Citrulline Effect Is a Characteristic Feature of Deiminated Peptides in Tandem Mass Spectrometry

Arnold Steckel,Gitta Schlosser

doi:10.1007/s13361-019-02271-x

Arnold Steckel, Gitta Schlosser

Open Access

https://doi.org/10.1007/s13361-019-02271-x

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Abstract

Tandem mass spectrometry of peptides is of utmost importance in proteomics. Collision-induced dissociation usually generates y type fragment ion series from tryptic peptides, carrying information on their primary structure. Amino acid side chains or differences in their basicity could alter fragmentation processes considerably. The well-known proline effect is a cleavage preference at the N-terminus of proline residues in peptides, usually yielding a very abundant y ion while suppressing others. Previously, we reported a similar phenomenon occurring at the C-terminus of citrulline residues and coined the term Cit effect. To confirm the presence of Cit effect in large proteomic datasets, we analyzed 293 peptides containing Cit residues based on the human proteome database mining work of Lee et al. (2018). The occurrence of Cit effect was found to be 44%. Comparing bond scissions at the amide linkage between Cit-Zzz (citrulline followed by a specified residue) to Aaa1-Aaa2 (Aaa can be any residue except Cit), 5 Cit-Zzz cleavages were significantly (CL = 95.0%) more frequent in > 85% of the cases in terms of relative sequential base beak occurrence. We used Pro effect to compare with Cit effect and obtained very similar results. On the other hand, our study showed that Cit effect is slightly inferior in the overall incidence to Pro effect (50% vs. 33%, CL = 95%) among deiminated peptides when Pro residues were also present in the sequence. Our results suggest that Cit effect is a characteristic feature and a possible biasing factor of deiminated peptides which can confirm the position of citrullination sites.

Highlights

Protein citrullination or deimination is a post-translational modification (PTM) converting certain arginines to citrullines [1]
We previously reported a similar phenomenon for Cit residues upon fragmenting Cit-containing model peptides, but in these cases, the cleavage occurred at the Cterminus of Cit residues (Cit-Aaa) [19] (Figure 1) as in the case of the aspartic acid effect, where the preferred cleavage is at the Asp-Aaa linkage [18]
We applied Newcombe-Wilson method—which is less sensitive for low sample sizes—for evaluating the difference between the confidence intervals based on sequential base peak generation

Summary

Introduction

Protein citrullination or deimination is a post-translational modification (PTM) converting certain arginines to citrullines [1]. Certain amino acids induce cleavages at their N- or C-termini with a higher preference, yielding the corresponding b or y ion with high intensity. These processes may hinder proper identification since they may suppress other valuable fragmentation routes. In 2018, a deep proteome mining was performed by Lee et al exploring the human citrullinome for 30 tissues by a thorough examination of MS/MS spectral repositories with rigorous methods [20] This group exploited the presence of Cit-selective iminium ions in the MS/MS spectra of deiminated peptides to confirm the Cit-content of the hits. We used their published data of validated Cit-peptide sequences for our statistical evaluation omitting repetitive sequences to improve our knowledge concerning the nature of Cit effect

Experimental Procedures

Results and Discussion

Conclusions