4.5 Review

What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Spectroscopy

On-tissue chemical derivatization in mass spectrometry imaging

Carla Harkin et al.

Summary: Mass spectrometry imaging (MSI) combines molecular and spatial information, making it a valuable tool in various applications. Chemical derivatization (CD) has proven to be an effective solution for ionization issues. On-tissue chemical derivatization (OTCD) is a powerful tool for studying the spatial distribution of poorly ionizable molecules within tissues.

MASS SPECTROMETRY REVIEWS (2022)

Article Chemistry, Analytical

Mass Spectrometry Imaging Techniques Enabling Visualization of Lipid Isomers in Biological Tissues

Antonin Bednarik et al.

ANALYTICAL CHEMISTRY (2022)

Review Spectroscopy

HIGH RESOLUTION MASS SPECTROMETRY IN LIPIDOMICS

Thomas Zuellig et al.

Summary: The rapid growth of lipidomics research in the past decade is closely linked to advancements in mass spectrometry instrumentation. The shift from low resolution to high-resolution lipidomics platforms is a key trend in the field.

MASS SPECTROMETRY REVIEWS (2021)

Article

Transparency and the Black Box Problem: Why We Do Not Trust AI

Warren J. von Eschenbach

Philosophy and Technology (2021)

Review Biochemical Research Methods

Recent developments of novel matrices and on-tissue chemical derivatization reagents for MALDI-MSI

Qiuqin Zhou et al.

Summary: MALDI-MSI is a rapidly growing technique for visualizing the distribution of biomolecules in tissue sections, with challenges such as sensitivity and specificity. Recent developments in small organic MALDI matrices and on-tissue chemical derivatization reagents play a crucial role in improving image quality and expanding application areas.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2021)

Review Chemistry, Physical

Quantitative Mass Spectrometry Imaging of Biological Systems

Daisy Unsihuay et al.

Summary: Mass spectrometry imaging (MSI) is a powerful label-free technique that can provide detailed maps of hundreds of molecules in complex samples with high sensitivity and subcellular spatial resolution. Accurate quantification in MSI requires a detailed understanding of matrix effects, extraction efficiency, and mass-dependent ion losses. Approaches developed for quantitative MSI of metabolites, lipids, and proteins in biological tissues are discussed for current and future applications.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 72 (2021)

Article Biochemistry & Molecular Biology

Mass spectrometry imaging of phosphatidylcholine metabolism in lungs administered with therapeutic surfactants and isotopic tracers

Shane R. Ellis et al.

Summary: In this study, mass spectrometry imaging with high mass resolution and stable isotope labeling was used to analyze spatial distribution of phosphatidylcholine (PC) metabolism in mouse lungs, revealing dysregulated surfactant metabolism and turnover of therapeutic pulmonary surfactants. The dual labeling strategy demonstrated lack of inhibition of endogenous PC synthesis by exogenous surfactant and showed the location of acyl chain remodeling processes leading to formation of polyunsaturated PC lipids. This ability to visualize discrete metabolic events has potential applications in both clinical and experimental studies.

JOURNAL OF LIPID RESEARCH (2021)

Article Biochemical Research Methods

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

Wanqiu Zhang et al.

Summary: This paper introduces the use of neural networks to extract high-level features from ion images and their application in ion image clustering. The results show that neural network-based pipelines provide better clustering outcomes and introduce a relative isotope ratio metric for clustering evaluation.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2021)

Review Biochemical Research Methods

Applications of stable isotopes in MALDI imaging: current approaches and an eye on the future

Angus C. Grey et al.

Summary: Matrix-assisted laser desorption/ionisation-imaging mass spectrometry (MALDI-IMS) is a valuable imaging modality in the study of biological, biomedical and pathological processes. The use of stable isotopically labelled (SIL) compounds in MALDI-IMS helps to overcome technical barriers and enhance accuracy and versatility. Studies delivering SIL compounds to live tissues provide insights into cell, tissue and inter-tissue metabolism while maintaining spatial resolution.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2021)

Article Chemistry, Analytical

Deep Learning-Based Annotation Transfer between Molecular Imaging Modalities: An Automated Workflow for Multimodal Data Integration

Alan M. Race et al.

