Biological injection therapy with leukocyte-poor platelet-rich plasma induces cellular alterations, enhancement of lubricin, and inflammatory downregulation in vivo in human knees: A controlled, prospective human clinical trial based on mass spectrometry imaging analysis.

Objective: To investigate the in vivo biological effects of leukocyte-poor platelet-rich plasma (LpPRP) treatment in human synovial layer to establish the cellular basis for a prolonged clinical improvement. Methods: Synovial tissues (n = 367) were prospectively collected from patients undergoing arthroscopic surgery. Autologous-conditioned plasma, LpPRP, was injected into the knees of 163 patients 1-7 days before surgery to reduce operative trauma and inflammation, and to induce the onset of regeneration. A total of 204 patients did not receive any injection. All samples were analyzed by mass spectrometry imaging. Data analysis was evaluated by clustering, classification, and investigation of predictive peptides. Peptide identification was done by tandem mass spectrometry and database matching. Results: Data analysis revealed two major clusters belonging to LpPRP-treated (LpPRP-1) and untreated (LpPRP-0) patients. Classification analysis showed a discrimination accuracy of 82%-90%. We identified discriminating peptides for CD45 and CD29 receptors (receptor-type tyrosine-protein phosphatase C and integrin beta 1), indicating an enhancement of musculoskeletal stem cells, as well as an enhancement of lubricin, collagen alpha-1-(I) chain, and interleukin-receptor-17-E, dampening the inflammatory reaction in the LpPRP-1 group following LpPRP injection. Conclusions: We could demonstrate for the first time that injection therapy using "autologic-conditioned biologics" may lead to cellular changes in the synovial membrane that might explain the reported prolonged beneficial clinical effects. Here, we show in vivo cellular changes, possibly based on muscular skeletal stem cell alterations, in the synovial layer. The gliding capacities of joints might be improved by enhancing of lubricin, anti-inflammation by activation of interleukin-17 receptor E, and reduction of the inflammatory process by blocking interleukin-17.

Imaging Mass Spectrometry for the Classification of Melanoma Based on BRAF/NRAS Mutational Status.

Mutations of the oncogenes v-raf murine sarcoma viral oncogene homolog B1 (BRAF) and neuroblastoma RAS viral oncogene homolog (NRAS) are the most frequent genetic alterations in melanoma and are mutually exclusive. BRAF V600 mutations are predictive for response to the two BRAF inhibitors vemurafenib and dabrafenib and the mitogen-activated protein kinase kinase (MEK) inhibitor trametinib. However, inter- and intra-tumoral heterogeneity and the development of acquired resistance to BRAF inhibitors have important clinical implications. Here, we investigated and compared the molecular profile of BRAF and NRAS mutated and wildtype melanoma patients' tissue samples using imaging mass spectrometry-based proteomic technology, to identify specific molecular signatures associated with the respective tumors. SCiLSLab and R-statistical software were used to classify peptide profiles using linear discriminant analysis and support vector machine models optimized with two internal cross-validation methods (leave-one-out, k-fold). Classification models showed molecular differences between BRAF and NRAS mutated melanoma, and identification of both was possible with an accuracy of 87-89% and 76-79%, depending on the respective classification method applied. In addition, differential expression of some predictive proteins, such as histones or glyceraldehyde-3-phosphate-dehydrogenase, correlated with BRAF or NRAS mutation status. Overall, these findings provide a new molecular method to classify melanoma patients carrying BRAF and NRAS mutations and help provide a broader view of the molecular characteristics of these patients that may help understand the signaling pathways and interactions involving the altered genes.

A Comparison of Different Sample Processing Protocols for MALDI Imaging Mass Spectrometry Analysis of Formalin-Fixed Multiple Myeloma Cells.

Sample processing of formalin-fixed specimens constitutes a major challenge in molecular profiling efforts. Pre-analytical factors such as fixative temperature, dehydration, and embedding media affect downstream analysis, generating data dependent on technical processing rather than disease state. In this study, we investigated two different sample processing methods, including the use of the cytospin sample preparation and automated sample processing apparatuses for proteomic analysis of multiple myeloma (MM) cell lines using imaging mass spectrometry (IMS). In addition, two sample-embedding instruments using different reagents and processing times were considered. Three MM cell lines fixed in 4% paraformaldehyde were either directly centrifuged onto glass slides using cytospin preparation techniques or processed to create paraffin-embedded specimens with an automatic tissue processor, and further cut onto glass slides for IMS analysis. The number of peaks obtained from paraffin-embedded samples was comparable between the two different sample processing instruments. Interestingly, spectra profiles showed enhanced ion yield in cytospin compared to paraffin-embedded samples along with high reproducibility compared to the sample replicate.

