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About the SASHIMI Project

Sashimi is a project that began at the Institute for Systems Biology in Seattle ISB in the proteomics group headed by Ruedi Aebersold. The goal of the project is to provide the scientific community with free open source software tools for the downstream analysis of mass spectrometric data. We hope to develop and distribute analysis tools that will facilitate the ability of labs worldwide to perform proteomics experiments.

Finding out more

The SPC Tools Wiki provides documentation for the Sashimi project tools as well as other software developed at the Seattle Proteome Center at ISB. Join our newsgroup spctools-discuss for an active support and discussion community surrounding the software produced by the Sashimi project. The newsgroup spctools-announce provides important update notification to the software.

Current projects

• MS glossolalia (a common file format for MS data).

  To address the difficulties presented by the introduction of a new mass spectrometer into a pre-existing data analysis framework, we developed an XML based common file format for MS data. The adoption of an open standard will provide programmers with an easy way to access this kind of information, thus facilitating development and distribution of software in this field. Additionally, the use of an architecture and operating system independent representation will ease the exchange of datasets between collaborators and ultimately allow for the creation of public data repositories. Although this format was created to address our specific needs in quantitative proteomics experiments, due to the expandable nature of XML, we believe that it will be easily amenable to other types of analysis.
  
  The Schema for the mzXML representation can be found here. Any feedback on this topic is appreciated.
  
  This project was presented at the 51st ASMS conference in Montreal. Pdf reprints of the poster can be found here. Here is the pdf of the extended abstract. And slides from the oral presentation can be found here (also in pdf format).
  
  These are the slides on the mzXML format and Pep3D presented during the ISB Proteomic/Informatics course. Current information on the ISB Proteomics course can be found here.
  
  This is a more general presentation on the ISB analysis pipeline that was used during the HUPO/PSI meeting in Carros (Fracne) in April 2004.

• Protein Quantification

  The aim of this part of the project is to provide software tools for the quantification of ICAT-like proteomic experiments.
  
  XPRESS and ASAPRatio are software tools for the relative quantification of isotopicaly labeled peptides. Thanks to the use of RAP they can directly read mzXML formatted datasets.
  

• Curation of Protein ID

  The aim of this part of the project is to provide software tools to help in the interpretation of the protein identifications.
  
  INTERACT was developed to address the need to curate large datasets (from tens to hundreds of LC-MS/MS runs covering multiple tens of thousands of MS/MS spectra).
  

• Probability Assignment

  • PeptideProphetTM

    By employing database search scores, number of tryptic termini, number of missed cleavages, and other information, the method learns to distinguish correctly from incorrectly assigned peptides in the data set and computes for each peptide assignment to a MS/MS spectrum a probability of being correct. PeptideProphetTM is hosted on a separate source forge project.
    
    

  • ProteinProphetTM

    Statistical model for validation of the identifications on the protein level. ProteinProphetTM is hosted on a separate source forge project.
    

Why open source?

I actually have an hard time believing anybody will ever read this, but if you actually are ...

• Open source software gives you a flexibility that cannot be equaled by any proprietary source software. It can be easily tailored to address your particular needs.

• Open source software gives you full insight on how your data is being handled.

• Open source software is probably the most democratic way to establish a widely accepted standard in data analysis.

How can I help?

There are many ways you can help us and you don't need to be a mass spectrometrist or a programmer in order to do it. The easiest way to help us is to provide us with feedback on our tools! Let us know if something doesn't work, if a change to a particular tool would make it more useful, if there's a useful tool or feature that's missing, etc. If you think you are qualified to help us in more specific ways, write to us! We'd love to add your name to the developers' section :) The SPC Tools Wiki provides documentation for the Sashimi project tools as well as other software developed at the Seattle Proteome Center at ISB. Join our newsgroup spctools-discuss for an active support and discussion community surrounding the software produced by the Sashimi project. The newsgroup spctools-announce provides important update notification to the software.