My question is that how can we select the unique peptides ?

Mr. Zeb,

For qualitative analysis of peptides, I would recommend to use vibrational spectroscopy, if the number of the components of your peptide mixture is relatively small (ca. 5-15 peptides, depending on the complexity of their molecular structures.)

There should be used, however, a set of data-processing methods and techniques for treatment of the vibrational spectroscopic patterns.

Please, consider in this context work [1] and the reference section, therein.

Because of, the qualitative analysis by means of mass spectrometry of complex mixtures of peptides does not represent a so trivial task, in particular, when there is a set of peptides with homopeptide-fragment chains. Such derivatives produce a set of structurally similar in qualitative terms fragment ions. Such fragment ions can be assigned precisely only via our quantitative method as I have already written to you.

Thus, a selection of a ''unique'' peptide by mass spectrometry (including chromatography) is significant doubtful; even it can be rather speculative, if the molecular structures of the analytes are very complex from the perspective of the number and type of the amino acid residues.

[1] Spectroscopic and structural elucidation of amino acid derivatives and small peptides: experimental and theoretical tools

Tsonko Kolev, Michael Spiteller, Bojidarka Koleva

Amino Acids, 38, 45–50 (2010)

If you have decided to use this approach: Vibrational spectroscopy to qualitative study of peptides; and if you have any questions regarding the application of the different methods and techniques for data-processing of the spectroscopic patterns, then please, do not hesitate to ask them, herein. I have a significant experience in vibrational spectroscopy of peptides, in addition to a developed, my-own method for 3D structural determination via linear polarized IR-spectroscopy. (Please, consider, for instance work [2] and relating references.)

[2] On the capability of the linear dichroic infrared spectroscopy, Bojidarka Ivanova

ISBN: 6139957893, 2018, pp. 72, Lap Lambert Academic Publishing

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