 1, concentration 6, replicate 4 (column number 36 in Spectra.txt), and serum 4, concentration 0, replicate 2. This left one empty spot on the plate (column number 280 in Spectra.txt) to which we spotted a sample containing only cytochrome c. The latter was not used in any subsequent analysis in [1], and no adjustment was made for former in the analysis in [1] (column #36 was used as is).

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MALDI Dilution Data: Randolph
FHCRC MALDI Dilution Processed Data
Timothy W. Randolph
Fred Hutchinson Cancer Research Center (Data Management and Coordinating Center)
Dale McLerran
Prostate and Urologic
Under Review
This work addresses the problem of extracting signal content from protein mass spectrometry data. A multiscale decomposition of these spectra is used to focus on local scale-based structure by defining scale-specific features. Quantification of features is accompanied by an efficient method for calculating the location of features which avoids estimation of signal-to-noise ratios or bandwidths.
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