SASPECT (version 0.1-1)

mouseTissue: LC MS/MS Data from Mouse Model

Description

An Example data for package SASPECT

Usage

data(mouseTissue)

Value

mouseTissue is a list of four components:

peptideData

a list of two numeric matrices, PeptideCount and PeptideConfidence. The columns correspond to 20 LC-MS/MS experiments, and rows correspond to 333 peptides. PeptideCount records the total spectral counts of each peptide in each experiment. PeptideConfidence tracks the highest PeptideProphet score of each peptide identification in each experiment in the database search procedure.

pep.set

a character vector of length 333, recording the peptide IDs.

pep.pro.name

a character matrix consisting of 15579 rows and 2 columns. The first column is a vector of mouse protein IDs (IPI numbers), while the second column gives the names of the peptides matching to the mouse proteins in the first column.

run.group.info

a data frame consiting of 2 rows and 2 columns, which indicates the case status and the sample size of each group.

Details

This data example is from the mouse study described in Whiteaker et. al. 2007. It contains the information of 333 peptides from 20 LC-MS/MS experiments (10 from the normal group and 10 from the control group).

References

Whiteaker, J. R., Zhang, H., Zhao, L., Wang, P., Kelly-Spratt, K. S., Ivey, R. G., Piening, B. D., Feng, L., Kasarda, E., Gurley, K. E., Eng, J. K., Chodosh, L. A., Kemp, C. J., McIntosh, M. W., Paulovich, A. G (2007) Integrated Pipeline for Mass Spectrometry-Based Discovery and Confirmation of Biomarkers Demonstrated in a Mouse Model of Breast Cancer. J. Proteome Res., 6(10); 3962-3975.

Wang, P., Liu, Y., McIntosh, M. W., Paulovich, A. G (2008) Significant analysis for comparative proteomics studies using label free LC-MS/MS experiments.