Top-down proteomics

Top-down vs bottom-up proteomics

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 dissociation or electron-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]

  1. ^ Sze SK, Ge Y, Oh H, McLafferty FW (2002). "Top-down mass spectrometry of a 29-kDa protein for characterization of any posttranslational modification to within one residue". Proc. Natl. Acad. Sci. U.S.A. 99 (4): 1774–9. Bibcode:2002PNAS...99.1774S. doi:10.1073/pnas.251691898. PMC 122269. PMID 11842225.
  2. ^ Kelleher NL (2004). "Top-down proteomics". Anal. Chem. 76 (11): 197A–203A. doi:10.1021/ac0415657. PMID 15190879.
  3. ^ Wright EP, Partridge MA, Padula MP, Gauci VJ, Malladi CS, Coorsen JR (2014). "Top-down proteomics: Enhancing 2D gel electrophoresis from tissue processing to high-sensitivity protein detection". Proteomics. 14 (7–8): 872–889. doi:10.1002/pmic.201300424. PMID 24452924. S2CID 29866065.
  4. ^ Durbin, Kenneth Robert; Fornelli, Luca; Fellers, Ryan T.; Doubleday, Peter F.; Narita, Masashi; Kelleher, Neil L. (2016). "Quantitation and Identification of Thousands of Human Proteoforms Below 30 kDa". Journal of Proteome Research. 15 (3): 976–982. doi:10.1021/acs.jproteome.5b00997. PMC 4794255. PMID 26795204.
  5. ^ Smith CL, Cantor CR (1989). "Evolving strategies for making physical maps of mammalian chromosomes". Genome. 31 (2): 1055–8. doi:10.1139/g89-181. PMID 2698822.
  6. ^ Bogdanov B, Smith RD (2005). "Proteomics by FTICR mass spectrometry: top down and bottom up". Mass Spectrometry Reviews. 24 (2): 168–200. Bibcode:2005MSRv...24..168B. doi:10.1002/mas.20015. PMID 15389855.
  7. ^ Tran, John C.; Zamdborg, Leonid; Ahlf, Dorothy R.; Lee, Ji Eun; Catherman, Adam D.; Durbin, Kenneth R.; Tipton, Jeremiah D.; Vellaichamy, Adaikkalam; Kellie, John F. (2011-12-08). "Mapping intact protein isoforms in discovery mode using top-down proteomics". Nature. 480 (7376): 254–258. Bibcode:2011Natur.480..254T. doi:10.1038/nature10575. ISSN 0028-0836. PMC 3237778. PMID 22037311.
  8. ^ Parks, Bryan A.; Jiang, Lihua; Thomas, Paul M.; Wenger, Craig D.; Roth, Michael J.; Boyne, Michael T.; Burke, Patricia V.; Kwast, Kurt E.; Kelleher, Neil L. (2007). "Top-Down Proteomics on a Chromatographic Time Scale Using Linear Ion Trap Fourier Transform Hybrid Mass Spectrometers". Analytical Chemistry. 79 (21): 7984–7991. doi:10.1021/ac070553t. PMC 2361135. PMID 17915963.