Here we describe a new instrument (SpiderMass) designed for in vivo and real-time analysis. In this instrument ion production is performed remotely from the MS instrument and the generated ions are transported in real-time to the MS analyzer. Ion production is promoted by Resonant Infrared Laser Ablation (RIR-LA) based on the highly effective excitation of O-H bonds in water molecules naturally present in most biological samples. The retrieved molecular patterns are specific to the cell phenotypes and benign versus cancer regions of patient biopsies can be easily differentiated. We also demonstrate by analysis of human skin that SpiderMass can be used under in vivo conditions with minimal damage and pain. Furthermore SpiderMass can also be used for real-time drug metabolism and pharmacokinetic (DMPK) analysis or food safety topics. SpiderMass is thus the first MS based system designed for in vivo real-time analysis under minimally invasive conditions.

Graphical AbstractHighlights d SpiderMass technology collects molecular information ex vivo and in vivo d Tumor classification by typing and grading is obtained by the technology d Found markers are cross-validated with mass spectrometry imaging d The technology was assessed ex vivo at the vet surgery room SUMMARY Histopathological diagnosis of biopsy samples and margin assessment of surgical specimens are challenging aspects in sarcoma. Using dog patient tissues, we assessed the performance of a recently developed technology for fast ex vivo molecular lipid-based diagnosis of sarcomas. The instrument is based on mass spectrometry (MS) molecular analysis through a laser microprobe operating under ambient conditions using excitation of endogenous water molecules. Classification models based on cancer/normal/necrotic, tumor grade, and subtypes showed a minimum of 97.63% correct classification. Specific markers of normal, cancer, and necrotic regions were identified by tandem MS and validated by MS imaging. Real-time detection capabilities were demonstrated by ex vivo analysis with direct interrogation of classification models.

This Protocol describes SpiderMass, a novel platform for in vivo and real time mass spectrometry analysis. The Procedure describes system setup and calibration, analysis of cell culture, tissue section and in vivo skin samples, and data processing. TWEET A new Protocol for in vivo and real time ambient mass spectrometry analysis of cultured cells, tissue sections, and in vivo skin. COVER TEASER In vivo and real-time ambient MS surface analysis Primary research articles where the protocol has been used and/or developed:

Rapid and accurate clinical diagnosis remains challenging. A component of diagnosis tool development is the design of effective classification models with Mass spectrometry (MS) data. Some Machine Learning approaches have been investigated but these models require time-consuming preprocessing steps to remove artifacts, making them unsuitable for rapid analysis. Convolutional Neural Networks (CNNs) have been found to perform well under such circumstances since they can learn representations from raw data. However, their effectiveness decreases when the number of available training samples is small, which is a common situation in medicine. In this work, we investigate transfer learning on 1D-CNNs, then we develop a cumulative learning method when transfer learning is not powerful enough. We propose to train the same model through several classification tasks over various small datasets to accumulate knowledge in the resulting representation. By using rat brain as the initial training dataset, a cumulative learning approach can have a classification accuracy exceeding 98% for 1D clinical MS-data. We show the use of cumulative learning using datasets generated in different biological contexts, on different organisms, and acquired by different instruments. Here we show a promising strategy for improving MS data classification accuracy when only small numbers of samples are available.

In vivo cancer margin delineation during surgery remains a major challenge. Despite the availability of several image guidance techniques and intraoperative assessment, clear surgical margins and debulking efficiency remain scarce. For this reason, there is particular interest in developing rapid intraoperative tools with high sensitivity and specificity to help guide cancer surgery in vivo. Recently, several emerging technologies including intraoperative mass spectrometry have paved the way for molecular guidance in a clinical setting. We evaluate these techniques and assess their relevance for intraoperative surgical guidance and how they can transform the future of molecular cancer surgery, diagnostics, patient management and care. HighlightsCancer surgery is the first treatment in many solid tumors. Quality of the initial surgery has a strong influence on the patient outcome. Tumors must be excised at best, but accurate delineation of their edges and margin definition is a huge challenge.

Mass Spectrometry Imaging (MSI) has shown to bring invaluable information for biological and clinical applications. However, conventional MSI is generally performed ex vivo from tissue sections. Here, we develop a novel MS-based method for in vivo mass spectrometry imaging. By coupling the SpiderMass technology -that provides in vivo minimally invasive analysis -to a robotic arm of high accuracy, we demonstrate that images can be acquired from any surface by moving the laser probe above the surface. By equipping the robotic arm with a sensor, we are also able to both get the topography image of the sample surface and the molecular distribution, and then and plot back the molecular data, directly to the 3D topographical image without the need for image fusion. This is shown for the first time with the 3D topographic MS-Based whole-body imaging of a mouse. Enabling fast in vivo MSI bridged to topography pave the way for surgical applications to excision margins.

Remote Infrared Matrix-Assisted Laser Desorption/Ionization (Remote IR-MALDI) system using tissue endogenous water as matrix was shown to enable in-vivo real-time mass spectrometry analysis with minimal invasiveness. Initially the system was used to detect metabolites and lipids. Here, we demonstrate its capability to detect and analyze peptides and proteins. Very interestingly, the corresponding mass spectra show ESI-like charge state distribution, opening many applications for structural elucidation to be performed in RUNNING TITLE: Remote IR-MALDI MS Analysis of Proteins

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