Summary: The article introduces a generic method for extracting information from different modalities using annotations from one microscopy modality and presents a fast, general multimodal registration workflow for automatic alignment of complex data sets. Experimental results demonstrate that the proposed methods help better understand tumor heterogeneity and the tumor microenvironment.

ANALYTICAL CHEMISTRY (2021)

Article Chemistry, Analytical

Transmission-Mode MALDI Mass Spectrometry Imaging of Single Cells: Optimizing Sample Preparation Protocols

Tanja Bien et al.

Summary: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has the potential to visualize the spatial distribution of biomolecules in cell cultures and tissue sections with high resolution, but sample preparation is crucial. A study found that a robust sample preparation protocol can preserve cell morphology and molecular integrity, contributing to the study of cell-to-cell heterogeneities at a molecular level. Advancements in single-cell MALDI imaging could benefit from these protocols.

ANALYTICAL CHEMISTRY (2021)

Article Chemistry, Analytical

Native Mass Spectrometry Imaging of Proteins and Protein Complexes by Nano-DESI

Oliver J. Hale et al.

Summary: By utilizing nanospray-desorption electrospray ionization (nano-DESI), native mass spectrometry imaging (native MSI) has achieved significant improvements in resolution compared to native LESA MSI, allowing for more precise imaging. This technique can also be used for location-targeted proteomic analysis directly from tissues.

ANALYTICAL CHEMISTRY (2021)

Article Chemistry, Applied

MALDI-TOF/TOF tandem mass spectrometry imaging reveals non-uniform distribution of disaccharide isomers in plant tissues

Lingpeng Zhan et al.

Summary: Mass spectrometry imaging (MSI) is a powerful technique for studying biomolecular locations in tissues, but often struggles to differentiate isomeric compounds. Coupling tandem mass spectrometry with MSI can help differentiate isomers effectively. This study utilized MALDI-TOF/TOF tandem mass spectrometry imaging to successfully differentiate isomeric disaccharides in plant tissues, highlighting the importance of considering isobaric compounds in research.

FOOD CHEMISTRY (2021)

Article Computer Science, Artificial Intelligence

A Survey of the Usages of Deep Learning for Natural Language Processing

Daniel W. Otter et al.

Summary: This article provides a brief introduction to the recent developments in natural language processing driven by deep learning models, discusses their applications and research findings, and offers recommendations for future research directions.

IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS (2021)

Article Biochemical Research Methods

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Florian Huber et al.

PLoS Computational Biology (2021)

Article Chemistry, Analytical

Perspective on Multimodal Imaging Techniques Coupling Mass Spectrometry and Vibrational Spectroscopy: Picturing the Best of Both Worlds

Stefania Alexandra Iakab et al.

Summary: Combining mass spectrometry imaging and vibrational spectroscopy imaging in multimodal strategies has shown advantages for studying biological samples and overcoming challenges, with potential for greater impact in clinical applications in the future.

ANALYTICAL CHEMISTRY (2021)

Article Biochemical Research Methods

OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data

Mateusz K. Lacki et al.

Summary: The Bruker timsTOF Pro instrument combines TIMS with TOF mass spectrometry for proteomics, lipidomics, and metabolomics applications. Computer programs like OpenTIMS, TimsR, and TimsPy provide swift and user-friendly access to the raw data, extending the interaction possibilities to macOS and enabling easy analysis through the vaex module.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Chemistry, Analytical

rMSIannotation: A peak annotation tool for mass spectrometry imaging based on the analysis of isotopic intensity ratios

Lluc Semente et al.

