Mass Spectrometry of Lipids SPPs

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== Proposals and discussion points<br>  ==
== Proposals and discussion points<br>  ==
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''Write here any proposals and discussion points you may have.''  
''Write here any proposals and discussion points you may have.''  
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[http://www.lipidomicnet.org/index.php/User:Jos_Brouwers Jos Brouwers]:<br>
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#Several MS data analysis packages are already available. Some of them in the public domain, such as [http://mzmine.sourceforge.net/ MZmine], [http://www.bioconductor.org/packages/bioc/1.6/src/contrib/html/xcms.html XCMS] and [http://sourceforge.net/projects/open-ms/ OpenMS]. Is it considered to adopt one of these packages for further development to suit our needs?
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#Sciex also has a software package available (at no cost): Lipidprofiler<sup>TM</sup>, based on a MS Acces database for identification/annotation purposes. With very few modifications, the database structure may be usable as a template for identification in to-be-written software (-front-ends).
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#Most of the text I read on SPP pages only deal with MS data. I know that I'm not the only person that finds HPLC indispensable in many analyses.&nbsp; Am I missing the LC/MS pages or do they still have to be written?
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#Is there agreement within the bioinformatics group about the data format that is most desirable from their point of view? mzXML? netCDF? RAW? Wiff? Or is it all the same (also with respect to multi-dimensional MS)? It might be a good idea to agree on a data format before data collection is started.
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[[Standard Processing Procedures|Back to Standard Processing Procedures]]
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[[Category:Lipid_mass_spectrometry]] [[Category:Standard_Processing_Procedures]]
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[[Standard Processing Procedures|Back to Standard Processing Procedures]]  
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[[Category:Lipid_mass_spectrometry]] [[Category:Standard Processing Procedures]]
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[[Category:Lipid_mass_spectrometry]] [[Category:Standard_Processing_Procedures]]

Revision as of 17:16, 29 October 2008

Contents

Input

1) Raw MS files of lipid analysis (massspectrometry files).
2) Template file which describes each sample analyzed.
3) List of identified lipids andd amount? (in case if lipids are identified by data producers)

Output

Data records in LipidomicNet database.
Raw MS files, sample information, identified lipids, lipid measurements (peak intensities/areas, relative abundance, absolute concentrations, mol.ratios) will be recorded into a database with a data retrieval interface connected to it.

Processing

General information about the experiment
Information from an MS experiment should be submitted to a LipidomicNet server for further recording into a database.

Prior to submission, format of the files, compliance of file entries with nomenclature adopted by LipidomicNet will be checked. Furthermore, quality of experiments should be assessed in order to assure that only high quality data reach the database.
Data recording starts with filling in or selecting already recoded information about the data producer.
In order to assure, that full information about analytical method is available before the data upload, method should be recorded on LipidomicNet WikiPages ().
After method is recorded its identification number (ID) can be used to identify all experiments performed with that method.

Information about samples

The following information about samples analyzed should be provided:
Sample Id, biological species, tissue/cell type, extraction method used etc.
During taskforce VIII workshop, it was decided to use controlled vocabularies (CV) and ontologies developed at EBI. When sample information is uploaded it will be checked for compliance with these ontologies. Data provider will have to edit all entries that don’t match the common format and resubmit the file.

Lipid information
Data providers that identify lipids from MS spectra can upload the list of lipids together with measures of lipid quantity. This file should contain sample id for with a lipid was identified (sample id should be in the list uploaded as described in the previous section). There should be a description of measurement units used and normalization steps performed (such as protein amount normalization, internal standard normalization etc).
Lipid list will be checked against a table of standard lipid names created by members of Task_Force_I

QC
In order to avoid recording and analysis of problematic dataset a quality control system will check results before uploading the data. QC will be evaluated based on reproducibility of lipid signal (if experiment contains replicas), ratios of internal standard and other measures depending on which MS method is used (Category:Lipid_mass_spectrometry).

Lipid identification from MS spectra files
Help to data providers who are interested in assistance with lipid identification will be provided upon request. Due to great variety of analytical MS platforms used by project members it is rather difficult and unpractical to develop a common framework for lipid identification. Instead, a custom solution will be provided based on analytical platform and method used to generate the data.

Proposals and discussion points

Write here any proposals and discussion points you may have.

Jos Brouwers:

  1. Several MS data analysis packages are already available. Some of them in the public domain, such as MZmine, XCMS and OpenMS. Is it considered to adopt one of these packages for further development to suit our needs?
  2. Sciex also has a software package available (at no cost): LipidprofilerTM, based on a MS Acces database for identification/annotation purposes. With very few modifications, the database structure may be usable as a template for identification in to-be-written software (-front-ends).
  3. Most of the text I read on SPP pages only deal with MS data. I know that I'm not the only person that finds HPLC indispensable in many analyses.  Am I missing the LC/MS pages or do they still have to be written?
  4. Is there agreement within the bioinformatics group about the data format that is most desirable from their point of view? mzXML? netCDF? RAW? Wiff? Or is it all the same (also with respect to multi-dimensional MS)? It might be a good idea to agree on a data format before data collection is started.



Back to Standard Processing Procedures



Back to Standard Processing Procedures

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