4.8 Article

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

Related references

Note: Only part of the references are listed.
Review Radiology, Nuclear Medicine & Medical Imaging

Experimental and Data Analysis Considerations for Three-Dimensional Mass Spectrometry Imaging in Biomedical Research

D. R. N. Vos et al.

Summary: Mass spectrometry imaging (MSI) has expanded into the 3D realm, allowing visualization of molecular distributions within 3D samples for a more comprehensive understanding of spatial and molecular complexity in biological samples. Successful 3D-MSI studies require consideration of experimental and data analysis aspects. Ongoing developments have enabled routine application of 3D-MSI to multi-sample studies.

MOLECULAR IMAGING AND BIOLOGY (2021)

Article Biochemical Research Methods

Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow

Andrea McCann et al.

Summary: MALDI mass spectrometry imaging (MSI) allows mapping and tentative identification of compounds based on their m/z value. However, mass shifts can degrade resolution and accuracy in the average spectrum. Mitigating sources of mass shift, adapting sample preparation, carefully selecting data acquisition settings, and applying post-processing methods are key factors in improving image quality and annotations. A recommended workflow successfully applied to complex samples acquired on MALDI ToF and MALDI FT-ICR instruments.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2021)

Article Biochemical Research Methods

Batch Effects in MALDI Mass Spectrometry Imaging

Benjamin Balluff et al.

Summary: Mass spectrometry imaging has become essential for spatially resolved molecular investigation of tissues, particularly in biomedical research, with MALDI MSI being widely used. However, batch effects could significantly hinder reliable data comparison in midsize studies. This critical insight will discuss the potential consequences of batch effects on biomarker discovery or multivariate classification and suggest measures to recognize and minimize these effects.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2021)

Article Biochemistry & Molecular Biology

The Impact of Histological Annotations for Accurate Tissue Classification Using Mass Spectrometry Imaging

Juliana Pereira Lopes Goncalves et al.

Summary: Spatial proteomics techniques, particularly mass spectrometry imaging combined with machine learning methods, have been proven to be valuable tools in addressing histopathology challenges and improving tissue classification accuracy. The intrinsic heterogeneity of tissues directly impacts the effectiveness of histological annotations, with a more significant effect on highly heterogeneous tissues.

METABOLITES (2021)

Article Chemistry, Analytical

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

Tobias Boskamp et al.

Summary: The study introduces a novel spectral cross-normalization algorithm and successfully applies it to multiple tissue sample sets, reducing batch effects. The results indicate that this method can be used for data analysis across different labs and protocols, showing promising outcomes.

ANALYTICAL CHEMISTRY (2021)

Article Medical Laboratory Technology

Implementation of Mass Spectrometry Imaging in Pathology: Advances and Challenges

Juliana Pereira Lopes Goncalves et al.

Summary: An accurate and precise diagnosis is crucial for treating diseases, especially in cancer therapy, where pathology utilizes a variety of tests and technologies to assist in better diagnosis. Mass spectrometry has been granted the status of the method of choice for analyzing proteins, peptides, and metabolites due to its high sensitivity and specificity. However, limitations such as low spatial resolution and complex sample processing are still being overcome in mass spectrometry analysis.

CLINICS IN LABORATORY MEDICINE (2021)

Article Oncology

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

Rita Casadonte et al.

Summary: This study utilized imaging mass spectrometry to compare the proteomic profiles of cutaneous melanomas and melanocytic nevi in a large cohort, identifying a signature that can distinguish malignant melanoma from benign nevus with an overall accuracy of over 98%. The prediction model was validated in an independent set with an accuracy of 93% in classifying melanoma from nevi. Statistical analysis of the imaging mass spectrometry data revealed significant variations in mass-to-charge ratio peaks between the two tissue types. This study represents the largest imaging mass spectrometry investigation of cutaneous melanoma and nevi to date, demonstrating the potential for IMS to discriminate between melanocytic nevi and melanoma.

CANCERS (2021)

Review Pathology

Next-generation protein analysis in the pathology department

Melek Ahmed et al.

JOURNAL OF CLINICAL PATHOLOGY (2020)

Article Biochemical Research Methods

Combined Immunohistochemistry after Mass Spectrometry Imaging for Superior Spatial Information

Katharina Kriegsmann et al.

PROTEOMICS CLINICAL APPLICATIONS (2019)

Editorial Material Medical Laboratory Technology

Mass Spectrometry-Based Tissue Imaging: The Next Frontier in Clinical Diagnostics?

Felix Leung et al.

CLINICAL CHEMISTRY (2019)

Article Chemistry, Analytical

Multicenter Validation Study of Quantitative Imaging Mass Spectrometry

Jeremy A. Barry et al.

ANALYTICAL CHEMISTRY (2019)

Article Biochemical Research Methods

An external quality assurance trial to assess mass spectrometry protein testing facilities for identifying multiple human peptides

Martin P. Horan et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2019)

Article Biochemical Research Methods

A test metric for assessing single-cell RNA-seq batch correction

Maren Buettner et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

Increases in Tumor N-Glycan Polylactosamines Associated with Advanced HER2-Positive and Triple-Negative Breast Cancer Tissues

Danielle A. Scott et al.

PROTEOMICS CLINICAL APPLICATIONS (2019)

Article Biochemical Research Methods

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

Alice Ly et al.

PROTEOMICS CLINICAL APPLICATIONS (2019)

Article Oncology

HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides

Andrew Janowczyk et al.

JCO CLINICAL CANCER INFORMATICS (2019)

Article Biochemical Research Methods

Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry

Peggi M. Angel et al.

JOURNAL OF PROTEOME RESEARCH (2018)

Article Biochemical Research Methods

Round robin study of formalin-fixed paraffin-embedded tissues in mass spectrometry imaging

Achim Buck et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2018)

Article Biochemical Research Methods

Tumor classification with MALDI-MSI data of tissue microarrays: A case study

Nadine E. Mascini et al.

METHODS (2018)

Article Biochemistry & Molecular Biology

Typing of colon and lung adenocarcinoma by high throughput imaging mass spectrometry

Mark Kriegsmann et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2017)

Article Dermatology

Imaging mass spectrometry assists in the classification of diagnostically challenging atypical Spitzoid neoplasms

Rossitza Lazova et al.

JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY (2016)

Article Biochemical Research Methods

Using collective expert judgements to evaluate quality measures of mass spectrometry images

Andrew Palmer et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Towards imaging metabolic pathways in tissues

Tim J. A. Dekker et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2015)

Article Biochemical Research Methods

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

Jeffrey T. Leek et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Normalization in MALDI-TOF imaging datasets of proteins: practical considerations

Soeren-Oliver Deininger et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2011)

Article Biochemical Research Methods

Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry

Rita Casadonte et al.

NATURE PROTOCOLS (2011)