Summary: The paper introduces a peak annotation algorithm rMSIannotation for annotating carbon isotopes and adducts in metabolomics and lipidomics imaging mass spectrometry datasets. The algorithm measures and evaluates the intensity ratio between carbon isotopic peaks and annotates them based on the distribution model across the m/z axis of compounds. The study shows that monoisotopic peaks can serve as a data reduction method, retaining most of the biological variance in the dataset.

ANALYTICA CHIMICA ACTA (2021)

Article Chemistry, Analytical

Determination of Abundant Metabolite Matrix Adducts Illuminates the Dark Metabolome of MALDI-Mass Spectrometry Imaging Datasets

Moritz Janda et al.

Summary: Spatial metabolomics using mass spectrometry imaging is a powerful tool to map hundreds to thousands of metabolites in biological systems. However, annotation of m/z values is a major challenge in MSI, complicated by background ions introduced during experimental procedures. Adduct formation, particularly with sodium or potassium ions, significantly increases total m/z peak counts, and current data analyses often neglect matrix adducts, leading to an overestimation of metabolite numbers.

ANALYTICAL CHEMISTRY (2021)

Article Multidisciplinary Sciences

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

G. Guo et al.

Summary: Spatial proteomics using MALDI-MSI is a powerful tool for direct detection of protein distribution in tissues but faces challenges in peptide quantification and identification. The development of HIT-MAP provides an open-source bioinformatics workflow for accurate protein annotation and spatial mapping from MALDI-MSI data.

NATURE COMMUNICATIONS (2021)

Article Multidisciplinary Sciences

Peak learning of mass spectrometry imaging data using artificial neural networks

Walid M. Abdelmoula et al.

Summary: This study demonstrates the application of artificial intelligence in mining Mass Spectrometry Imaging (MSI) data to reveal biologically relevant metabolomic and proteomic information acquired from different mass spectrometry platforms. By utilizing a fully connected variational autoencoder, the researchers developed the msiPL method to learn and visualize the underlying non-linear spectral manifold in MSI data, uncovering biologically relevant clusters of tissue anatomy and tumor heterogeneity in various tissue types.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

Sample preparation of formalin-fixed paraffin-embedded tissue sections for MALDI-mass spectrometry imaging

Juliane Hermann et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2020)

Article Biochemical Research Methods

rMSIproc: an R package for mass spectrometry imaging data processing

Pere Rafols et al.

BIOINFORMATICS (2020)

Article Biochemical Research Methods

ColocML: machine learning quantifies co-localization between mass spectrometry images

Katja Ovchinnikova et al.

BIOINFORMATICS (2020)

Article Biochemical Research Methods

LipostarMSI: Comprehensive, Vendor-Neutral Software for Visualization, Data Analysis, and Automated Molecular Identification in Mass Spectrometry Imaging

Sara Tortorella et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2020)

Article Biochemical Research Methods

Influence of Lipid Fragmentation in the Data Analysis of Imaging Mass Spectrometry Experiments

Jone Garate et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2020)

Article Chemistry, Analytical

Toward the Rational Design of Universal Dual Polarity Matrix for MALDI Mass Spectrometry

Penghsuan Huang et al.

ANALYTICAL CHEMISTRY (2020)

Article Biochemical Research Methods

OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images

Katja Ovchinnikova et al.

BMC BIOINFORMATICS (2020)

Article Chemistry, Analytical

MALDI-2 for the Enhanced Analysis of N-Linked Glycans by Mass Spectrometry Imaging

Bram Heijs et al.

ANALYTICAL CHEMISTRY (2020)

Article Biochemical Research Methods

Bromopyrylium Derivatization Facilitates Identification by Mass Spectrometry Imaging of Monoamine Neurotransmitters and Small Molecule Neuroactive Compounds

Reza Shariatgorji et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2020)

Article Biochemical Research Methods

Ion Mobility-Mass Spectrometry Imaging Workflow

Daniela Mesa Sanchez et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2020)

Review Genetics & Heredity

Opening the Black Box: Interpretable Machine Learning for Geneticists

Christina B. Azodi et al.

