Peptrix Files

Welcome to the Peptrix label-free peptide profiling application

Version : 3.2
Date    : 2015 march 5
Author  : Dr. M.K. Titulaer, mktitulaer@telfort.nl

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DESCRIPTION:

Peprix is a software application for label-free peptide
profiling written in Java, using a MySQL database. 
Peptrix is able to detect and identify significantly 
differentially expressed peptides in peptide profiles obtained 
from body fluids of patient and control groups. 
The presented modular software is capable of central storage of 
mass spectra and results in fast analysis. 

The software architecture consists of 4 pillars

1) a Graphical User Interface written in Java, 
2) a MySQL database, which contains all metadata, such as 
   experiment numbers and sample codes, 
3) a FTP (File Transport Protocol) server to store all raw mass 
   spectrometry files and processed data, and 
4) the software package R, which is used for modular 
   statistical calculations, such as the Wilcoxon-Mann-Whitney 
   rank sum test. 

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HISTORY:

version 3.2 : Implementation of msconvert.exe as 
              Thermo Fischer Scientific Orbitrap™ 
              raw to mzxml file converter 
              (http://proteowizard.sourceforge.net/)
version 3.0 : processing Thermo Fischer Scientific Orbitrap™ 
              mass spectrometry data and MS2 identifications
version 2.0 : processing Bruker-Daltonics FT-ICR mass 
              spectrometry data
Version 1.0 : processing Bruker-Daltonics MALDI-TOF mass 
              spectrometry data

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INSTALLATION, SYSTEM REQUIREMENTS, AND BUGS:

see the file installation_instructions.TXT

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DOCUMENTATION:

1) M.K. Titulaer, Candidate Biomarker Discovery for Angiogenesis 
   by Automatic Integration of Orbitrap MS1 Spectral- and X!Tandem 
   MS2 Sequencing Information, Genomics, Proteomics & 
   Bioinformatics 2013 Jun;11(3):182-94. 
   doi: 10.1016/j.gpb.2013.02.002. Epub 2013 Apr 2.

2) M.K. Titulaer, D. de Costa, C. Stingl, Dekker L.J., 
   P.A. Sillevis Smitt, T.M. Luider, Label-free peptide profiling 
   of Orbitrap full mass spectra, BMC Res Notes. 2011 Jan 27; 
   4(1):21. 

3) M.K. Titulaer, D.A.N. Mustafa, I. Siccama, M. Konijnenburg, 
   P.C. Burgers, A.C. Andeweg, P.A.E. Sillevis Smitt, J.M. Kros, 
   and Th. M Luider, A software application for comparing large 
   numbers of high resolution MALDI-FTICR MS spectra demonstrated 
   by searching candidate biomarkers for glioma blood vessel 
   formation, BMC Bioinformatics 9 (2008) 133

4) M.K. Titulaer, I. Siccama, L.J. Dekker, Angelique L.C.T. 
   van.Rijswijk, R.M.A. Heeren, Peter A. Sillevis Smitt, and 
   Theo M. Luider, A database application for pre-processing, 
   storage and comparison of mass spectra derived from patients 
   and controls, BMC Bioinformatics 7 (2006) 403