Multimodal Lung Cancer Subtyping Using Deep Learning Neural Networks on Whole Slide Tissue Images and MALDI MSI.

Artificial intelligence (AI) has shown potential for facilitating the detection and classification of tumors. In patients with non-small cell lung cancer, distinguishing between the most common subtypes, adenocarcinoma (ADC) and squamous cell carcinoma (SqCC), is crucial for the development of an effective treatment plan. This task, however, may still present challenges in clinical routine. We propose a two-modality, AI-based classification algorithm to detect and subtype tumor areas, which combines information from matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) data and digital microscopy whole slide images (WSIs) of lung tissue sections. The method consists of first detecting areas with high tumor cell content by performing a segmentation of the hematoxylin and eosin-stained (H&E-stained) WSIs, and subsequently classifying the tumor areas based on the corresponding MALDI MSI data. We trained the algorithm on six tissue microarrays (TMAs) with tumor samples from N = 232 patients and used 14 additional whole sections for validation and model selection. Classification accuracy was evaluated on a test dataset with another 16 whole sections. The algorithm accurately detected and classified tumor areas, yielding a test accuracy of 94.7% on spectrum level, and correctly classified 15 of 16 test sections. When an additional quality control criterion was introduced, a 100% test accuracy was achieved on sections that passed the quality control (14 of 16). The presented method provides a step further towards the inclusion of AI and MALDI MSI data into clinical routine and has the potential to reduce the pathologist's work load. A careful analysis of the results revealed specific challenges to be considered when training neural networks on data from lung cancer tissue.

Multicenter Evaluation of Tissue Classification by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging.

Many studies have demonstrated that tissue phenotyping (tissue typing) based on mass spectrometric imaging data is possible; however, comprehensive studies assessing variation and classifier transferability are largely lacking. This study evaluated the generalization of tissue classification based on Matrix Assisted Laser Desorption/Ionization (MALDI) mass spectrometric imaging (MSI) across measurements performed at different sites. Sections of a tissue microarray (TMA) consisting of different formalin-fixed and paraffin-embedded (FFPE) human tissue samples from different tumor entities (leiomyoma, seminoma, mantle cell lymphoma, melanoma, breast cancer, and squamous cell carcinoma of the lung) were prepared and measured by MALDI-MSI at different sites using a standard protocol (SOP). Technical variation was deliberately introduced on two separate measurements via a different sample preparation protocol and a MALDI Time of Flight mass spectrometer that was not tuned to optimal performance. Using standard data preprocessing, a classification accuracy of 91.4% per pixel was achieved for intrasite classifications. When applying a leave-one-site-out cross-validation strategy, accuracy per pixel over sites was 78.6% for the SOP-compliant data sets and as low as 36.1% for the mistuned instrument data set. Data preprocessing designed to remove technical variation while retaining biological information substantially increased classification accuracy for all data sets with SOP-compliant data sets improved to 94.3%. In particular, classification accuracy of the mistuned instrument data set improved to 81.3% and from 67.0% to 87.8% per pixel for the non-SOP-compliant data set. We demonstrate that MALDI-MSI-based tissue classification is possible across sites when applying histological annotation and an optimized data preprocessing pipeline to improve generalization of classifications over technical variation and increasing overall robustness.

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue.

Among neonates, tested positive for SARS-CoV-2, the majority of infections occur through postpartum transmission. Only few reports describe intrauterine or intrapartum SARS-CoV-2 infections in newborns. To understand the route of transmission, detection of the virus or virus nucleic acid in the placenta and amniotic tissue are of special interest. Current methods to detect SARS-CoV-2 in placental tissue are immunohistochemistry, electron microscopy, in-situ hybridization, polymerase chain reaction (PCR) and next-generation sequencing. Recently, we described an alternative method for the detection of viral ribonucleic acid (RNA), by combination of reverse transcriptase-PCR and mass spectrometry (MS) in oropharyngeal and oral swabs. In this report, we could detect SARS-CoV-2 in formal-fixed and paraffin-embedded (FFPE) placental and amniotic tissue by multiplex RT-PCR MS. Additionally, we could identify the British variant (B.1.1.7) of the virus in this tissue by the same methodology. Combination of RT-PCR with MS is a fast and easy method to detect SARS-CoV-2 viral RNA, including specific variants in FFPE tissue.

