Welcome to the bioinformatics tools webpage of the Protein Chemistry and Proteomics Laboratory
In this page you will find information about several programs developed by our group for the analysis and intepretation of mass spectrometry data obtained in high-througput proteomics experiments
About us
Our group are devoted to the development and implementation of novel mass spectrometry and proteomics approaches and their application to several research projects in the cardiovascular area. They currently include the study of molecular mechanisms underlying angiogenesis in vascular endothelium, the analysis of protein modifications in response to oxidative stress, the study of protein-protein interactions related to endothelium functionality and the dynamic study of the mitochondrial membrane proteome in animal models of vascular disfunction.
Among our developments are novel bioinformatics tools for de novo peptide sequencing, validation of peptide identifications in large-scale protein characterization experiments and relative protein quantification by stable-isotope labeling. Some of these tools are available for the public domain and can be downloaded from this webpage.
Proteomics lectures in Universidad Francisco de Vitoria 2008/2009
Here you can find some resources for the bioinformatics practical lesson:
- The powerpoint presentation is available here
- Statistical validation methods ppt presentation is available here
- Proposed exercises list
- MS/MS spectra for the 2nd exercise: dtas_300.zip
- The data for the 3rd exercise: ppw_A23.txt
pRatio 5.0.1 has been released!
News: isoelectric point calculation. Coming soon an integration of isoelectric point value to calculate the FDR.
- ask for the program at: pnavarro.at.cbm.uam.es
QuiXoT 1.1.00 Released
- QuiXoT is a program developed for the comparative analysis of proteomes by stable 18O-isotope labeling in a large-scale experiments using linear ion trap mass spectrometry
- QuiXoT determines the proportion of peptides coming from the control and the target samples and at the same time calculates labeling efficiency of ech one of the peptides. This is done by fitting the ZoomScan envelope using a kinetic model, as described in our recent papers ( López-Ferrer et al, 2006; Ramos et al, MCP, 2007 ). Calculation of labeling efficiency avoids artifacts due to incomplete labelling and is particularly useful to check the validity of large-scale peptide quantification experiments. It is also very useful to tune up methods aimed to optimizing labeling conditions.
- QuiXoT includes a powerful statistical tool based on a novel model that allows for a highly automated interpretation and validation of quantitative proteomics data even in very large quantification experiments (hundreds of fractions). Details about this new algorithm will be published soon.
- A demo version of QuiXoT is available upon request.
pRatio 4.0.6 has been released!
Now the pRatio includes a CSV output, in order to make a faster insight into the identified peptides.
- pRatio instructions
- pRatio program download
- pRatio source code in C# download
RAW data from Jurkat nucleii available
For the MCP manuscript "Properties of average score distributions of SEQUEST: the Probability Ratio method", Mol.Cell.Proteomics, feb 25 2008, in Press
Salvador Martínez Bartolomé#,Ω,$, Pedro Navarro#,$, Fernando Martín-Maroto&,$, Daniel López Ferrer#,δ, Antonio Ramos-Fernández#,Ω, Margarita Villar,#,£ Josefa P. García-Ruiz#, and Jesús Vázquez#,*
from the #Protein Chemistry and Proteomics Laboratory, Centro de Biología Molecular “Severo Ochoa”-CSIC, 28049 Cantoblanco, Madrid, Spain, and &ThermoElectron Corp, River Oaks Parkway 355, San Jose, CA, USA
- Raw data available clicking here
Proteomics lectures in Universidad Francisco de Vitoria 2007/2008
Here you can find some resources for the bioinformatics practical lesson:
- The powerpoint presentation is available here
- Proposed exercises list
- The data for the 1st exercise: ppw_A23.txt
- MS/MS spectra for the 3rd exercise: ppw_A23_MSMS.zip
pRatio 4.0.4
- pRatio is a tool that calculates the probability ratio in large-scale peptide identification experiments.
- The probability ratio is a probability-based score that incorporates a correction for spectrum quality. This new algorithm is described in a paper that is currently under revision and that will be published soon.
- pRatio is a robust and non-parametric program that does not need any kind of spectra classification and is hence recommened for a fully automated, unattended peptide validation.
- The program also calculates the false discovery rate (FDR) associated to each one of the tentative peptide identifications from the data obtained by a parallel search against a decoy database.
- pRatio instructions
- pRatio program download
- pRatio source code in C# download
QuiXoT 1.0.83
- QuiXoT is a program developed for the comparative analysis of proteomes by stable 18O-isotope labeling in a large-scale experiments using linear ion trap mass spectrometry
- QuiXoT determines the proportion of peptides coming from the control and the target samples and at the same time calculates labeling efficiency of ech one of the peptides. This is done by fitting the ZoomScan envelope using a kinetic model, as described in our recent papers ( López-Ferrer et al, 2006; Ramos et al, MCP, 2007 ). Calculation of labeling efficiency avoids artifacts due to incomplete labelling and is particularly useful to check the validity of large-scale peptide quantification experiments. It is also very useful to tune up methods aimed to optimizing labeling conditions.
- QuiXoT includes a powerful statistical tool based on a novel model that allows for a highly automated interpretation and validation of quantitative proteomics data even in very large quantification experiments (hundreds of fractions). Details about this new algorithm will be published soon.
- A demo version of QuiXoT is available upon request.