Peptide mass fingerprinting

Peptide mass fingerprinting (PMF) (also known as protein fingerprinting) is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF.[1] The method was developed in 1993 by several groups independently.[2][3][4][5][6] The peptide masses are compared to either a database containing known protein sequences or even the genome. This is achieved by using computer programs that translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides, and calculate the absolute masses of the peptides from each protein. They then compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match.
The advantage of this method is that only the masses of the peptides have to be known. Time-consuming de novo peptide sequencing is then unnecessary. A disadvantage is that the protein sequence has to be present in the database of interest. Additionally most PMF algorithms assume that the peptides come from a single protein.[7] The presence of a mixture can significantly complicate the analysis and potentially compromise the results. Typical for the PMF based protein identification is the requirement for an isolated protein. Mixtures exceeding a number of 2-3 proteins typically require the additional use of MS/MS based protein identification to achieve sufficient specificity of identification (6). Therefore, the typical PMF samples are isolated proteins from two-dimensional gel electrophoresis (2D gels) or isolated SDS-PAGE bands. Additional analyses by MS/MS can either be direct, e.g., MALDI-TOF/TOF analysis or downstream nanoLC-ESI-MS/MS analysis of gel spot eluates.[7][8]

Sample preparation

Protein samples can be derived from SDS-PAGE[7] and are then subject to some chemical modifications. Disulfide bridges in proteins are reduced and cysteine amino acids are carbamidomethylated chemically or acrylamidated during the gel electrophoresis.

Then the proteins are cut into several fragments using proteolytic enzymes such as trypsin, chymotrypsin or Glu-C. A typical sample:protease ratio is 50:1. The proteolysis is typically carried out overnight and the resulting peptides are extracted with acetonitrile and dried under vacuum. The peptides are then dissolved in a small amount of distilled water or further concentrated and purified using ZipTip Pipette tips and are ready for mass spectrometric analysis.

Mass spectrometric analysis

The digested protein can be analyzed with different types of mass spectrometers such as ESI-TOF or MALDI-TOF. MALDI-TOF is often the preferred instrument because it allows a high sample throughput and several proteins can be analyzed in a single experiment, if complemented by MS/MS analysis.

A small fraction of the peptide (usually 1 microliter or less) is pipetted onto a MALDI target and a chemical called a matrix is added to the peptide mix. The matrix molecules are required for the desorption of the peptide molecules. Matrix and peptide molecules co-crystallize on the MALDI target and are ready to be analyzed.

The target is inserted into the vacuum chamber of the mass spectrometer and the desorption and ionisation of the polypeptide fragments is initiated by a pulsed laser beam which transfers high amounts of energy into the matrix molecules. The energy transfer is sufficient to promote the ionisation and transition of matrix molecules and peptides from the solid phase into the gas phase. The ions are accelerated in the electric field of the mass spectrometer and fly towards an ion detector where their arrival is detected as an electric signal. Their mass-to-charge ratio is proportional to their time of flight (TOF) in the drift tube and can be calculated accordingly.

Computational analysis

The mass spectrometric analysis produces a list of molecular weights of the fragments which is often called a peak list. The peptide masses are compared to protein databases such as Swissprot, which contain protein sequence information. Software performs in silico digests on proteins in the database with the same enzyme (e.g. trypsin) used in the chemical cleavage reaction. The mass of these peptide fragments is then calculated and compared to the peak list of measured peptide masses. The results are statistically analyzed and possible matches are returned in a results table.

See also

References

  1. ↑ Clauser KR, Baker P, Burlingame AL (1999). "Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching". Anal. Chem. 71 (14): 2871–82. doi:10.1021/ac9810516. PMID 10424174.
  2. ↑ Pappin DJ, Hojrup P, Bleasby AJ (1993). "Rapid identification of proteins by peptide-mass fingerprinting". Curr. Biol. 3 (6): 327–32. doi:10.1016/0960-9822(93)90195-T. PMID 15335725.
  3. ↑ Henzel WJ, Billeci TM, Stults JT, Wong SC, Grimley C, Watanabe C (1993). "Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases". Proc. Natl. Acad. Sci. U.S.A. 90 (11): 5011–5. Bibcode:1993PNAS...90.5011H. doi:10.1073/pnas.90.11.5011. PMC 46643Freely accessible. PMID 8506346.
  4. ↑ Mann M, Højrup P, Roepstorff P (1993). "Use of mass spectrometric molecular weight information to identify proteins in sequence databases". Biol. Mass Spectrom. 22 (6): 338–45. doi:10.1002/bms.1200220605. PMID 8329463.
  5. ↑ James P, Quadroni M, Carafoli E, Gonnet G (1993). "Protein identification by mass profile fingerprinting". Biochem. Biophys. Res. Commun. 195 (1): 58–64. doi:10.1006/bbrc.1993.2009. PMID 8363627.
  6. ↑ Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993). "Peptide mass maps: a highly informative approach to protein identification". Anal. Biochem. 214 (2): 397–408. doi:10.1006/abio.1993.1514. PMID 8109726.
  7. 1 2 3 Shevchenko A, Jensen ON, Podtelejnikov AV, Sagliocco F, Wilm M, Vorm O, Mortensen P, Shevchenko A, Boucherie H, Mann M (1996). "Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels". Proc. Natl. Acad. Sci. U.S.A. 93 (25): 14440–5. Bibcode:1996PNAS...9314440S. doi:10.1073/pnas.93.25.14440. PMC 26151Freely accessible. PMID 8962070.
  8. ↑ Wang W, Sun J, Nimtz M, Deckwer WD, Zeng AP (2003). "Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences". Proteome Science. 1 (1): 6. doi:10.1186/1477-5956-1-6. PMC 317362Freely accessible. PMID 14653859.

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