Robust subtyping of non-small cell lung cancer whole sections through MALDI mass spectrometry imaging.

Subtyping of the most common non-small cell lung cancer (NSCLC) tumor types adenocarcinoma (ADC) and squamous cell carcinoma (SqCC) is still a challenge in the clinical routine and a correct diagnosis is crucial for an adequate therapy selection. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has shown potential for NSCLC subtyping but is subject to strong technical variability and has only been applied to tissue samples assembled in tissue microarrays (TMAs). To our knowledge, a successful transfer of a classifier from TMAs to whole sections, which are generated in the standard clinical routine, has not been presented in the literature as of yet. We introduce a classification algorithm using extensive preprocessing and a classifier (either a neural network or a linear discriminant analysis (LDA)) to robustly classify whole sections of ADC and SqCC lung tissue. The classifiers were trained on TMAs and validated and tested on whole sections. Vital for a successful application on whole sections is the extensive preprocessing and the use of whole sections for hyperparameter selection. The classification system with the neural network/LDA results in 99.0%/98.3% test accuracy on spectra level and 100.0%/100.0% test accuracy on whole section level, respectively, and, therefore, provides a powerful tool to support the pathologist's decision making process. The presented method is a step further towards a clinical application of MALDI MSI and artificial intelligence for subtyping of NSCLC tissue sections.

Cross-Normalization of MALDI Mass Spectrometry Imaging Data Improves Site-to-Site Reproducibility.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is an established tool for the investigation of formalin-fixed paraffin-embedded (FFPE) tissue samples and shows a high potential for applications in clinical research and histopathological tissue classification. However, the applicability of this method to serial clinical and pharmacological studies is often hampered by inevitable technical variation and limited reproducibility. We present a novel spectral cross-normalization algorithm that differs from the existing normalization methods in two aspects: (a) it is based on estimating the full statistical distribution of spectral intensities and (b) it involves applying a non-linear, mass-dependent intensity transformation to align this distribution with a reference distribution. This method is combined with a model-driven resampling step that is specifically designed for data from MALDI imaging of tryptic peptides. This method was performed on two sets of tissue samples: a single human teratoma sample and a collection of five tissue microarrays (TMAs) of breast and ovarian tumor tissue samples (N = 241 patients). The MALDI MSI data was acquired in two labs using multiple protocols, allowing us to investigate different inter-lab and cross-protocol scenarios, thus covering a wide range of technical variations. Our results suggest that the proposed cross-normalization significantly reduces such batch effects not only in inter-sample and inter-lab comparisons but also in cross-protocol scenarios. This demonstrates the feasibility of cross-normalization and joint data analysis even under conditions where preparation and acquisition protocols themselves are subject to variation.

Imaging Mass Spectrometry-Based Proteomic Analysis to Differentiate Melanocytic Nevi and Malignant Melanoma.

The discrimination of malignant melanoma from benign nevi may be difficult in some cases. For this reason, immunohistological and molecular techniques are included in the differential diagnostic toolbox for these lesions. These methods are time consuming when applied subsequently and, in some cases, no definitive diagnosis can be made. We studied both lesions by imaging mass spectrometry (IMS) in a large cohort (n = 203) to determine a different proteomic profile between cutaneous melanomas and melanocytic nevi. Sample preparation and instrument setting were tested to obtain optimal results in term of data quality and reproducibility. A proteomic signature was found by linear discriminant analysis to discern malignant melanoma from benign nevus (n = 113) with an overall accuracy of >98%. The prediction model was tested in an independent set (n = 90) reaching an overall accuracy of 93% in classifying melanoma from nevi. Statistical analysis of the IMS data revealed mass-to-charge ratio (m/z) peaks which varied significantly (Area under the receiver operating characteristic curve > 0.7) between the two tissue types. To our knowledge, this is the largest IMS study of cutaneous melanoma and nevi performed up to now. Our findings clearly show that discrimination of melanocytic nevi from melanoma is possible by IMS.