TRENDS IN GENETICS (2020)

Article Biochemical Research Methods

Feature-based molecular networking in the GNPS analysis environment

Louis-Felix Nothias et al.

NATURE METHODS (2020)

Article Biochemical Research Methods

diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition

Florian Meier et al.

NATURE METHODS (2020)

Article Biotechnology & Applied Microbiology

Evaluation of freely available software tools for untargeted quantification of 13C isotopic enrichment in cellular metabolome from HR-LC/MS data

Manohar C. Dange et al.

METABOLIC ENGINEERING COMMUNICATIONS (2020)

Article Physics, Atomic, Molecular & Chemical

Ultra-high resolution MALDI-FTICR-MSI analysis of intact proteins in mouse and human pancreas tissue

Isabella Piga et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2019)

Article Physics, Atomic, Molecular & Chemical

A quantitative map of glutathione in the aging human lens

Angus C. Grey et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2019)

Article Chemistry, Analytical

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

Nils Hoffmann et al.

ANALYTICAL CHEMISTRY (2019)

Review Biochemical Research Methods

Advanced MALDI mass spectrometry imaging in pharmaceutical research and drug development

Sandra Schulz et al.

CURRENT OPINION IN BIOTECHNOLOGY (2019)

Review Biochemistry & Molecular Biology

Protein identification strategies in MALDI imaging mass spectrometry: a brief review

Daniel J. Ryan et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2019)

Article Biochemical Research Methods

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

Kai Duhrkop et al.

NATURE METHODS (2019)

Article Chemistry, Analytical

Metal Oxide Laser Ionization Mass Spectrometry Imaging (MOLI MSI) Using Cerium(IV) Oxide

Sankha S. Basu et al.

ANALYTICAL 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

Precise co-registration of mass spectrometry imaging, histology, and laser microdissection-based omics

Frederic Dewez et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2019)

Article Chemistry, Analytical

3-Aminophthalhydrazide (Luminol) As a Matrix for Dual-Polarity MALDI MS Imaging

Bin Li et al.

ANALYTICAL CHEMISTRY (2019)

Article Biochemistry & Molecular Biology

CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification

Yannick Djoumbou-Feunang et al.

METABOLITES (2019)

Review Physiology

METABOLOMICS FOR INVESTIGATING PHYSIOLOGICAL AND PATHOPHYSIOLOGICAL PROCESSES

David S. Wishart

PHYSIOLOGICAL REVIEWS (2019)

Article Chemistry, Analytical

Deciphering Metabolic Heterogeneity by Single-Cell Analysis

Tom M. J. Evers et al.

ANALYTICAL CHEMISTRY (2019)

Article Chemistry, Analytical

Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics

Lin Wang et al.

ANALYTICAL CHEMISTRY (2019)

Article Biochemical Research Methods

Sputter-Coated Metal Screening for Small Molecule Analysis and High-Spatial Resolution Imaging in Laser Desorption Ionization Mass Spectrometry

Rebecca L. Hansen et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2019)

Article Physics, Atomic, Molecular & Chemical

Class-specific depletion of lipid ion signals in tissues upon formalin fixation

D. R. N. Vos et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2019)

Article Biochemistry & Molecular Biology

PubChem 2019 update: improved access to chemical data

Sunghwan Kim et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Three-Dimensional Mass Spectrometry Imaging Identifies Lipid Markers of Medulloblastoma Metastasis

Martin R. L. Paine et al.

SCIENTIFIC REPORTS (2019)

Article Biochemical Research Methods

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

Mark T. Bokhart et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2018)

Article Biochemical Research Methods

Towards High-Resolution Tissue Imaging Using Nanospray Desorption Electrospray Ionization Mass Spectrometry Coupled to Shear Force Microscopy

Son N. Nguyen et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2018)

Article Biochemistry & Molecular Biology

HMDB 4.0: the human metabolome database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Biochemical Research Methods

MALDI matrices for low molecular weight compounds: an endless story?

