Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS

Gustafsson, Ove J. R.; Eddes, James S.; Meding, Stephan; Koudelka, Tomas; Oehler, Martin K.; McColl, Shaun R.; Hoffmann, Peter

doi:10.1016/j.jprot.2012.04.054

Cited by 50 publications

(105 citation statements)

References 30 publications

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“…[35] 2.2 Protocol-specific solutions 2.2.1 10 mM citric acid monohydrate pH 6 [29,36] ▪ 1.05 g citric acid monohydrate (Sigma-Aldrich, Japan) ▪ Dissolve in 480 mL H 2 O ▪ pH to 6.0 using 1 M NaOH (~13 mL) (Merck, Darmstadt, Germany) ▪ Make up volume to 500 mL with H 2 O 2.2.2 100 mM ammonium bicarbonate (NH 4 [32] ▪ 0.4 pmol/mL angiotensin I [34][35][36][37][38][39][40][41][42][43] ( Figure 1. Protocol for mapping the distribution and determining the identity of tryptic peptides generated in situ.…”

Section: Chemicals Consumables and Equipmentmentioning

confidence: 99%

“…SNAP using averagine [39] peptide composition) ○ Re-calibration [32] (quadratic internal re-calibration, 300 ppm tolerance using a custom mass control list [.mcl] containing the following calibrants): Figure 3. Typical MALDI-TOF/TOF spectrum (single) from an in situ acquisition (500 laser shot sum) on an FFPE ovarian cancer section prepared using the described tryptic MALDI-IMS protocol in a previous research article.…”

Section: 4mentioning

confidence: 99%

“…[ 32] ▪ First, .xml peak lists are extracted from the folders containing each individual spectrum. ▪ Peak lists are combined into a single list sorted by m/z.…”

Section: Maldi-ims Cancer-specific Peptide Visualization and Calculatmentioning

confidence: 99%

“…4) was found to have an AWM m/z of 1905.981, as calculated from all spectra using a single linkage distance of 0.05 m/z units. [32] 6.7 The AWM m/z values for peaks of interest can now be matched to LC/MS/MS data generated from a tryptic digest of an adjacent section of cancer tissue.…”

Section: Examplementioning

confidence: 99%

“…[6,29] The methods necessary to prepare FFPE samples, perform MALDI-IMS, analyze data and characterize the resulting peptide features have not yet been standardized and are largely developed in-house by individual laboratories. [6,7,14,30,31] As such, the need to add to the limited number of detailed protocols in the field [14] prompted the current manuscript, in which the methods developed and published in two previous manuscripts by our group [29,32] have been described in a single detailed experimental workflow combining tryptic peptide MALDI-IMS and subsequent liquid chromatographic/tandem mass spectrometric (LC/MS/MS) identification of the peptides which localize to a region of interest (e.g. tumour tissue).…”

Section: Introductionmentioning

confidence: 99%

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Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Gustafsson

Eddes

Meding

et al. 2013

Rapid Comm Mass Spectrometry

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RATIONALE: Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the means to map the in situ distribution of tryptic peptides in formalin-fixed clinical tissue samples. The ability to analyze clinical samples is of great importance to further developments in the imaging field. However, there is a requirement in this field of research for additional methods describing the characterization of tryptic peptides by MALDI imaging. METHODS AND RESULTS: This protocol gives highly detailed instructions, with examples, for (1) successfully performing tryptic peptide MALDI imaging on formalin-fixed cancer tissue using a MALDI-TOF/TOF MS instrument, (2) tentatively generating identifications through nLC/MS/MS, and (3) validating these identifications by in situ MS/MS of peptides of interest. CONCLUSIONS: This protocol provides a detailed and straightforward description of the methods required for groups new to MALDI imaging to begin analysis of formalin-fixed clinical samples.

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Section: Chemicals Consumables and Equipmentmentioning

confidence: 99%

Section: 4mentioning

confidence: 99%

“…[ 32] ▪ First, .xml peak lists are extracted from the folders containing each individual spectrum. ▪ Peak lists are combined into a single list sorted by m/z.…”

Section: Maldi-ims Cancer-specific Peptide Visualization and Calculatmentioning

confidence: 99%

Section: Examplementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Gustafsson

Eddes

Meding

et al. 2013

Rapid Comm Mass Spectrometry

Self Cite

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Emerging Computational Methods in Mass Spectrometry Imaging

Laskin

2022

Advanced Science

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Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high-spatial resolution and high-throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation-driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods.

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Detection of early proteomic alterations in 5xFAD Alzheimer's disease neonatal mouse model via MALDI‐MSI

Uras

Karayel-Basar

Sahin

et al. 2023

Alzheimer's & Dementia

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Alzheimer's disease (AD) is a debilitating neurodegenerative disorder, characterized by memory deficit and dementia. AD is considered a multifactorial disorder where multiple processes like amyloid‐beta and tau accumulation, axonal degeneration, synaptic plasticity, and autophagic processes plays an important role. In this study, the spatial proteomic differences in the neonatal 5xFAD brain tissue were investigated using MALDI‐MSI coupled to LC‐MS/MS, and the statistically significantly altered proteins were associated with AD. Thirty‐five differentially expressed proteins (DEPs) between the brain tissues of neonatal 5xFAD and their littermate mice were detected via MALDI‐MSI technique. Among the 35 proteins identified, 26 of them were directly associated with AD. Our results indicated a remarkable resemblance in the protein expression profiles of neonatal 5xFAD brain when compared to AD patient specimens or AD mouse models. These findings showed that the molecular alterations in the AD brain existed even at birth and that some proteins are neurodegenerative presages in neonatal AD brain.Highlights Spatial proteomic alterations in the 5xFAD mouse brain compared to the littermate. 26 out of 35 differentially expressed proteins associated with Alzheimer's disease (AD). Molecular alterations and neurodegenerative presages in neonatal AD brain. Alterations in the synaptic function an early and common neurobiological thread.

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Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS

Cited by 50 publications

References 30 publications

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Emerging Computational Methods in Mass Spectrometry Imaging

Detection of early proteomic alterations in 5xFAD Alzheimer's disease neonatal mouse model via MALDI‐MSI

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