Peptides mass spectral interpretation

Progress is also made in software for mass spectral interpretation, especially for the so-called deconvolution of (mixed) ion envelopes of multiply charged protein ions generated by electrospray ionization, and for the peptide sequencing by MS-MS techniques. In that respect, the development of tools to search extensive protein and DNA databases using peptide maps, peptide molecular masses, LC retention time data, and sequence tags is an enormous... 

Most small peptides derived from protein sources contain a variety of polar and non-polar amino acids and as such are more difficult to handle. Nevertheless appreciation of the problems and considered chemical manipulation have allowed their MS elucidation [177-184] although a practical limit of about six amino acids in the peptide is reached before degradative procedures become advisable. An important step before sequencing a peptide by mass spectrometry is whenever possible to obtain the amino acid content by hydrolysis and conventional column chromatographic analysis. This assists in the selection of any chemical pretreatment and with the spectral interpretation. A variety of small peptides has been identified by a combination of methods and include 5 - 0X0 - L - prolyl - L - histadyl - L - prolinamide (2-pyrollidone-5-carboxylyl-... 

In the past, sequencing of peptides was accomplished using the Edman degradation procedure (see Section 8.2) [3]. Currently, this objective is more often accomplished by interpretation of a peptide s product-ion spectrum. As discussed above, one easy way is to submit the mass spectral data to the database search. Often, this search fails to provide an unequivocal identification of a peptide or protein. Therefore, one needs to resort to a manual interpretation of the mass spectrum. This procedure, known as de novo peptide sequencing, requires a detailed, complete, and... 

There are a number of substantial technical issues involved in de novo sequencing that arise from the fact that peptides do not fragment in an ideal manner. One result of this is that skilled spectral interpreters have devised sets of rules that can be used to convert mass differences between ions of a spectrum into amino acid sequences unfortunately, these rules are complicated and are not always followed. In addition, the fragmentations do not occur in a manner that gives rise to uniform ion intensities. This phenomenon results in spectra that have a substantial range of intensities which, depending on the ionization and mass analyzer used. 

The heptapeptide ulicyclamide (15) and the octapeptide ulithiacyclamide (16) were the first representatives of a series of cyclic peptides to be isolated from Lissoclinum patella. Their structures were elucidated by interpretation of spectral data [44], A revised structure was later put forward for ulicyclamide (15) as a result of a detailed analysis of the fast atom bombardment (FAB) mass spectrum. The same paper reported the isolation of two more polar cyclic peptides and another, which was present as a minor component. These heptapeptides were called lissoclinamides 1-3 (17-19) [45]. An unidentified tunicate from the Great Barrier Reef contained ulithiacyclamide (16) and ascidiacyclamide (14) [46]. Two syntheses of ulithiacyclamide (16)... 

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