Mass Spectrometry Imaging for Reliable and Fast Classification of Non-Small Cell Lung Cancer Subtypes.

Subtyping of non-small cell lung cancer (NSCLC) is paramount for therapy stratification. In this study, we analyzed the largest NSCLC cohort by mass spectrometry imaging (MSI) to date. We sought to test different classification algorithms and to validate results obtained in smaller patient cohorts. Tissue microarrays (TMAs) from including adenocarcinoma (ADC, n = 499) and squamous cell carcinoma (SqCC, n = 440), were analyzed. Linear discriminant analysis, support vector machine, and random forest (RF) were applied using samples randomly assigned for training (66%) and validation (33%). The m/z species most relevant for the classification were identified by on-tissue tandem mass spectrometry and validated by immunohistochemistry (IHC). Measurements from multiple TMAs were comparable using standardized protocols. RF yielded the best classification results. The classification accuracy decreased after including less than six of the most relevant m/z species. The sensitivity and specificity of MSI in the validation cohort were 92.9% and 89.3%, comparable to IHC. The most important protein for the discrimination of both tumors was cytokeratin 5. We investigated the largest NSCLC cohort by MSI to date and found that the classification of NSCLC into ADC and SqCC is possible with high accuracy using a limited set of m/z species.

Mass Spectrometry Imaging Differentiates Chromophobe Renal Cell Carcinoma and Renal Oncocytoma with High Accuracy.

Background: While subtyping of the majority of malignant chromophobe renal cell carcinoma (cRCC) and benign renal oncocytoma (rO) is possible on morphology alone, additional histochemical, immunohistochemical or molecular investigations are required in a subset of cases. As currently used histochemical and immunohistological stains as well as genetic aberrations show considerable overlap in both tumors, additional techniques are required for differential diagnostics. Mass spectrometry imaging (MSI) combining the detection of multiple peptides with information about their localization in tissue may be a suitable technology to overcome this diagnostic challenge. Patients and Methods: Formalin-fixed paraffin embedded (FFPE) tissue specimens from cRCC (n=71) and rO (n=64) were analyzed by MSI. Data were classified by linear discriminant analysis (LDA), classification and regression trees (CART), k-nearest neighbors (KNN), support vector machine (SVM), and random forest (RF) algorithm with internal cross validation and visualized by t-distributed stochastic neighbor embedding (t-SNE). Most important variables for classification were identified and the classification algorithm was optimized. Results: Applying different machine learning algorithms on all m/z peaks, classification accuracy between cRCC and rO was 85%, 82%, 84%, 77% and 64% for RF, SVM, KNN, CART and LDA. Under the assumption that a reduction of m/z peaks would lead to improved classification accuracy, m/z peaks were ranked based on their variable importance. Reduction to six most important m/z peaks resulted in improved accuracy of 89%, 85%, 85% and 85% for RF, SVM, KNN, and LDA and remained at the level of 77% for CART. t-SNE showed clear separation of cRCC and rO after algorithm improvement. Conclusion: In summary, we acquired MSI data on FFPE tissue specimens of cRCC and rO, performed classification and detected most relevant biomarkers for the differential diagnosis of both diseases. MSI data might be a useful adjunct method in the differential diagnosis of cRCC and rO.

Microproteomics and Immunohistochemistry Reveal Differences in Aldo-Keto Reductase Family 1 Member C3 in Tissue Specimens of Ulcerative Colitis and Crohn's Disease.

PURPOSE: Differential diagnosis of ulcerative colitis (UC) and Crohn's disease (CD) is of utmost importance for the decision making of respective therapeutic treatment strategies but in about 10-15% of cases, a clinical and histopathological assessment does not lead to a definite diagnosis. The aim of the study is to characterize proteomic differences between UC and CD. EXPERIMENTAL DESIGN: Microproteomics is performed on formalin-fixed paraffin-embedded colonic tissue specimens from 9 UC and 9 CD patients. Protein validation is performed using immunohistochemistry (IHC) (nUC =51, nCD =62, nCTRL =10) followed by digital analysis. RESULTS: Microproteomic analyses reveal eight proteins with higher abundance in CD compared to UC including proteins related to neutrophil activity and damage-associated molecular patterns. Moreover, one protein, Aldo-keto reductase family 1 member C3 (AKR1C3), is present in eight out of nine CD and absent in all UC samples. Digital IHC analysis reveal a higher percentage and an increased expression intensity of AKR1C3-positive epithelial cells in CD compared to UC and in controls compared to inflammatory bowel disease (IBD). CONCLUSION AND CLINICAL RELEVANCE: Overall, the results suggest that microproteomics is an adequate tool to highlight protein patterns in IBD. IHC and digital pathology might support future differential diagnosis of UC and CD.