Cosima Damiana Calvano et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2018)

Review Biochemistry & Molecular Biology

Advances in mass spectrometry imaging coupled to ion mobility spectrometry for enhanced imaging of biological tissues

Marta Sans et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2018)

Article Robotics

The limits and potentials of deep learning for robotics

Niko Suenderhauf et al.

INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH (2018)

Article Chemistry, Multidisciplinary

Mapping of drug distribution in the rabbit liver tumor model by complementary fluorescence and mass spectrometry imaging

Katrin Fuchs et al.

JOURNAL OF CONTROLLED RELEASE (2018)

Review Chemistry, Analytical

Nanoparticle assisted laser desorption/ionization mass spectrometry for small molecule analytes

Hani Nasser Abdelhamid

MICROCHIMICA ACTA (2018)

Article Biochemical Research Methods

Automated, parallel mass spectrometry imaging and structural identification of lipids

Shane R. Ellis et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

Erica M. Forsberg et al.

NATURE PROTOCOLS (2018)

Article Biochemistry & Molecular Biology

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

Jasmine Chong et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Chemistry, Multidisciplinary

Advances in mass spectrometry-based metabolomics for investigation of metabolites

Jun-Ling Ren et al.

RSC ADVANCES (2018)

Article Chemistry, Analytical

Data-Driven Restoring of Metabolite Annotations Significantly Improves Sensitivity

Ana S. C. Silva et al.

ANALYTICAL CHEMISTRY (2018)

Review Radiology, Nuclear Medicine & Medical Imaging

Mass Spectrometry Imaging and Integration with Other Imaging Modalities for Greater Molecular Understanding of Biological Tissues

Tiffany Porta Siegel et al.

MOLECULAR IMAGING AND BIOLOGY (2018)

Article Biochemical Research Methods

Evaluation of Digital Image Recognition Methods for Mass Spectrometry Imaging Data Analysis

Mans Ekelof et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2018)

Review Biochemistry & Molecular Biology

Recent Developments of Useful MALDI Matrices for the Mass Spectrometric Characterization of Lipids

Jenny Leopold et al.

BIOMOLECULES (2018)

Article Biochemical Research Methods

Deep learning for tumor classification in imaging mass spectrometry

Jens Behrmann et al.

BIOINFORMATICS (2018)

Review Chemistry, Analytical

Mass Spectrometry Imaging: A Review of Emerging Advancements and Future Insights

Amanda Rae Buchberger et al.

ANALYTICAL CHEMISTRY (2018)

Article Biochemical Research Methods

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Andrew Palmer et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution

Mario Kompauer et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Mass Spectrometry Imaging, Laser Capture Microdissection, and LC-MS/MS of the Same Tissue Section

Marialaura Dilillo et al.

JOURNAL OF PROTEOME RESEARCH (2017)

Article Biochemical Research Methods

Overlapping MALDI-Mass Spectrometry Imaging for In-Parallel MS and MS/MS Data Acquisition without Sacrificing Spatial Resolution

Rebecca L. Hansen et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2017)

Review Microbiology

Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples

Jesse P. Harrison et al.

FRONTIERS IN MICROBIOLOGY (2017)

Review Biochemistry & Molecular Biology

Quantification of low molecular weight compounds by MALDI imaging mass spectrometry - A tutorial review

Ignacy Rzagalinski et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2017)

Article Chemistry, Analytical

On Mass Ambiguities in High-Resolution Shotgun Lipidomics

Chris Bielow et al.

ANALYTICAL CHEMISTRY (2017)

Article Biochemical Research Methods

MALDI MSI and LC-MS/MS: Towards preclinical determination of the neurotoxic potential of fluoroquinolones

Adeola Shobo et al.

