Quality Control Study for Proteomics of Nipple Aspirate Fluid

In the paper by Coombes et al, (Proteomics 2005; to appear; see also the preliminary Technical Report (UTMDABTR-001-04)), we described the Cromwell package that we use to process mass spectrometry data. In that paper, we illustrate the method using a set of 24 quality control spectra from a breast cancer study. These raw spectra and additional scripts used in the p[rocessing are available here:

• Text file containing an outline of the processing steps and file organization.
• Zip file containing 24 XML files with the raw spectra.
• Zip file containing the additional 72 XML files with the raw spectra from 2 spots per chip.
• Version 4 binary MATLAB file containing all 24 raw spectra oin a single matrix.
• Version 4 binary MATLAB file containing the vector of M/Z values.
• Comma-separated values file containing the list of peaks found by the Ciphergen spectra using the default settings.
• Comma-separated values file containing the list of peaks found by the Ciphergen spectra after setting the sensitivity to "maximum".
• Tab-separated-values text file containing the union of all peaks found in the 24 spectra by the Cromwell package.
• Tab-separated-values text file containing a summary, after merging, of the distinct peaks found in this data set.
• Zip file containing additional perl scripts and MATLAB scripts used in processing the data.
• The Cromwell Package
• Cromwell uses the Rice Wavelet Toolbox

More details on the breast cancer study from which these QC spectra were derived can be found in:

1. Pawlik TM, Fritsche H, Coombes KR, Xiao L, Krishnamurthy S, Hunt KK, Pusztai L, Chen JN, Clarke CH, Arun B, Hung MC, Kuerer HM. 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 Res Treat. 2005 Jan;89(2):149-57. Abstract
2. Kuerer HM, Coombes KR, Chen JN, Xiao L, Clarke C, Fritsche H, Krishnamurthy S, Marcy S, Hung MC, Hunt KK. Association between ductal fluid proteomic expression profiles and the presence of lymph node metastases in women with breast cancer. Surgery. 2004 Nov;136(5):1061-9. Abstract
3. Coombes KR, Fritsche HA Jr, Clarke C, Chen JN, Baggerly KA, Morris JS, Xiao LC, Hung MC, Kuerer HM. Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization. Clin Chem. 2003 Oct;49(10):1615-23. Abstract