Innovations in mass spectrometry (MS) instrumentation continue to emerge, driven primarily by the need to identify and characterize proteins with greater confidence. Simultaneously, fragmentation schemes are an essential performance component of any MS platform, delivering detailed structural and sequence data necessary for precise identifications. Here we report on the latest advances...
We demonstrate top-down sequencing and detailed PTM characterization of intact histone proteoforms using a novel timsOMNI mass spectrometry platform. We prepared well defined acetylated and methylated proteoforms of histones H3 and H4 that were analyzed and sequenced by nanoESI interfaced to a modified timsTOF Ultra mass spectrometer equipped with the omnitrap technology (FasmaTech, Bruker...
Quantitative analysis of intact proteoforms in mass-limited, complex samples remains challenging due to the low ion intensity in MS detection and peak overlap caused by insufficient separation. While targeted top-down proteomics methods such as parallel reaction monitoring (PRM) have been developed for LC-MS, they typically require microgram-level sample input, limiting their utility for...
The “proteoform hypothesis” postulates that the proteome-to-phenotype connection is better explained through the characterization of the actual molecules present in a cell or tissue, or proteoforms, than by cataloguing “protein groups” that represent undistinguished molecule ensembles. The top-down (TD) approach to proteomics (i.e., the direct analysis of proteoforms) can theoretically ensure...
Most top-down proteomics workflows rely on deconvolution of intact and fragment ion m/z values using modeled isotope distributions, typically via an “averagine” approximation. This step often limits accuracy: poor fits to distorted isotope patterns can lead to incorrect monoisotopic mass assignment, widened mass tolerances, and inflated false discovery rates. To address these limitations, we...