DRUG TESTING AND ANALYSIS (2016)

Article Biochemistry & Molecular Biology

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Chemistry, Analytical

Absolute Quantitative MALDI Imaging Mass Spectrometry: A Case of Rifampicin in Liver Tissues

Chad W. Chumbley et al.

ANALYTICAL CHEMISTRY (2016)

Article Biochemical Research Methods

Untargeted Metabolomics Strategies-Challenges and Emerging Directions

Alexandra C. Schrimpe-Rutledge et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2016)

Article Multidisciplinary Sciences

Can we open the black box of AI?

Davide Castelvecchi

NATURE (2016)

Editorial Material Biochemical Research Methods

What more can TOF-SIMS bring than other MS imaging methods?

David Touboul et al.

BIOANALYSIS (2016)

Article Chemistry, Multidisciplinary

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

Christoph Ruttkies et al.

JOURNAL OF CHEMINFORMATICS (2016)

Article Multidisciplinary Sciences

3D Mass Spectrometry Imaging Reveals a Very Heterogeneous Drug Distribution in Tumors

S. Giordano et al.

SCIENTIFIC REPORTS (2016)

Article Biochemical Research Methods

The challenge of on-tissue digestion for MALDI MSI- a comparison of different protocols to improve imaging experiments

Hanna C. Diehl et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2015)

Article Chemistry, Analytical

Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees

Martin Loos et al.

ANALYTICAL CHEMISTRY (2015)

Article Biochemical Research Methods

Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments

Kyle D. Bemis et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

The SwissLipids knowledgebase for lipid biology

Lucila Aimo et al.

BIOINFORMATICS (2015)

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

Pyrylium Salts as Reactive Matrices for MALDI-MS Imaging of Biologically Active Primary Amines

Mohammadreza Shariatgorji et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Article Biochemical Research Methods

Imaging MS in Toxicology: An Investigation of Juvenile Rat Nephrotoxicity Associated with Dabrafenib Administration

M. Reid Groseclose et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Article Biochemical Research Methods

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

Hiroshi Tsugawa et al.

NATURE METHODS (2015)

Article Multidisciplinary Sciences

Mass spectrometry imaging with laser-induced postionization

Jens Soltwisch et al.

SCIENCE (2015)

Article Biochemical Research Methods

Distribution and quantification of irinotecan and its active metabolite SN-38 in colon cancer murine model systems using MALDI MSI

Achim Buck et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2015)

Article Biochemical Research Methods

Discussion point: reporting guidelines for mass spectrometry imaging

Liam A. McDonnell et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2015)

Article Biochemical Research Methods

A spiked tissue-based approach for quantification of phosphatidylcholines in brain section by MALDI mass spectrometry imaging

Laure Jadoul et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2015)

Review Chemistry, Analytical

Mass Spectrometry Imaging of Biomolecular Information

Bernhard Spengler

ANALYTICAL CHEMISTRY (2015)

Article Biochemical Research Methods

Comprehensive Lipidome Analysis by Shotgun Lipidomics on a Hybrid Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer

Reinaldo Almeida et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Editorial Material Engineering, Environmental

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

Emma L. Schymanski et al.

ENVIRONMENTAL SCIENCE & TECHNOLOGY (2014)

Article Biochemistry & Molecular Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Ron Caspi et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Chemistry, Analytical

Lipid imaging by mass spectrometry - a review

David Gode et al.

ANALYST (2013)

Article Chemistry, Analytical

Surface-Transfer Mass Spectrometry Imaging on a Monoisotopic Silver Nanoparticle Enhanced Target

Joanna Niziol et al.

ANALYTICAL CHEMISTRY (2013)

Article Chemistry, Analytical

Orbitrap Mass Spectrometry

Roman A. Zubarev et al.

