INTRO
This package was produced as part of National Cancer Institute's caBIG project
(https://cabig.nci.nih.gov/) and is also aviable for download from NCI Center 
for Bioinformatics (http://ncicb.nci.nih.gov/download/index.jsp) website as 
well as CRAN (http://cran.r-project.org/) website. 

INSTALATION FAQ
In current version of R (2.1.1 and up) some people expirience problems with 
installing the package due to inability to find 'PROcess' package, which resides 
in "BioConductor" repository. To make the process smoother one should add 
"BioConductor" to the list of repositories, before the instalation of the 
package. Use "utils::setRepositories()" or "Pakages / Select repositories" 
menu.

DOCUMENTATION
See R_home/library/caMassClass/doc for  following documentation:
- 'caMassClass-road_map.pdf' - one-page flow chart showing how 
   functions in this library suppose to interract with each other.
- 'caMassClass-presentation.pdf' - up-to-date presentation showing how to use 
   the package including some examples.
- 'caMassClass-old_manual.pdf' - older document, not always up to date.

DATA SOURCES
The package was tested on SELDI data produced by:
- Center for Prostate Disease Research (http://www.cpdr.org/) 
- Eastern Virginia Medical School's The Virginia Prostate Center 
  (http://www.evms.edu/vpc/seldi/index.html) 
- NCI's Center for Cancer Research 
  (http://home.ccr.cancer.gov/ncifdaproteomics/ppatterns.asp)

OTHER RELATED PROJECTS
Other packages related to proteomics mass spectrometry, availble from CRAN or 
BioConductor websites:
- PROcess - "A package for processing protein mass spectrometry data"
- ppc - "Sample classification of protein mass spectra by peak probabilty 
        contrasts"
- msBase - "Basic classes and methods for mass spectrometric mass list 
  manipulation"
- msCalib - "Calibration and filtering methods for calibration of mass 
  spectrometric peptide mass lists. Includes methods for internal, external 
  calibration of mass lists. Provides methods for filtering chemical noise and 
  peptide contaminants."
- msInspect - "msInspect allows you to view mass spectrometry (MS1) data in an 
  mzXML file. You can use msInspects built-in tools to inspect data, identify 
  peptide features, generate peptide arrays using data from multiple runs, and 
  export data to external applications for further analysis and collaboration. 
  We are also developing tools for protein identification directly from MS1 
  data using Fasta files. msInspect is an open source application written in 
  Java". Found at edi.fhcrc.org/download/ms1/msInspect_UserGuide_070105.pdf and
  proteomics.fhcrc.org/CPAS
- RProtiomics - NCI funded project not in form of R packages:
  http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/rproteomics/

====================================================\==========================                 
 Jarek Tuszynski, PhD.                           o / \ 
 Science Applications International Corporation  <\__,|  
 (703) 676-4192                                   ">   \
 Jaroslaw.W.Tuszynski@saic.com                     `    \

