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\begin{document}

\title{MassSpecPreppy - an end-to-end solution for automated protein
concentration determination and flexible sample digestion for proteomics
applications}



\author[1]{Alexander Reder}%
\author[1]{Christian Hentschker}%
\author[1]{Leif Steil}%
\author[1]{Manuela Gesell Salazar}%
\author[1]{Elke Hammer}%
\author[1]{Vishnu M. Dhople}%
\author[1]{Thomas Sura}%
\author[1]{Ulrike Lissner}%
\author[1]{Hannes Wolfgramm}%
\author[1]{Denise Dittmar}%
\author[1]{Marco Harms}%
\author[1]{Kristin Surmann}%
\author[1]{Uwe Volker}%
\author[1]{Stephan Michalik}%
\affil[1]{University Medicine Greifswald}%


\vspace{-1em}



  
  \date{June 18, 2024}


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\selectlanguage{english}
\begin{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: \selectlanguage{ngerman}±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.%
\end{abstract}\selectlanguage{ngerman}%



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\textbf{Hosted file}

\verb`MassSpecPreppy_manuscript_PROTEOMICS_line_numbering.docx`  available at \url{https://authorea.com/users/650415/articles/658922-massspecpreppy-an-end-to-end-solution-for-automated-protein-concentration-determination-and-flexible-sample-digestion-for-proteomics-applications}\selectlanguage{english}
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\includegraphics[width=0.70\columnwidth]{figures/FIGURE-2-BCA-single-concentrations/FIGURE-2-BCA-single-concentrations}

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\end{figure}\selectlanguage{english}
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\includegraphics[width=0.70\columnwidth]{figures/FIGURE-3-BCA-various-concentrations/FIGURE-3-BCA-various-concentrations}

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\end{figure}\selectlanguage{english}
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\end{center}
\end{figure}\selectlanguage{english}
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\end{figure}

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