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Besides the “In-lab” analysis, performed using the lab’s own tools, a second “centralized” analysis is going to be performed by sharing the data in standard formats and using different software tools available for comparison. |
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Raw data conversion to the mzXML standard: |
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The working data format for the centralized analysis is going to be the standard mzXML because nowadays is the most supported format for the open-source quantitation tools that we want to use to analyze the data. |
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The workflow that we are going to follow to convert all the propietary data format files is showed in the following picture: |
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Vendor's RAW files will be converted to mzXML using open-source tools as proteoWizard or OpenMS without the need of having the vendor’s libraries. |
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Identification analysis workflows: |
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The centralized identification analysis of the data will be performed using the Omics-Hub software from Integromics. |
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Peak list files will be extracted using open-source tools. That peak lists, will be imported by Omics-Hub* and database searches will be performed.
(*) Omics-Hub is able to import automatically raw files from MALDI-TOF TOF 4700-4800 from Applied Biosystems. |
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Quantitation analysis workflows: |
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Analysis workflow for ICPL or iTRAQ/TMT labelling |
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Analysis workflow for label-free |
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