Lymph node metastasis of primary endometrial cancers: Associated proteins revealed by MALDI imaging

Mittal, Parul; Klingler‐Hoffmann, Manuela; Arentz, Georgia; Winderbaum, Lyron; Lokman, Noor A.; Zhang, Chao; Anderson, Lyndal; Scurry, James; Leung, Yee; Stewart, Colin J.R.; Carter, Jonathan; Kaur, Gurjeet; Oehler, Martin K.; Hoffmann, Peter

doi:10.1002/pmic.201500455

Cited by 27 publications

(34 citation statements)

References 37 publications

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“…Similar to journal checklists, MSIcheck allows for rapid nonexhaustive publication assessment. Application here to two specific previous publications [ 36 , 37 ] (Supplementary Table S6 ) highlighted that MSIcheck can be completed in less than 10 minutes, with time noted as the most important factor. Secondary, but still important, was the inclusion of MSIcheck for journal article reviewers.…”

Section: Msicheckmentioning

confidence: 95%

Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments

et al. 2018

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Reproducibility, or a lack thereof, is an increasingly important topic across many research fields. A key aspect of reproducibility is accurate reporting of both experiments and the resulting data. Herein, we propose a reporting guideline for mass spectrometry imaging (MSI). Previous standards have laid out guidelines sufficient to guarantee a certain quality of reporting; however, they set a high bar and as a consequence can be exhaustive and broad, thus limiting uptake.To help address this lack of uptake, we propose a reporting supplement—Minimum Information About a Mass Spectrometry Imaging Experiment (MIAMSIE)—and its abbreviated reporting standard version, MSIcheck. MIAMSIE is intended to improve author-driven reporting. It is intentionally not exhaustive, but is rather designed for extensibility and could therefore eventually become analogous to existing standards that aim to guarantee reporting quality. Conversely, its abbreviated form MSIcheck is intended as a diagnostic tool focused on key aspects in MSI reporting.We discuss how existing standards influenced MIAMSIE/MSIcheck and how these new approaches could positively impact reporting quality, followed by test implementation of both standards to demonstrate their use. For MIAMSIE, we report on author reviews of four articles and a dataset. For MSIcheck, we show a snapshot review of a one-month subset of the MSI literature that indicated issues with data provision and the reporting of both data analysis steps and calibration settings for MS systems. Although our contribution is MSI specific, we believe the underlying approach could be considered as a general strategy for improving scientific reporting.

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Section: Msicheckmentioning

confidence: 95%

Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments

et al. 2018

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“…This has been particularly useful for investigating clinically relevant questions where typical histomorphological analysis may be ambiguous, e.g., classifying thyroid cancers, identifying metastasis origin, and discriminating between benign and malignant skin lesions . MALDI–MSI has been used for retrospective studies, such as identifying proteins associated with lymph node metastases from primary endometrial cancer . Another benefit is the possibility to perform classification on a single tissue section, thereby saving tissue material for subsequent analyses.…”

Section: Introductionmentioning

confidence: 99%

“…A number of obstacles still prevent the acceptance of MALDI–MSI as a clinical tool. First, the spatial resolution of peptide MALDI–MSI was inferior to traditional microscopy, with raster sizes for FFPE samples generally being between 50 and 100 µm . Second, sample preparation protocols for peptide MALDI‐MSI of FFPE tissues require many steps that can potentially introduce variability .…”

Section: Introductionmentioning

confidence: 99%

Site‐to‐Site Reproducibility and Spatial Resolution in MALDI–MSI of Peptides from Formalin‐Fixed Paraffin‐Embedded Samples

Longuespée

Casadonte³

et al. 2019

Proteomics Clinical Apps

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Purpose To facilitate the transition of MALDI–MS Imaging (MALDI–MSI) from basic science to clinical application, it is necessary to analyze formalin‐fixed paraffin‐embedded (FFPE) tissues. The aim is to improve in situ tryptic digestion for MALDI–MSI of FFPE samples and determine if similar results would be reproducible if obtained from different sites. Experimental Design FFPE tissues (mouse intestine, human ovarian teratoma, tissue microarray of tumor entities sampled from three different sites) are prepared for MALDI–MSI. Samples are coated with trypsin using an automated sprayer then incubated using deliquescence to maintain a stable humid environment. After digestion, samples are sprayed with CHCA using the same spraying device and analyzed with a rapifleX MALDI Tissuetyper at 50 µm spatial resolution. Data are analyzed using flexImaging, SCiLS, and R. Results Trypsin application and digestion are identified as sources of variation and loss of spatial resolution in the MALDI–MSI of FFPE samples. Using the described workflow, it is possible to discriminate discrete histological features in different tissues and enabled different sites to generate images of similar quality when assessed by spatial segmentation and PCA. Conclusions and Clinical Relevance Spatial resolution and site‐to‐site reproducibility can be maintained by adhering to a standardized MALDI–MSI workflow.

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“…IR melting employs an IR laser to melt a thermoplastic film that covers the tissue section and is removed together with the ROI . LCM has been coupled with LC‐MS/MS and MALDI MSI …”

Section: Introductionmentioning

confidence: 99%

MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics

et al. 2019

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A multimodal workflow for mass spectrometry imaging was developed that combines MALDI imaging with protein identification and quantification by liquid chromatography tandem mass spectrometry (LC-MS/MS). Thin tissue sections were analyzed by MALDI imaging, and the regions of interest (ROI) were identified using a smoothing and edge detection procedure. A midinfrared laser at 3-μm wavelength was used to remove the ROI from the brain tissue section after MALDI mass spectrometry imaging (MALDI MSI). The captured material was processed using a single-pot solidphase-enhanced sample preparation (SP3) method and analyzed by LC-MS/MS using ion mobility (IM) enhanced data independent acquisition (DIA) to identify and quantify proteins; more than 600 proteins were identified. Using a modified database that included isoform and the post-translational modifications chain, loss of the initial methionine, and acetylation, 14 MALDI MSI peaks were identified. Comparison of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the identified proteins was achieved through an evolutionary relationships classification system.

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Lymph node metastasis of primary endometrial cancers: Associated proteins revealed by MALDI imaging

Cited by 27 publications

References 37 publications

Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments

Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments

Site‐to‐Site Reproducibility and Spatial Resolution in MALDI–MSI of Peptides from Formalin‐Fixed Paraffin‐Embedded Samples

MALDI imaging directed laser ablation tissue microsampling for data independent acquisition proteomics

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