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Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Incorrectly annotated keratin derived peptide sequences lead to misleading MS/MS data interpretation.

Robert Nawrot¹, Jakub Barylski, Waltraud X Schulze

¹Department of Molecular Virology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, PL-61-614 Poznań, Poland.

Journal of Proteomics

|July 31, 2013

Summary

A common 12 amino acid peptide, TNAENEFVTIKK, identified in plant proteomic studies, is likely a keratin contaminant, not a plant protein. This highlights the need for caution in interpreting such data to avoid misinterpretation.

Keywords:

Database contamination Keratin NanoLC–nanoESI-MS/MS Plant proteomics Unknown protein 1 Unknown protein 18

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Area of Science:

Proteomics
Molecular Biology
Biochemistry

Background:

The peptide TNAENEFVTIKK has been identified in proteomic analyses of plant species, including Chelidonium majus.
This peptide has been erroneously annotated as plant proteins, such as Unknown protein 18 from Pseudotsuga menziesii and Unknown protein 1 from Vitis rotundifolia.

Purpose of the Study:

To investigate the origin of the abundant peptide TNAENEFVTIKK detected in plant proteomic samples.
To determine if this peptide represents a genuine plant protein or a common contaminant.
To provide evidence for re-annotating or flagging this peptide in proteomic databases.

Main Methods:

Nano-liquid chromatography coupled with nano-electrospray ionization tandem mass spectrometry (nanoLC-nanoESI-MS/MS).
Database searching using Mascot against NCBInr with taxonomic restrictions.
Comparative analysis of peptide sequences with known keratin proteotypic peptides.

Main Results:

The peptide TNAENEFVTIKK was found to be identical to sequences associated with type II cytoskeletal keratin.
Empirical evidence showed the peptide's presence in various keratin-contaminated samples.
The sequence matches known proteotypic peptides of keratins, suggesting a contaminant origin.

Conclusions:

The peptide TNAENEFVTIKK is likely derived from keratin contamination, not from the analyzed plant species.
Existing annotations of this peptide as plant proteins (e.g., P85925, P86104, P84718) are questionable and may lead to data misinterpretation.
Researchers should exercise caution and perform thorough quality assessment when encountering this peptide in plant proteomic data to avoid biological misinterpretations.