massarrayanalyzer 4 maldi tof mass spectrometer  (agena bioscience)

Journal: PLoS ONE

Article Title: Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular Identity

doi: 10.1371/journal.pone.0052299

Figure Lengend Snippet: Methylation status of CpG sites 87 ctDMRs was analyzed by MassARRAY. Individual CpG and sample types were ordered by hierarchical clustering. Within heatmap, red and green correspond to hypermethylation and hypomethylation respectively.

Article Snippet: Samples were rotated for 5–10 minutes at room temperature and a portion of each reaction (∼15 nL) was then spotted on to SpectroCHIP II chips (Sequenom) and analyzed using a MassARRAY Analyzer 4 MALDI-TOF mass spectrometer (Sequenom).

Techniques: Methylation

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: Workflow and molecular principle of SARS-CoV-2 RNA detection in FFPE tissue by MALDI-TOF mass spectrometry. RNA extraction from FFPE placental and amniotic tissue was performed using the Maxwell RSC RNA FFPE Kit (Promega) according to manufacturer’s instructions. Extracted viral RNA is then reverse transcribed into cDNA and amplified by a one-step RT-PCR reaction. The figure schematically depicts specific amplification of the SARS-CoV-2 targets N1 and N2. The forward primers are indicated in green, the reverse primers in blue. Thereafter, PCR products are treated with the shrimp alkaline phosphatase (SAP) enzyme to remove unincorporated nucleotides (dNTPs). Next, a single nucleotide extension reaction is performed, in which target-specific extension primers are elongated by a single mass-modified terminator nucleotide (A, T, C or G) complementary to the cDNA template sequence. The extension products (EP) are then analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) using the MassARRAY system (Agena Bioscience) and mass spectra of the SARS-CoV-2-specific detected cDNA fragments are generated. In the absence of viral RNA, RT-PCR as well as single nucleotide extension reactions cannot be performed and consequently, no cDNA fragments are detected by MALDI-TOF analysis. EP: extension product; UEP: unextended extension primer.

Article Snippet: The resultant extension products (analytes) are then desalted, transferred to a silicon chip with pre-spotted matrix material (SpectroCHIP ® Array), and loaded onto the MALDI-TOF mass spectrometer (MassARRAY Analyzer 4, Agena Bioscience).

Techniques: RNA Detection, Mass Spectrometry, RNA Extraction, Reverse Transcription, Amplification, One Step RT-PCR, Modification, Sequencing, Generated, Reverse Transcription Polymerase Chain Reaction

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: Detection of SARS-CoV-2 RNA in placental and amniotic tissue. Placental and amniotic tissue were analyzed by MALDI-TOF MS using the CE-IVD-certified MassARRAY SARS-CoV-2 Panel ( A ) and by RT-PCR using the EURORealTime SARS-CoV-2 Kit ( B ). ( A ): The plots display the intensity of the peaks corresponding to the 5 targets ORF1, ORF1ab, N1, N2 and N3 included in the CE-IVD-certified MassARRAY SARS-CoV-2 Panel. The intensity threshold considering a peak as detected is 5. All 5 SARS-CoV-2 targets were detected in both placental and amniotic tissue. ( B ). The graphs show the fluorescence intensity ( y -axis) for each cycle ( x -axis) of the real-time amplification of the SARS-CoV-2 -specific target regions (amplification curve). The amplification curve of the positive control (PC) is highlighted in green, the one of the negative control (NC) in red. The crossing point (Cp) value is indicated for both placental tissue (p.tissue) and amniotic tissue (a.tissue).

Article Snippet: The resultant extension products (analytes) are then desalted, transferred to a silicon chip with pre-spotted matrix material (SpectroCHIP ® Array), and loaded onto the MALDI-TOF mass spectrometer (MassARRAY Analyzer 4, Agena Bioscience).

Techniques: Reverse Transcription Polymerase Chain Reaction, Fluorescence, Amplification, Positive Control, Negative Control

Journal: Viruses

Article Title: Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including Variant Analysis by Mass Spectrometry in Placental Tissue

doi: 10.3390/v14030604

Figure Lengend Snippet: SARS-CoV-2 variant analysis of amniotic and placental tissue by MALDI-TOF MS. Placental and amniotic tissue were analyzed by MALDI-TOF MS using the MassARRAY SARS-CoV-2 Variant Panel v1. The figure shows the specific mutations within the SARS-CoV-2 spike gene that are assigned to the different variants B 1.1.7 ( A ), B 1.351 ( B ), P.1 ( C ) and Cluster 5/Mink ( D ). Detected mutations in placental tissue (p.tissue), amniotic tissue (a.tissue), positive controls (PC) B 1.1.7 and B 1.351 and negative control (NC) are illustrated by green-colored squares.

Article Snippet: The resultant extension products (analytes) are then desalted, transferred to a silicon chip with pre-spotted matrix material (SpectroCHIP ® Array), and loaded onto the MALDI-TOF mass spectrometer (MassARRAY Analyzer 4, Agena Bioscience).

Techniques: Variant Assay, Negative Control