Breast2003QC {msBreast}R Documentation

Mass Spectra from a Breast Cancer Quality Control Sample

Description

A data object of class msSet, consisting of 96 mass spectra generated from a pooled sample of nipple aspirate fluid (NAF) from healthy breasts and breasts with cancer. The data set was derived from Breast2003QCList by eliminating the mass region below 950 Da/charge. Please see the references for more details.

Usage

Breast2003QC

Format

An object of msSet. See msSet in package msProcess for details.

Source

http://bioinformatics.mdanderson.org/pubdata.html

References

Coombes, K.R., Tsavachidis, S., Morris, J.S., Baggerly, K.A., and Kuerer, H.M., "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, 5:4107–17, 2005.

Pawlik, T.M., Fritsche, H., Coombes, K.R., Xiao, L., Krishnamurthy, S., Hunt, K.K., Pusztai, L., Chen, J.N., Clarke, C.H., Arun, B., Hung, M.C., and Kuerer, H.M., "Significant differences in nipple aspirate fluid protein expression between healthy women and those with breast cancer demonstrated by time-of-flight mass spectrometry," Breast Cancer Research and Treatment, 89(2):149–57, 2005.

Kuerer, H.M., Coombes, K.R., Chen, J.N., Xiao, L., Clarke, C., Fritsche, H., Krishnamurthy, S., Marcy, S., Hung, M.C., and Hunt, K.K., "Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer," Surgery, 136(5):1061–9, 2004.

Coombes, K.R., Fritsche, Jr., H.A., Clarke, C., Chen, J.N., Baggerly, K.A., Morris, J.S., Xiao, L.C., Hung, M.C., and Kuerer, H.M., "Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization," Clinical Chemistry, 49(10):1615–23, 2003.

See Also

Breast2003QCList.

Examples

if (require("msProcess")) {
if (!exists("Breast2003QC")) data("Breast2003QC", package="msBreast")

## plot a few spectra 
plot(Breast2003QC, subset=1:5)

## image of all spectra 
image(Breast2003QC)
}

[Package msBreast version 1.0.2 Index]