Journal: Nucleic Acids Research

Article Title: The human methyltransferase ZCCHC4 catalyses N 6 -methyladenosine modification of 28S ribosomal RNA

doi: 10.1093/nar/gkz1147

Figure Lengend Snippet: ZCCHC4-dependent methylation of A4220 in 28S rRNA in cells. ( A ) Localization of m 6 A4220 in the 28S RNA structure. m 6 A4220 (green) is shown on the 28S rRNA structure, together with other known, snoRNA-independent methyl modifications (m 1 A1322, purple; m 3 C3782, blue; Gm4196, olive; m 5 C4447, pink; Um4498, cyan; Gm4499, yellow; m 3 U4530, red). The figure was adapted from Sergiev et al. , and made based on the corresponding published structure (PDB ID: 4UG0). Note that m 6 A4220, by an alternative numbering system, previously has been referred to as m 6 A4190. ( B ) Structure of the A4220-containing stem–loop. Shown is a schematic representation of the stem–loop, based on secondary structure prediction, as well as the structure of the corresponding segments in the context of the intact ribosome (generated from PDB ID: 4UG0; shown with orange backbone). Also indicated are the previously reported proximity and interaction between A4220 and C4211 (shown as stick representation in upper right panel, and indicated by a red, dotted line on the cartoon representation of the sequence) . ( C ) ZCCHC4 is required for methylation of A4220. 28S rRNA sub-fragment isolated from ZCCHC4 KO HAP-1 cells or corresponding WT cells was digested with RNase T1, and the resulting products analysed by MALDI mass spectrometry. Peaks corresponding to products derived from the A4220-containing stem–loop are indicated. Arrows indicate the A4220-encompassing product. Asterisks indicate 2′-3′ cyclic phosphate intermediates from the RNase T1 digestion. The m / z 1914.2 fragment was occasionally observed in both WT and KO rRNA preparations (but was detected only in the KO preparation in the shown experiment). Sequence information was not obtained, but the calculated stoichiometry (C 3 A 1 U 1 Gp) suggests that this fragment represents a truncated version, CACCUGp, of the m / z 2549.34 RNase T1 digestion product (shown in green); heterogeneity at the termini is commonly observed with this approach to purify rRNA sub-fragments. Um and Gm are 2′- O -ribose methylated versions of U and G, respectively.

Article Snippet: The desired 28S rRNA sub-fragment was purified by polyacrylamide gel electrophoresis and digested with RNase T1 for analysis on a Bruker UltraFlex MALDI mass spectrometer ( ).

Techniques: Methylation, Generated, Sequencing, Isolation, Mass Spectrometry, Derivative Assay

Journal: Journal of the American Society for Mass Spectrometry

Article Title: Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

doi: 10.1021/jasms.0c00439

Figure Lengend Snippet: Example single cell imaging results from TG-MALDI-2 in the analysis of Vero-B4 cell culture: (a) Bright-field microscopy image of Vero B cells with deposited DHB matrix; (b) background ( m / z = 633.042) and (c–e) single ion images of PE (36:2), PC (34:1), and PC (34:1). (f) High resolution bright-field microscopy image of highlighted red region in a, and (g) overlay of ion images in b, c, and e. (h) in-line bright-field microscopy image from the TG-MALDI-2 source outlined region in f. Adapted with permission from ref . 2019 Nature Research.

Article Snippet: There have also been many new instrumental designs developed to increase the imaging speed of MALDI-MSI since imaging overall large (tissue level) areas at single cell resolution increases the number of data points (pixels) needed to be obtained., Recently, Potocnik et al. used continuous laser acquisition to image lipids at a rate of 50 pixel/s and a lateral resolution of 10 μm in sections of mouse brain using a Bruker rapifleX MALDI Tissuetyper TOF-MS instrument.

Techniques: Single Cell, Imaging, Cell Culture, Microscopy

Journal: Journal of the American Society for Mass Spectrometry

Article Title: Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

doi: 10.1021/jasms.0c00439

Figure Lengend Snippet: Example of TOF-SIMS subcellular imaging, where the distribution of a drug is visualized in a single cell using the hybrid OrbiSIMS. (a) A sequence of total ion images captured every ∼400 nm of depth, as the cell was sputtered away. (b) Overlaid ion images of the PC headgroup in gray, m / z 157 (a nuclear marker) in magenta, and the drug (amiodarone) in green at each of the respective spatial locations in a , and (c) a 3D rendering of the cell that tomographically illustrates the location of PC, nucleus, and drug markers. Mass spectrum obtained from the ToF-MS (black) and the Orbitrap-MS (blue) of the (d) PC headgroup and (e) nuclear marker. Adapted with permission from ref . 2017 Nature Research.

