Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification
Created: 7th Oct 2009 at 14:07
Last updated: 8th Nov 2017 at 15:21
Institutions: University of Leidenorcid.org/0000-0002-1279-5133
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
This investigation contains spreadsheet templates and examples for SEEK users to download and use for structuring experimental data. These templates were developed by the SysMO-DB team and the SysMO PALs
Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, Metabolomics Master Template, NimbleGen Transcriptomics Templates, Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry), RT-PCR Excel Template
Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources
Person responsible: Katy Wolstencroft
Snapshots: No snapshots
This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)
An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.
The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies
An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).
MIAPE (Minimum Information About a Proteomics Experiment) is the recommended format for proteomics data in SysMO-SEEK. The document attached provides more information and links to tools and resources.