2D and 3D MALDI-imaging: Conceptual strategies for visualization and data mining

Thiele, Herbert; Heldmann, Stefan; Trede, Dennis; Strehlow, Jan; Wirtz, Stefan; Dreher, Wolfgang; Berger, Judith; Oetjen, Janina; Kobarg, Jan Hendrik; Fischer, Bernd; Maaß, Peter

doi:10.1016/j.bbapap.2013.01.040

Cited by 72 publications

(81 citation statements)

References 43 publications

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“…The 2D MALDI Imaging data of rostral (R1) caudal (C1) and lesion (L) sections after 3 days of SCI (n ϭ 1) were analyzed with SCiLS Lab 2015a (30). The baseline was removed by iterative convolution and the data were normalized based on the total ion count (TIC) method (31).…”

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confidence: 99%

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Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair

Devaux¹,

Cizkova²,

Quanico³

et al. 2016

Molecular & Cellular Proteomics

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Spinal cord injury (SCI) represents a major debilitating health issue with a direct socioeconomic burden on the public and private sectors worldwide. Although several studies have been conducted to identify the molecular progression of injury sequel due from the lesion site, still the exact underlying mechanisms and pathways of injury development have not been fully elucidated. In this work, based on OMICs, 3D matrix-assisted laser desorption ionization (MALDI) imaging, cytokines arrays, confocal imaging we established for the first time that molecular and cellular processes occurring after SCI are altered between the lesion proximity, i.e. rostral and caudal segments nearby the lesion (R1-C1) whereas segments distant from R1-C1, i.e. R2-C2 and R3-C3 levels coexpressed factors implicated in neurogenesis. Delay in T regulators recruitment between R1 and C1 favor discrepancies between the two segments. This is also reinforced by presence of neurites outgrowth inhibitors in C1, absent in R1. Moreover

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confidence: 99%

“…The PLSA was performed with random initialization with a threshold of 29.0588, maximum interval processing mode, lower m/z range threshold mode and individual spectrum mode. The PCA was performed with no scaling, a threshold of 29.0588, maximum interval processing mode, lower m/z range threshold mode and individual spectrum mode (30).…”

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confidence: 99%

Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair

Devaux¹,

Cizkova²,

Quanico³

et al. 2016

Molecular & Cellular Proteomics

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“…Since that time IMS has been successfully employed in cancer research, neuroscience, reproductive biology and pharmaceutics for the study and development of new drugs [2]. Most of the IMS applications in cancer research are connected with identification of spectrally unique regions within a sample by spatial segmentation [3,4]. In this paper we are resolving a reverse problem -specific tissue areas are delineated by an experienced pathologist giving information for each spectrum about region affiliation, which gives an opportunity to find biomarkers with increased or decreased concentration level across regions.…”

Section: Introductionmentioning

confidence: 99%

Modeling of Imaging Mass Spectrometry Data and Testing by Permutation for Biomarkers Discovery in Tissues

Marczyk

Drazek

Pietrowska

et al. 2015

Procedia Computer Science

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Exploration of tissue sections by imaging mass spectrometry reveals abundance of different biomolecular ions in different sample spots, allowing finding region specific features. In this paper we present computational and statistical methods for investigation of protein biomarkers i.e. biological features related to presence of different pathological states. Proposed complete processing pipeline includes data pre-processing, detection and quantification of peaks by using Gaussian mixture modeling and identification of specific features for different tissue regions by performing permutation tests. Application of created methodology provides detection of proteins/peptides with concentration levels specific for tumor area, normal epithelium, muscle or saliva gland regions with high confidence.

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“…To analyze several consecutive tissue sections at a time we generated a 3D MALDI imaging and a 3D high resolution histological image model respectively [16,17]. The simultaneous analysis should give us a more complex insight into cancer tissue.…”

Section: Introductionmentioning

confidence: 99%

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition

Lotz

Hoffmann

Lotz

et al. 2017

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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2D and 3D MALDI-imaging: Conceptual strategies for visualization and data mining

Cited by 72 publications

References 43 publications

Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair

Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair

Modeling of Imaging Mass Spectrometry Data and Testing by Permutation for Biomarkers Discovery in Tissues

Integration of 3D multimodal imaging data of a head and neck cancer and advanced feature recognition

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