ANALYTICAL CHEMISTRY (2013)

Article Chemistry, Analytical

A Mimetic Tissue Model for the Quantification of Drug Distributions by MALDI Imaging Mass Spectrometry

M. Reid Groseclose et al.

ANALYTICAL CHEMISTRY (2013)

Article Biochemical Research Methods

Testing for presence of known and unknown molecules in imaging mass spectrometry

Theodore Alexandrov et al.

BIOINFORMATICS (2013)

Review Biochemical Research Methods

MALDI imaging mass spectrometry and analysis of endogenous peptides

Bijon Chatterji et al.

EXPERT REVIEW OF PROTEOMICS (2013)

Article Physics, Atomic, Molecular & Chemical

Bioimaging of copper deposition in Wilson's diseases mouse liver by laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI)

M-M Pornwilard et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2013)

Article Biochemical Research Methods

Multiplex mass spectrometry imaging for latent fingerprints

Gargey B. Yagnik et al.

JOURNAL OF MASS SPECTROMETRY (2013)

Article Biochemical Research Methods

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

Guillaume Robichaud et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2013)

Article Biochemical Research Methods

The mzQuantML Data Standard for Mass Spectrometry-based Quantitative Studies in Proteomics

Mathias Walzer et al.

MOLECULAR & CELLULAR PROTEOMICS (2013)

Article Biochemistry & Molecular Biology

Detection of high molecular weight proteins by MALDI imaging mass spectrometry

Veronica Mainini et al.

MOLECULAR BIOSYSTEMS (2013)

Article Biochemical Research Methods

LipidBlast in silico tandem mass spectrometry database for lipid identification

Tobias Kind et al.

NATURE METHODS (2013)

Article Biochemistry & Molecular Biology

MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data

Kenneth Haug et al.

NUCLEIC ACIDS RESEARCH (2013)

Review Chemistry, Analytical

High Resolution Mass Spectrometry

Feng Xian et al.

ANALYTICAL CHEMISTRY (2012)

Article Biochemical Research Methods

MALDIquant: a versatile R package for the analysis of mass spectrometry data

Sebastian Gibb et al.

BIOINFORMATICS (2012)

Article Computer Science, Artificial Intelligence

Gaussian mixture decomposition in the analysis of MALDI-TOF spectra

Joanna Polanska et al.

EXPERT SYSTEMS (2012)

Article Biochemical Research Methods

imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data

Thorsten Schramm et al.

JOURNAL OF PROTEOMICS (2012)

Article Biochemical Research Methods

Automated MALDI Matrix Coating System for Multiple Tissue Samples for Imaging Mass Spectrometry

William P. Mounfield et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2012)

Article Biochemical Research Methods

Advanced Mass Calibration and Visualization for FT-ICR Mass Spectrometry Imaging

Donald F. Smith et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2012)

Article Biochemical Research Methods

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

Andrew R. Jones et al.

MOLECULAR & CELLULAR PROTEOMICS (2012)

Review Cell Biology

Metabolomics: the apogee of the omics trilogy

Gary J. Patti et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Mass spectrometry imaging (MSI) of metals in mouse spinal cord by laser ablation ICP-MS

J. Sabine Becker et al.

METALLOMICS (2012)

Article Multidisciplinary Sciences

mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra

Timo H. J. Niedermeyer et al.

PLOS ONE (2012)

Article Chemistry, Analytical

Protein identification in mass-spectrometry imaging

Nadine E. Mascini et al.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2012)

Review Biochemical Research Methods

Matrix-assisted laser desorption ionization imaging mass spectrometry in lipidomics

J. A. Fernandez et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2011)

Article Biochemical Research Methods

Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data

Juergen Hartler et al.

