scholarly journals Using Biological Signals for Mass Recalibration of Mass Spectrometry Imaging Data

2020 ◽  
Author(s):  
Raphaël La Rocca ◽  
Christopher Kune ◽  
Mathieu Tiquet ◽  
Lachlan Stuart ◽  
Theodore Alexandrov ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Samples ◽  
Mass Spectrometry Imaging ◽  
Mass Shift ◽  
High Mass ◽  
Whole Body ◽  
Imaging Data ◽  
Data Adaptive ◽  
The Impact ◽  
Mass Shifts

<p>Mass spectrometry imaging (MSI) is a powerful and convenient method to reveal the spatial chemical composition of different biological samples. The molecular annotation of the detected signals is only possible when high mass accuracy is maintained across the entire image and the <i>m/z</i> range. However, the heterogeneous molecular composition of biological samples could result in fluctuations in the detected <i>m/z</i>-values, called mass shift. Mass shifts impact the interpretability of the detected signals by decreasing the number of annotations and by affecting the spatial consistency and accuracy of ion images. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. The selection of internal calibrating signals for a global MSI acquisition is not trivial, prone to false positive detection of calibrating signals and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of internal calibrating ions generated automatically in a data-adaptive manner. The method exploits RANSAC (<i>Random Sample Consensus</i>) algorithm, to select, in a robust manner, the experimental signal corresponding to internal calibrating signals by filtering out calibration points with infrequent mass errors and by using the remaining points to estimate a linear model of the mass shifts. We applied the method to a zebrafish whole body section acquired at high mass resolution to demonstrate the impact of mass shift on data analysis and the capacity of our algorithm to recalibrate MSI data. We illustrate the broad applicability of the method by recalibrating 31 different public MSI datasets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations, especially the high-confident annotations at a low false discovery rate.</p>

scholarly journals Adaptive pixel mass recalibration for mass spectrometry imaging based on locally endogenous biological signals.

2020 ◽  
Author(s):  
Raphaël La Rocca ◽  
Christopher Kune ◽  
Mathieu Tiquet ◽  
Lachlan Stuart ◽  
Gauthier Eppe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Samples ◽  
Mass Spectrometry Imaging ◽  
A Priori ◽  
Mass Shift ◽  
High Mass ◽  
Whole Body ◽  
False Positive Detection ◽  
Data Adaptive ◽  
The Impact

<p>Mass spectrometry imaging (MSI) is a powerful and convenient method for revealing the spatial chemical composition of different biological samples. Molecular annotation of the detected signals is only possible if a high mass accuracy is maintained over the entire image and the m/z range. However, the heterogeneous molecular composition of biological samples could lead to small fluctuations in the detected m/z-values, called mass shift. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. Their “a priori” selection for a global MSI acquisition is prone to false positive detection and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of pixel specific internal calibrating ions, automatically generated in a data-adaptive manner (https://github.com/LaRoccaRaphael/MSI_recalibration). Through a practical example, we applied the methodology to a zebrafish whole body section acquired at high mass resolution to demonstrate the impact of mass shift on data analysis and the capability of our algorithm to recalibrate MSI data. In addition, we illustrate the broad applicability of the method by recalibrating 31 different public MSI datasets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations (gaining from 20 up to 400 additional annotations), particularly the high-confidence annotations with a low false discovery rate.<br></p>

scholarly journals Adaptive pixel mass recalibration for mass spectrometry imaging based on locally endogenous biological signals.

2020 ◽  
Author(s):  
Raphaël La Rocca ◽  
Christopher Kune ◽  
Mathieu Tiquet ◽  
Lachlan Stuart ◽  
Gauthier Eppe ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Samples ◽  
Mass Spectrometry Imaging ◽  
A Priori ◽  
Mass Shift ◽  
High Mass ◽  
Whole Body ◽  
False Positive Detection ◽  
Data Adaptive ◽  
The Impact

<p>Mass spectrometry imaging (MSI) is a powerful and convenient method for revealing the spatial chemical composition of different biological samples. Molecular annotation of the detected signals is only possible if a high mass accuracy is maintained over the entire image and the m/z range. However, the heterogeneous molecular composition of biological samples could lead to small fluctuations in the detected m/z-values, called mass shift. The use of internal calibration is known to offer the best solution to avoid, or at least to reduce, mass shifts. Their “a priori” selection for a global MSI acquisition is prone to false positive detection and therefore to poor recalibration. To fill this gap, this work describes an algorithm that recalibrates each spectrum individually by estimating its mass shift with the help of a list of pixel specific internal calibrating ions, automatically generated in a data-adaptive manner (https://github.com/LaRoccaRaphael/MSI_recalibration). Through a practical example, we applied the methodology to a zebrafish whole body section acquired at high mass resolution to demonstrate the impact of mass shift on data analysis and the capability of our algorithm to recalibrate MSI data. In addition, we illustrate the broad applicability of the method by recalibrating 31 different public MSI datasets from METASPACE from various samples and types of MSI and show that our recalibration significantly increases the numbers of METASPACE annotations (gaining from 20 up to 400 additional annotations), particularly the high-confidence annotations with a low false discovery rate.<br></p>

