Publications by authors named "Joshua Charkow"
With the increased usage and diversity of methods and instruments being applied to analyze Data-Independent Acquisition (DIA) data, visualization is becoming increasingly important to validate automated software results. Here we present MassDash, a cross-platform DIA mass spectrometry visualization and validation software for comparing features and results across popular tools. MassDash provides a web-based interface and Python package for interactive feature visualizations and summary report plots across multiple automated DIA feature detection tools, including OpenSwath, DIA-NN, and dreamDIA.
View Article and Find Full Text PDFIn bottom-up mass spectrometry-based proteomics, deep proteome coverage is limited by high cofragmentation rates. Cofragmentation occurs when more than one analyte is isolated by the quadrupole and the subsequent fragmentation event produces fragment ions of heterogeneous origin. One strategy to reduce cofragmentation rates is through effective peptide separation techniques such as chromatographic separation and, the more recently popularized, ion mobility (IM) spectrometry, which separates peptides by their collisional cross section.
View Article and Find Full Text PDFArticle Synopsis
- Truncating variants in exons 33 and 34 of the SRCAP gene are linked to Floating-Harbor syndrome, a neurodevelopmental disorder with symptoms like short stature and speech delay.
- In a study of 33 individuals with different clinical features than FLHS, most had de novo SRCAP variants, revealing shared issues like developmental delays and behavioral problems.
- The research found distinct DNA methylation signatures for these individuals compared to FLHS, leading to the classification of their condition as "non-FLHS SRCAP-related NDD," emphasizing the relationship between variant location, DNA methylation, and clinical symptoms.