Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases

Ejvind Mørtz*, Peter B. O'Connor, Peter Roepstorff, Neil L. Kelleher, Troy D. Wood, Fred W. McLafferty, Matthias Mann

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

204 Scopus citations


Molecular and fragment ion data of intact 8-to 43-kDa proteins from electrospray Fourier-transform tandem mass spectrometry are matched against the corresponding data in sequence data bases. Extending the sequence tag concept of Mann and Wilm for matching peptides, a partial amino acid sequence in the unknown is first identified from the mass differences of a series of fragment ions, and the mass position of this sequence is defined from molecular weight and the fragment ion masses. For three studied proteins, a single sequence tag retrieved only the correct protein from the data base; a fourth protein required the input of two sequence tags. However, three of the data base proteins differed by having an extra methionine or by missing an acetyl or heme substitution. The positions of these modifications in the protein examined were greatly restricted by the mass differences of its molecular and fragment ions versus those of the data base. To characterize the primary structure of an unknown represented in the data base, this method is fast and specific and does not require prior enzymatic or chemical degradation.

Original languageEnglish (US)
Pages (from-to)8264-8267
Number of pages4
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number16
StatePublished - Aug 6 1996


  • data base search
  • electrospray mass spectrometry
  • protein modification
  • protein sequencing

ASJC Scopus subject areas

  • General


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