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Projects lead by the ICAR group

[ Popitam ] [ Aldente ] [ swissPIT ] [ SPUMS ] [ ClinicalMS ]

Introduction

The Identification and Characterisation (ICAR) axis is one of the three principle research axes of the PIG group. Identification and characterization of all proteins expressed by a genome in biological samples represent major challenges in proteomics. Today commonly used approaches combine protein separation with mass spectrometry (MS) analysis, including peptide mass fingerprinting (PMF) analysis and tandem MS (MS/MS) analysis. Although automation is often possible, a number of limitations still adversely affect the rate of protein identification and annotation in databases. Mass spectrometry produces large volumes of data that can be used, on the one hand to search protein as well as genomic databases in order to identify the analysed proteins, and on the other hand to partially characterize the proteins previously separated, that is to search for possible post-translational modifications. One important activity of the group is the design of new algorithms for the identification and characterisation of proteins from PMF and MS-MS data.

Popitam

web interface

Description

Popitam is a method designed to characterize peptides with mutations or unexpected post-translational modifications using MS/MS data. In short, Popitam reduces the spectrum space by using database information to exclusively extract tags that are consistent with theoretical peptides and constructs several tag scenarios for each theoretical peptide. Each scenario is scored according to a function that has been generated using Genetic Programming. The theoretical peptide with the highest scoring scenario is proposed as identification of the spectrum. Possible modifications on one (or any of several adjacent amino acids) are represented by their delta mass values.

Publications

Hernandez P, Peptide Identification by Tandem Mass Spectrometry: A Tag-Oriented Open-Modification Search Method, Thesis work, 2005. [pdf]
Hernandez P, Gras R, Frey J, Appel RD, Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data, Proteomics. 2003 Jun;3(6):870-8. [PubMed]

Aldente

web interface

Description

Aldente is a tool to identify proteins from peptide mass fingerprinting data. Aldente uses the Hough transform to determine the mass spectrometer deviation, to realign the experimental masses and to exclude outliers. This tool has other unique advantages and features: it extensively uses the Swiss-Prot annotations (PTM, alternative splicing, etc.) and it is completely interconnected with other ExPASy proteomics tools, offering the functionality of protein characterization as part of the identification procedure; the scores may be tailored by fully customizable parameters; besides from the usual chemical amino acid modifications, it also considers any user-defined modifications, such as alkylation products on cysteine residues, with the possibility to define their contribution to the score.

Publications

Tuloup M, Hernandez C, Coro I, Hoogland C, Binz PA, Appel RD. Aldente and BioGraph : An improved peptide mass fingerprinting protein identification environment, Congress of the Swiss Proteomics Society. Basel: Dec. 2003: 174-176. [Abstract]

swissPIT

web interface

Description

SwissPIT (swiss Protein Identification Toolbox) is a pipeline for knowledge extraction from MS data. Too often, proteomics scientists multiply manual procedures to efficiently analyse mass spectrometry data. Software tools are run several times in order to empirically discover the best parameter settings. When various strategies of MS analysis are used, the results are manually selected and combined. In most situations though, only one single tool is used for protein identification along with a unique parameter setting. Many spectra are thus missed due to inappropriate parameter values, to inadequate filtering or simply to under-performance of certain scoring schemes for the quality of the spectra at hand. The swissPIT platform aims at providing a flexible automation of computer tasks, as well as a combination of different workflow strategies, which are thus necessary to enhance data analysis, to improve the quality and confidence in the identification and characterization results, to reduce human interaction and to achieve high-throughput analysis.

Publications

Quandt A, Hernandez P, Kunzst P, Pautasso C, Tuloup M, Hernandez C, Appel RD, Grid-based analysis of tandem mass spectrometry data in clinical proteomics, Stud Health Technol Inform. 2007;126:13-22. [PubMed]

SPUMS

The goal of SPUMS is to design and implement an efficient platform (software and database) that can automatically and quickly recognise the effect(s) induced by the variable presence of drug chemical fragments on circulating peptides in mass spectra obtained from patient blood samples.

ClinicalMS

The goal of ClinicalMS is to design and implement an efficient platform (software and database) that can automatically and quickly recognise circulating drug chemical fragments in mass spectra obtained from patient blood samples.

People working at ICAR:

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