Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis[1][2] or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS.[3] Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins.[4] The name is derived from the similar approach to DNA sequencing.[5] During mass spectrometry intact proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance (Penning trap),[6] quadrupole ion trap (Paul trap) or Orbitrap mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron-capture dissociationorelectron-transfer dissociation. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry (MS).[7] Top-down MS (non-gel) proteomics interrogates protein structure through measurement of an intact mass followed by direct ion dissociation in the gas phase.[8]
Study One: Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa
Study Two: Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics