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MassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications
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  • Alexander Reder,
  • Christian Hentschker,
  • Leif Steil,
  • Manuela Gesell Salazar,
  • Elke Hammer,
  • Vishnu M. Dhople,
  • Thomas Sura,
  • Ulrike Lissner,
  • Hannes Wolfgramm,
  • Denise Dittmar,
  • Marco Harms,
  • Kristin Surmann,
  • Uwe Volker,
  • Stephan Michalik
Alexander Reder
University Medicine Greifswald
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Christian Hentschker
University Medicine Greifswald
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Leif Steil
University Medicine Greifswald
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Manuela Gesell Salazar
University Medicine Greifswald
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Elke Hammer
University Medicine Greifswald
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Vishnu M. Dhople
University Medicine Greifswald
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Thomas Sura
University Medicine Greifswald
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Ulrike Lissner
University Medicine Greifswald
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Hannes Wolfgramm
University Medicine Greifswald
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Denise Dittmar
University Medicine Greifswald
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Marco Harms
University Medicine Greifswald
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Kristin Surmann
University Medicine Greifswald
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Uwe Volker
University Medicine Greifswald
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Stephan Michalik
University Medicine Greifswald

Corresponding Author:stephan.michalik@uni-greifswald.de

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Abstract

In proteomics, fast, efficient and highly reproducible sample preparation is of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open science OT-2 liquid handling robot from Opentrons. This platform can prepare up to 96 samples at once, performing tasks like BCA protein concentration determination, sample digestion with normalization, reduction/alkylation and peptide elution into vials or loading specified peptide amounts onto Evotips in an automated and flexible manner. The performance of the developed workflows using MassSpecPreppy was compared with standard manual sample preparation workflows. The BCA assay experiments revealed an average recovery of 101.3% (SD: ±7.82%) for the MassSpecPreppy workflow, while the manual workflow had a recovery of 96.3% (SD: ±9.73%). The species mix used in the evaluation experiments showed that 94.5% of protein groups for OT-2 digestion and 95% for manual digestion passed the significance thresholds with comparable peptide level coefficient of variations. These results demonstrate that MassSpecPreppy is a versatile and scalable platform for automated sample preparation, producing injection-ready samples for proteomics research.
31 Jul 2023Submitted to PROTEOMICS
08 Aug 2023Submission Checks Completed
08 Aug 2023Assigned to Editor
08 Aug 2023Review(s) Completed, Editorial Evaluation Pending
08 Aug 2023Reviewer(s) Assigned
24 Aug 2023Editorial Decision: Revise Minor
13 Sep 2023Review(s) Completed, Editorial Evaluation Pending
13 Sep 20231st Revision Received
14 Sep 2023Reviewer(s) Assigned
14 Sep 2023Editorial Decision: Accept