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\begin{document}

\title{Guided analysis of ambient ionization mass spectrometry data with the
MQ\_Assistant}



\author[1]{Héctor Guillén-Alonso}%
\author[1]{Nancy Shyrley García-Rojas}%
\author[1]{R Winkler}%
\affil[1]{Cinvestav UGA-LANGEBIO}%


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  \date{May 24, 2024}


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\begin{abstract}
RATIONALE Ambient ionization mass spectrometry (AIMS) delivers realistic
data from samples in their native state. In addition, AIMS methods
reduce time and costs for sample preparation and have less environmental
impact. However, AIMS data are often complex and require substantial
processing before interpretation. METHODS We developed an interactive R
script for the guided processing of mass spectrometry (MS) data. The
`MQ\_Assistant' is based on MALDIquant, a popular R package for MS data
processing. In each step, the user can try and pre-view the effect of
chosen parameters before deciding on the values with the best result and
proceeding to the next stage. The outcome of the MQ\_Assistant is a
feature matrix that can be further analyzed in R and statistics tools
such as MetaboAnalyst. RESULTS Using 360 AIMS example spectra, we
demonstrate the step-by-step processing for creating a feature matrix.
In addition, we show how to visualize the results of tree biological
replicates of a plant-microbe interaction between Arabidopsis and
Trichoderma as a heatmap using R and upload them to MetaboAnalyst. The
final parameter set can be saved for reuse in MALDIquant workflows of
similar data. CONCLUSIONS The MQ\_Assistant helps novices and
experienced users to develop workflows for (AI)MS data processing. The
interactive procedure supports the quick finding of appropriate
settings. These parameters can be exported and reused in future
projects. The step-wise operation with visual feedback also suggests the
use of the MQ\_Assistant in education.%
\end{abstract}%



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\textbf{Hosted file}

\verb`MQ_Assistant-RCM-V0_230307.docx`  available at \url{https://authorea.com/users/593624/articles/628531-guided-analysis-of-ambient-ionization-mass-spectrometry-data-with-the-mq\_assistant}

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