BIOINFORMATICS (2011)

Article Physics, Atomic, Molecular & Chemical

Mass spectrometric imaging (MSI) of metals using advanced BrainMet techniques for biomedical research

Johanna Sabine Becker et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2011)

Article Biochemical Research Methods

MALDI Mass Spectrometric Imaging of Lipids in Rat Brain Injury Models

Joseph A. Hankin et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2011)

Article Biochemical Research Methods

Compelling Evidence for Lucky Survivor and Gas Phase Protonation: The Unified MALDI Analyte Protonation Mechanism

Thorsten W. Jaskolla et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2011)

Article Biochemical Research Methods

mzML-a Community Standard for Mass Spectrometry Data

Lennart Martens et al.

MOLECULAR & CELLULAR PROTEOMICS (2011)

Review Biochemical Research Methods

A concise review of mass spectrometry imaging

Erika R. Amstalden van Hove et al.

JOURNAL OF CHROMATOGRAPHY A (2010)

Article Biochemical Research Methods

MassBank: a public repository for sharing mass spectral data for life sciences

Hisayuki Horai et al.

JOURNAL OF MASS SPECTROMETRY (2010)

Article Biochemical Research Methods

Calibration Function for the Orbitrap FTMS Accounting for the Space Charge Effect

Mikhail V. Gorshkov et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2010)

Article Biochemical Research Methods

Mass spectrometry image correlation: Quantifying colocalization

Liam A. McDonnell et al.

JOURNAL OF PROTEOME RESEARCH (2008)

Article Endocrinology & Metabolism

Proposed minimum reporting standards for chemical analysis

Lloyd W. Sumner et al.

METABOLOMICS (2007)

Article Biochemical Research Methods

Sublimation as a method of matrix application for mass spectrometric imaging

Joseph A. Hankin et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2007)

Article Biochemical Research Methods

Analysis of erlotinib and its metabolites in rat tissue sections by MALDI quadrupole time-of-flight mass spectrometry

Luca Signor et al.

JOURNAL OF MASS SPECTROMETRY (2007)

Article Biochemical Research Methods

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Tobias Kind et al.

BMC BIOINFORMATICS (2007)

Article Physics, Atomic, Molecular & Chemical

Compound and metabolite distribution measured by MALDI mass spectrometric imaging in whole-body tissue sections

Markus Stoeckli et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2007)

Article Physics, Atomic, Molecular & Chemical

Processing MALDI mass spectra to improve mass spectral direct tissue analysis

Jeremy L. Norris et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2007)

Article Physics, Atomic, Molecular & Chemical

Development of capabilities for imaging mass spectrometry under ambient conditions with desorption electrospray ionization (DESI)

Demian R. Ifa et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2007)

Article Biochemical Research Methods

Imaging mass spectrometry of neuropeptides in decapod crustacean neuronal tissues

Stephanie S. DeKeyser et al.

JOURNAL OF PROTEOME RESEARCH (2007)

Article Biochemistry & Molecular Biology

LMSD: LIPID MAPS structure database

Manish Sud et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Chemistry, Analytical

Direct molecular analysis of whole-body animal tissue sections by imaging MALDI mass spectrometry

Sheerin Khatib-Shahidi et al.

ANALYTICAL CHEMISTRY (2006)

Article Biochemical Research Methods

The HUPO proteomics standards initiative - Overcoming the fragmentation of proteomics data

Henning Hermjakob

PROTEOMICS (2006)

Article Biochemical Research Methods

Gas chromatography mass spectrometry-based metabolite profiling in plants

Jan Lisec et al.

NATURE PROTOCOLS (2006)

Article Biochemistry & Molecular Biology

The PeptideAtlas project

Frank Desiere et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Medical Laboratory Technology

METLIN - A metabolite mass spectral database

CA Smith et al.

THERAPEUTIC DRUG MONITORING (2005)

Review Biochemical Research Methods

Fluorescence microscopy

JW Lichtman et al.

NATURE METHODS (2005)

Review Spectroscopy

Accurate mass measurements by Fourier transform mass spectrometry

LK Zhang et al.

MASS SPECTROMETRY REVIEWS (2005)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)