scholarly journals Exemplifying the Screening Power of Mass Spectrometry Imaging over Label-Based Technologies for Simultaneous Monitoring of Drug and Metabolite Distributions in Tissue Sections

2015 ◽  
Vol 21 (2) ◽  
pp. 187-193 ◽  
Author(s):  
Richard J. A. Goodwin ◽  
Anna Nilsson ◽  
C. Logan Mackay ◽  
John G. Swales ◽  
Maria K. Johansson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Cyclic Peptide ◽  
Analysis Data ◽  
Resolving Power ◽  
High Mass ◽  
Whole Body ◽  
Ion Cyclotron Resonance ◽  
Label Free ◽  
Tissue Sections

Mass spectrometry imaging (MSI) provides pharmaceutical researchers with a suite of technologies to screen and assess compound distributions and relative abundances directly from tissue sections and offer insight into drug discovery–applicable queries such as blood-brain barrier access, tumor penetration/retention, and compound toxicity related to drug retention in specific organs/cell types. Label-free MSI offers advantages over label-based assays, such as quantitative whole-body autoradiography (QWBA), in the ability to simultaneously differentiate and monitor both drug and drug metabolites. Such discrimination is not possible by label-based assays if a drug metabolite still contains the radiolabel. Here, we present data exemplifying the advantages of MSI analysis. Data of the distribution of AZD2820, a therapeutic cyclic peptide, are related to corresponding QWBA data. Distribution of AZD2820 and two metabolites is achieved by MSI, which [14C]AZD2820 QWBA fails to differentiate. Furthermore, the high mass-resolving power of Fourier transform ion cyclotron resonance MS is used to separate closely associated ions.

Correcting mass shifts: A lock mass-free recalibration procedure for mass spectrometry imaging data

2015 ◽  
Vol 407 (25) ◽  
pp. 7603-7613 ◽  
Author(s):  
Purva Kulkarni ◽  
Filip Kaftan ◽  
Philipp Kynast ◽  
Aleš Svatoš ◽  
Sebastian Böcker
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Imaging Data ◽  
Mass Shifts

scholarly journals Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
G. Guo ◽  
M. Papanicolaou ◽  
N. J. Demarais ◽  
Z. Wang ◽  
K. L. Schey ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Spatial Distribution ◽  
High Resolution ◽  
Mass Spectrometry Imaging ◽  
Direct Detection ◽  
High Mass ◽  
Imaging Data ◽  
Distribution Maps ◽  
Automated Annotation ◽  
Peptide Mass

AbstractSpatial proteomics has the potential to significantly advance our understanding of biology, physiology and medicine. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful tool in the spatial proteomics field, enabling direct detection and registration of protein abundance and distribution across tissues. MALDI-MSI preserves spatial distribution and histology allowing unbiased analysis of complex, heterogeneous tissues. However, MALDI-MSI faces the challenge of simultaneous peptide quantification and identification. To overcome this, we develop and validate HIT-MAP (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets and generate customisable spatial distribution maps. HIT-MAP will be a valuable resource for the spatial proteomics community for analysing newly generated and retrospective datasets, enabling robust peptide and protein annotation and visualisation in a wide array of normal and disease contexts.

scholarly journals Spatially-Aware Clustering of Ion Images in Mass Spectrometry Imaging Data Using Deep Learning

2020 ◽  
Author(s):  
Wanqiu Zhang ◽  
Marc Claesen ◽  
Thomas Moerman ◽  
M. Reid Groseclose ◽  
Etienne Waelkens ◽  
...  
Keyword(s):  
Neural Network ◽  
Mass Spectrometry ◽  
Deep Learning ◽  
Mass Spectrometry Imaging ◽  
Spatial Information ◽  
Image Clustering ◽  
Imaging Data ◽  
The Neural Network ◽  
Clustering Quality ◽  
The Impact