Using the Chemical Noise Background in MALDI Mass Spectrometry Imaging for Mass Alignment and Calibration.

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is an established tool for the investigation of formalin fixed paraffin embedded (FFPE) tissue samples and shows a high potential for applications in clinical research and histopathological diagnosis. The applicability and accuracy of this method, however, heavily depends on the quality of the acquired data, and in particular mass misalignment in axial time-of-flight (TOF) MSI continues to be a serious issue. We present a mass alignment and recalibration method that is specifically designed to operate on MALDI peptide imaging data. The proposed method exploits statistical properties of the characteristic chemical noise background observed in peptide imaging experiments. By comparing these properties to a theoretical peptide mass model, the effective mass shift of each spectrum is estimated and corrected. The method was evaluated on a cohort of 31 FFPE tissue samples, pursuing a statistical validation approach to estimate both the reduction of relative misalignment, as well as the increase in absolute mass accuracy. Our results suggest that a relative mass precision of approximately 5 ppm and an absolute accuracy of approximately 20 ppm are achievable using our method.

Combined Immunohistochemistry after Mass Spectrometry Imaging for Superior Spatial Information.

OBJECTIVE: Tissue slides analyzed by MS imaging (MSI) are stained by H&E (Haematoxylin and Eosin) to identify regions of interest. As it can be difficult to identify specific cells of interest by H&E alone, data analysis may be impaired. Immunohistochemistry (IHC) can highlight cells of interest but single or combined IHC on tissue sections analyzed by MSI have not been performed. METHODS: We performed MSI on bone marrow biopsies from patients with multiple myeloma and stained different antibodies (CD38, CD138, MUM1, kappa- and lambda). A combination of CK5/6/TTF1 and Napsin-A/p40 is stained after MSI on adenocarcinoma and squamous cell carcinoma of the lung. Staining intensities of p40 after MSI and on a serial section are quantified on a tissue microarray (n = 44) by digital analysis. RESULTS: Digital evaluation reveals weaker staining intensities after MSI as compared to serial sections. Staining quality and quantity after MSI enables to identify cells of interest. On the tissue microarray, one out of 44 tissue specimens shows no staining of p40 after MSI, but weak nuclear staining on a serial section. CONCLUSION: We demonstrated that single and double IHC staining is feasible on tissue sections previously analyzed by MSI, with decreased staining intensities.

Microproteomic Profiling of High-Grade Squamous Intraepithelial Lesion of the Cervix: Insight into Biological Mechanisms of Dysplasia and New Potential Diagnostic Markers.

PURPOSE: High-grade squamous intraepithelial lesion (HSIL) is a known precursor for squamous cell carcinoma of uterine cervix. Although it is known that SILs are associated to infection by human papillomavirus, downstream biological mechanisms are still poorly described. In this study, we compared the microproteomic profile of HSIL to normal tissues: ectocervix (ectoC) and endocervix (endoC). EXPERIMENTAL DESIGN: Tissue regions of endoC, ectoC, and HSlL were collected by laser microdissection (3500 cells each) from five patients. Samples were processed and analyzed using our recently developed laser microdissection-based microproteomic method. Tissues were compared in order to retrieve HSIL's proteomic profile. Potentially interesting proteins for pathology were stained by immunohistochemistry. RESULTS: We identified 3072 proteins among the fifteen samples and 2386 were quantified in at least four out of the five biological replicates of at least one tissue type. We found 236 proteins more abundant in HSIL. Gene ontology enrichments revealed mechanisms of DNA replication and RNA splicing. Despite the squamous nature of HSIL, a common signature between HSIL and endoC could be found. Finally, potential new markers could support diagnosis of dysplasia in SILs. CONCLUSION AND CLINICAL RELEVANCE: This microproteomic investigation of HSIL gives insights into the biology of cervical precancerous lesions.

