democratization of proteomics data lennart martens - - PowerPoint PPT Presentation

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democratization of proteomics data
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democratization of proteomics data lennart martens - - PowerPoint PPT Presentation

Mar 28, 2023 241 likes •532 views

democratization of proteomics data lennart martens lennart.martens@vib-ugent.be computational omics and systems biology group VIB / Ghent University, Ghent, Belgium We should never forget The land of opportunity What about our

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democratization of proteomics data

lennart martens

lennart.martens@vib-ugent.be computational omics and systems biology group VIB / Ghent University, Ghent, Belgium

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We should never forget The land of opportunity What about our quali(ty|fications)?

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We should never forget The land of opportunity What about our quali(ty|fications)?

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J.R.R. Tolkien, A Conversation with Smaug

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Due to the large volume of data, LIMS systems are required to manage data locally

Helsens, Proteomics, 2010 Review in Stephan, Proteomics, 2010

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A little light searching in ms_lims

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We should never forget The land of opportunity What about our quali(ty|fications)?

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Vaudel, Proteomics, revision submitted

(Public) proteomics data can be used in different ways, opening up many opportunities

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Vaudel, Proteomics, revision submitted

Ideally, the data ecosystem will even allow in silico proteomics experiments

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We should never forget The land of opportunity What about our quali(ty|fications)?

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Target: peppermint icicles Result: peppermint ... eh … erm…

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The big quality control poll (n=86, 8 days) How would you describe yourself?

With Bas van Breukelen, Utrecht

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The big quality control poll (n=86, 8 days) Do you already use quality control tools?

With Bas van Breukelen, Utrecht

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The big quality control poll (n=86, 8 days) Is it easy to obtain quality control software?

With Bas van Breukelen, Utrecht

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The big quality control poll (n=86, 8 days) How important is quality control for …

With Bas van Breukelen, Utrecht

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The big quality control poll (n=86, 8 days) How easy is it for you to …

With Bas van Breukelen, Utrecht

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The NIST/NCI CPTAC panel of metrics

Rudnick, MCP, 2010

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NIST metrics in actual use

Rudnick, MCP, 2010

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Tabb lab implementation: QuaMeter

Ma, Anal. Chem., 2012

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OpenMS supports TOPPAS and KNIME quality control pipelines

Walzer, MCP, 2014 Junker, Journal of Proteome Research, 2012

TOPPAS KNIME

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qcML is intended to be transparent, acting as the relay format of QC metrics

Walzer, MCP, 2014

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Ideally, longitudinal analysis of QC metrics allows the easy detection of outlying data

Walzer, MCP, 2014

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However, different types of data sets will exhibit different ranges of QC metrics

Walzer, MCP, 2014

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If you get down and dirty, the instrument logs are very interesting fodder too

Bittremieux, Journal of Proteome Research, 2015

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The journey from quality control to accreditation can be taken in steps

  • Given the right software:
  • Routine local QC on a local standard
  • Routine local QC on all runs
  • Longitudinal QC data on standard and runs
  • Given data standards and infrastructure:
  • Routine deposition of QC metrics in public domain
  • Mandatory deposition of QC metrics in public domain
  • Given reference samples
  • Voluntary, non-binding performance tests
  • Voluntary accreditation
  • Official standards for accreditation
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www.compomics.com

@compomics