Article Snippet: There have also been many new instrumental designs developed to increase the imaging speed of MALDI-MSI since imaging overall large (tissue level) areas at single cell resolution increases the number of data points (pixels) needed to be obtained., Recently, Potocnik et al. used continuous laser acquisition to image lipids at a rate of 50 pixel/s and a lateral resolution of 10 μm in sections of mouse brain using a Bruker rapifleX MALDI Tissuetyper TOF-MS instrument.

Techniques: Imaging, Single Cell, Sequencing, Marker

Journal: Frontiers in Microbiology

Article Title: MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

doi: 10.3389/fmicb.2015.00791

Figure Lengend Snippet: Microbial detection methods used in clinical microbiology.

Article Snippet: In the last 2 years, MALDI Biotyper CA System (Bruker Daltonics Inc.) has been approved by the US Food and Drug Administration (FDA) for identification of cultured bacteria from human specimens ( in vitro diagnosis).

Techniques: In Situ Hybridization, Fluorescence In Situ Hybridization, Staining, Real-time Polymerase Chain Reaction, Multiplex PCR, DNA Sequencing, Sequencing, Biomarker Discovery, Amplification, Lamp Assay

Journal: Frontiers in Microbiology

Article Title: MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

doi: 10.3389/fmicb.2015.00791

Figure Lengend Snippet: Schematic diagram showing the work-flow in a MALDI-TOF MS .

Article Snippet: In the last 2 years, MALDI Biotyper CA System (Bruker Daltonics Inc.) has been approved by the US Food and Drug Administration (FDA) for identification of cultured bacteria from human specimens ( in vitro diagnosis).

Techniques:

Journal: Frontiers in Microbiology

Article Title: MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

doi: 10.3389/fmicb.2015.00791

Figure Lengend Snippet: Bacteria in which MALDI-TOF MS was used for identification and strain typing.

Article Snippet: In the last 2 years, MALDI Biotyper CA System (Bruker Daltonics Inc.) has been approved by the US Food and Drug Administration (FDA) for identification of cultured bacteria from human specimens ( in vitro diagnosis).

Techniques: Bacteria

Journal: Frontiers in Microbiology

Article Title: MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

doi: 10.3389/fmicb.2015.00791

Figure Lengend Snippet: Fungi which have been identified using MALDI-TOF MS.

Article Snippet: In the last 2 years, MALDI Biotyper CA System (Bruker Daltonics Inc.) has been approved by the US Food and Drug Administration (FDA) for identification of cultured bacteria from human specimens ( in vitro diagnosis).

Techniques:

Journal: Mass Spectrometry Reviews

Article Title: The expanding role of mass spectrometry in the field of vaccine development

doi: 10.1002/mas.21571

Figure Lengend Snippet: An overview of the role of MS technologies in the vaccine development

Article Snippet: Meningococcal vaccine , Semi quantitative LC‐MS/MS analysis carried out to define conjugation of glycans to the lysines of Cross‐Reactive‐Material‐197 (CRM 197 ). Conjugate vaccines use CRM 197 as carrier protein. , NanoLC‐ESI‐MS analysis was carried out on an Ultimate 3000 RSLC‐nano system (Dionex/Thermo Scientific) coupled to an amaZon speed ETD ion trap (Bruker). LC‐MALDI‐TOF‐MS experiments were performed on an ultrafleXtreme MALDI‐TOF/TOF (Bruker). , Crotti et al .

Techniques: Recombinant, Sequencing, Glycoproteomics, Mass Spectrometry, Fractionation, Software, Stable Transfection, Membrane, Clinical Proteomics, Molecular Weight, Hydrophilic Interaction Liquid Chromatography, Virus, Vaccines, Isotope Dilution, Targeted Proteomics, Northern Blot, Fluorescence, Purification, Reversed-phase Chromatography, Quantitative Proteomics, Produced, Derivative Assay, Conjugation Assay, Binding Assay, Labeling, Multiplex sample analysis, Concentration Assay, Quantitation Assay