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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.

Dataset consisting of 3 biological conditions: 1) Arabidopsis thaliana 2) Trichoderma atroviride and 3) Trichoderma-Arabidopsis interaction. Three biological replicates and 40 measurements per sample were performed over 10 days. This experiment was to focus on 6-PP kinetic, a molecule produced by Trichoderma that help to establish interaction with plants. A custom Low-Temperature Plasma ambient ionization source were used, coupled to an LCQ-fleet ion trap (Thermo Scientific, USA). Mass spectra were taken in full spectra at 50-500 *m/z* range, on profile mode. Each MS scan consist of 10 micros cans. Data was saved under RAW property format of Thermo. To convert to mzML open format, Proteowizard were used.

3D-printing is revolutionizing the rapid prototyping in analytical chemistry. In the last few years, we observed the development of 3D-printed components for ion studies, such as ion sources, ion transfer and ion mobility spectrometry (IMS) devices. Often, 3D-printed gadgets add functions to existing mass spectrometry (MS) systems. Custom adapters improve the sensibility for coupling with ambient ionization and upstream chromatography methods, and sample preparation units optimize the following MS analyses. Besides, 3D-printer parts are suitable for constructing custom analytical robots and mass imaging systems. Some of those assemblies implement new concepts and are commercially not available. An essential aspect of using 3D-printing is the fast turnover of design improvements, which is motivated by permissive licenses. The easy reproducibility and exchange of ideas lead to a community-driven development, which is accompanied by economic advantages for public research and education.

Secondary metabolites of plants have important biological functions, which often depend on their localization in tissues. Ideally, a fresh untreated material should be directly analyzed to obtain a realistic view of the true sample chemistry. Therefore, there is a large interest for ambient mass-spectrometry-based imaging (MSI) methods. Our aim was to simplify this technology and to find an optimal combination of desorption/ionization principles for a fast ambient MSI of macroscopic plant samples. We coupled a 405 nm continuous wave (CW) ultraviolet (UV) diode laser to a three-dimensionally (3D) printed low-temperature plasma (LTP) probe. By moving the sample with a RepRap-based sampling stage, we could perform imaging of samples up to 16 × 16 cm2. We demonstrate the system performance by mapping mescaline in a San Pedro cactus (Echinopsis pachanoi) cross section, tropane alkaloids in jimsonweed (Datura stramonium) fruits and seeds, and nicotine in tobacco (Nicotiana tabacum) seedlings. In all cases, the ...

Mass spectrometry research laboratories reported multiple probes for ambient ionization in the last years. Combining them with a mechanical moving stage enables automated sampling and imaging applications. We developed a robotic platform, which is based on RepRap 3D-printer components, and therefore easy to reproduce and to adopt for custom prototypes. The minimal step width of the Open LabBot is 12.5 μm, and the sampling dimensions (x, y, z) are 18 × 15 × 20 cm. Adjustable rails in an aluminium frame construction facilitate the mounting of additional parts such as sensors, probes, or optical components. The Open LabBot uses industry-standard G-code for its control. The simple syntax facilitates the programming of the movement. We developed two programs: 1) LABI-Imaging, for direct control via a USB connection and the synchronization with MS data acquisition. 2) RmsiGUI, which integrates all steps of mass spectrometry imaging: The creation of G-code for robot control, the assembly of imzML files from raw data and the analysis of imzML files. We proved the functionality of the system by the automated sampling and classification of essential oils with a PlasmaChip probe. Further, we performed an ambient ionization mass spectrometry imaging (AIMSI) experiment of a lime slice with laser desorption low-temperature plasma (LD-LTP) ionization, demonstrating the integration of the complete workflow in RmsiGUI. The design of the Open LabBot and the software are released under open licenses to promote their use and adoption in the instrument developers’ community.

Low-temperature plasma (LTP) ionization represents an emerging technology in ambient mass spectrometry. LTP enables the solvent-free direct detection of a broad range of molecules and mass spectrometry imaging (MSI). The low energy consumption and modest technical requirements of these ion sources favors their employment in mobile applications and as a means to upgrade existing mass analyzers. However, the broad adoption of LTP is hindered by the lack of commercial devices, and constructing personal devices is tricky. Improper setup can result in equipment malfunction or may cause serious damage to instruments due to strong electromagnetic fields or arcing. With this in mind, we developed a reproducible LTP probe, which is designed exclusively from commercial and 3D printed components. The plasma jet generated by the device has a diameter of about 200 μm, which is satisfactory for the ambient imaging of macroscopic samples. We coupled the 3D-LTP probe to an ion trap analyzer and demonstrated the functionality of the ion source by detecting organic and chemical compounds from pure reference standards, biological substances, and pharmaceutical samples. Molecules were primarily detected in their protonated form or as water/ammonium adducts. The identification of compounds was possible by standard collision-induced dissociation (CID) fragmentation spectra. The files necessary to reproduce the 3D parts are available from the project page ( http://lababi.bioprocess.org/index.php/3d-ltp ) under a dual license model, which permits reproduction of the probe and further community-driven development for noncommercial use ("peer production"). Our reproducible probe design thus contributes to a facilitated adaption and evolution of low-temperature plasma technologies in analytical chemistry.