Targeted Feature Extraction in MALDI Mass Spectrometry Imaging to Discriminate Proteomic Profiles of Breast and Ovarian Cancer.

PURPOSE: To develop a mass spectrometry imaging (MSI) based workflow for extracting m/z values related to putative protein biomarkers and using these for reliable tumor classification. EXPERIMENTAL DESIGN: Given a list of putative breast and ovarian cancer biomarker proteins, a set of related m/z values are extracted from heterogeneous MSI datasets derived from formalin-fixed paraffin-embedded tissue material. Based on these features, a linear discriminant analysis classification model is trained to discriminate the two tumor types. RESULTS: It is shown that the discriminative power of classification models based on the extracted features is increased compared to the automatic training approach, especially when classifiers are applied to spectral data acquired under different conditions (instrument, preparation, laboratory). CONCLUSIONS AND CLINICAL RELEVANCE: Robust classification models not confounded by technical variation between MSI measurements are obtained. This supports the assumption that the classification of the respective tumor types is based on biological rather than technical differences, and that the selected features are related to the proteomic profiles of the tumor types under consideration.

In MALDI-Mass Spectrometry Imaging on Formalin-Fixed Paraffin-Embedded Tissue Specimen Section Thickness Significantly Influences m/z Peak Intensity.

BACKGROUND: In matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) standardized sample preparation is important to obtain reliable results. Herein, the impact of section thickness in formalin-fixed paraffin embedded (FFPE) tissue microarrays (TMA) on spectral intensities is investigated. PATIENTS AND METHODS: TMAs consisting of ten different tissues represented by duplicates of ten patients (n = 200 cores) are cut at 1, 3, and 5 µm. MSI analysis is performed and mean intensities of all evaluable cores are extracted. Measurements are merged and mean m/z intensities are compared. RESULTS: Visual inspection of spectral intensities between 1, 3, and 5 µm reveals generally higher intensities in thinner tissue sections. Specifically, higher intensities are observed in the vast majority of peaks (98.6%, p < 0.01) in 1 µm compared with 5 µm sections. Note that 28.4% and 2.1% of m/z values exhibit a at least two- and threefold intensity difference (p < 0.01) in 1 µm compared to 5 µm sections, respectively. CONCLUSION: A section thickness of 1 µm results in higher spectral intensities compared with 5 µm. The results highlight the importance of standardized protocols in light of recent efforts to identify clinically relevant biomarkers using MSI. The use of TMAs for comparative analysis seems advantageous, as section thickness displays less variability.

Digital PCR After MALDI-Mass Spectrometry Imaging to Combine Proteomic Mapping and Identification of Activating Mutations in Pulmonary Adenocarcinoma.

PURPOSE: Matrix assisted laser desorption/ionization time-of-flight mass spectrometry imaging (MALDI-MSI) is a powerful tool to analyze the spatial distribution of peptides in tissues. Digital PCR (dPCR) is a method to reliably detect genetic mutations. Biopsy material is often limited due to minimally invasive techniques, but information on diagnosis, prognosis, and prediction is required for subsequent clinical decision making. Thus, saving tissue material during diagnostic workup is highly warranted for best patient care. The possibility to combine proteomic analysis by MALDI-MSI and mutational analysis by dPCR from the same tissue section is evaluated. EXPERIMENTAL DESIGN: Ten 0.5 × 0.5 cm formalin-fixed paraffin embedded tissue samples of pulmonary adenocarcinomas with known EGFR or KRAS mutations are analyzed by MALDI-MSI. Subsequently, DNA is extracted from the analyzed tissue material and tested for the respective driver mutation by dPCR. RESULTS: Detection of driver gene mutations after MALDI MSI analysis is successful in all analyzed samples. Determined mutant allele frequencies are in good agreement with values assessed from untreated serial tissue sections with a mean absolute deviation of 0.16. CONCLUSION AND CLINICAL RELEVANCE: It has been demonstrated that MALDI-MSI can be combined with genetic analysis, like dPCR. Workflows enabling the subsequent analysis of proteomic and genetic markers are particularly promising for the analysis of limited sample material such as biopsy specimen.