AbstractComputational analysis is crucial to capitalize on the wealth of spatio-molecular information generated by mass spectrometry imaging (MSI) experiments. Currently, the spatial information available in MSI data is often under-utilized, due to the challenges of in-depth spatial pattern extraction.The advent of deep learning has greatly facilitated such complex spatial analysis. In this work, we use a pre-trained neural network to extract high-level features from ion images in MSI data, and test whether this improves downstream data analysis. The resulting neural network interpretation of ion images, coined neural ion images, are used to cluster ion images based on spatial expressions.We evaluate the impact of neural ion images on two ion image clustering pipelines, namely DBSCAN clustering, combined with UMAP-based dimensionality reduction, and k-means clustering. In both pipelines, we compare regular and neural ion images from two different MSI datasets. All tested pipelines could extract underlying spatial patterns, but the neural network-based pipelines provided better assignment of ion images, with more fine-grained clusters, and greater consistency in the spatial structures assigned to individual clusters.Additionally, we introduce the Relative Isotope Ratio metric to quantitatively evaluate clustering quality. The resulting scores show that isotopical m/z values are more often clustered together in the neural network-based pipeline, indicating improved clustering outcomes.The usefulness of neural ion images extends beyond clustering towards a generic framework to incorporate spatial information into any MSI-focused machine learning pipeline, both supervised and unsupervised.

scholarly journals Self-supervised Clustering of Mass Spectrometry Imaging Data Using Contrastive Learning

2021 ◽  
Author(s):  
Hang Hu ◽  
Jyothsna Padmakumar Bindu ◽  
Julia Laskin
Keyword(s):  
Mass Spectrometry ◽  
Biological Samples ◽  
Mass Spectrometry Imaging ◽  
Molecular Mapping ◽  
Label Free ◽  
Imaging Data ◽  
Supervised Clustering

Mass spectrometry imaging (MSI) is widely used for the label-free molecular mapping of biological samples. The identification of co-localized molecules in MSI data is crucial to the understanding of biochemical...

scholarly journals Time‐of‐flight secondary ion mass spectrometry imaging of biological samples with delayed extraction for high mass and high spatial resolutions

2015 ◽  
Vol 29 (13) ◽  
pp. 1187-1195 ◽  
Author(s):  
Quentin P. Vanbellingen ◽  
Nicolas Elie ◽  
Michael J. Eller ◽  
Serge Della‐Negra ◽  
David Touboul ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Samples ◽  
Mass Spectrometry Imaging ◽  
Secondary Ion Mass Spectrometry ◽  
Time Of Flight ◽  
High Mass ◽  
Ion Mass Spectrometry ◽  
Delayed Extraction ◽  
Secondary Ion

scholarly journals Spatially aware clustering of ion images in mass spectrometry imaging data using deep learning

2021 ◽  
Vol 413 (10) ◽  
pp. 2803-2819
Author(s):  
Wanqiu Zhang ◽  
Marc Claesen ◽  
Thomas Moerman ◽  
M. Reid Groseclose ◽  
Etienne Waelkens ◽  
...  
Keyword(s):  
Neural Network ◽  
Mass Spectrometry ◽  
Deep Learning ◽  
Mass Spectrometry Imaging ◽  
Spatial Information ◽  
Image Clustering ◽  
Imaging Data ◽  
The Neural Network ◽  
Clustering Quality ◽  
The Impact

AbstractComputational analysis is crucial to capitalize on the wealth of spatio-molecular information generated by mass spectrometry imaging (MSI) experiments. Currently, the spatial information available in MSI data is often under-utilized, due to the challenges of in-depth spatial pattern extraction. The advent of deep learning has greatly facilitated such complex spatial analysis. In this work, we use a pre-trained neural network to extract high-level features from ion images in MSI data, and test whether this improves downstream data analysis. The resulting neural network interpretation of ion images, coined neural ion images, is used to cluster ion images based on spatial expressions. We evaluate the impact of neural ion images on two ion image clustering pipelines, namely DBSCAN clustering, combined with UMAP-based dimensionality reduction, and k-means clustering. In both pipelines, we compare regular and neural ion images from two different MSI datasets. All tested pipelines could extract underlying spatial patterns, but the neural network-based pipelines provided better assignment of ion images, with more fine-grained clusters, and greater consistency in the spatial structures assigned to individual clusters. Additionally, we introduce the relative isotope ratio metric to quantitatively evaluate clustering quality. The resulting scores show that isotopical m/z values are more often clustered together in the neural network-based pipeline, indicating improved clustering outcomes. The usefulness of neural ion images extends beyond clustering towards a generic framework to incorporate spatial information into any MSI-focused machine learning pipeline, both supervised and unsupervised. Graphical abstract

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