Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Dec 14;12 Suppl 14(Suppl 14):S8.
doi: 10.1186/1471-2105-12-S14-S8.

Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs

Chiyong Kang  1 , Gwan-Su Yi
Affiliations

Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs

Chiyong Kang et al. BMC Bioinformatics. .

Abstract

Background: Various solutions have been introduced for the identification of post-translational modification (PTM) from tandem mass spectrometry (MS/MS) in proteomics field but the identification of peptide modifiers, such as Ubiquitin (Ub) and ubiquitin-like proteins (Ubls), is still a challenge. The fragmentation of peptide modifier produce complex shifted ion mass patterns in combination with other PTMs, which makes it difficult to identify and locate the PTMs on a protein sequence. Currently, most PTM identification methods do not consider the complex fragmentation of peptide modifier or deals it separately from the other PTMs.

Results: We developed an advanced PTM identification method that inspects possible ion patterns of the most known peptide modifiers as well as other known biological and chemical PTMs to make more comprehensive and accurate conclusion. The proposed method searches all detectable mass differences of measured peaks from their theoretical values and the mass differences within mass tolerance range are grouped as mass shift classes. The most possible locations of multiple PTMs including peptide modifiers can be determined by evaluating all possible scenarios generated by the combination of the qualified mass shift classes.The proposed method showed excellent performance in the test with simulated spectra having various PTMs including peptide modifiers and in the comparison with recently developed methods such as QuickMod and SUMmOn. In the analysis of HUPO Brain Proteome Project (BPP) datasets, the proposed method could find the ubiquitin modification sites that were not identified by other conventional methods.

Conclusions: This work presents a novel method for identifying bothpeptide modifiers that generate complex fragmentation patternsand PTMs that are not fragmented during fragmentation processfrom tandem mass spectra.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Various mass shifts that could be generated from a Ubl. (a) An example of theoretical fragmentation patterns and cleavage sites from UFM1_HUMAN. (b) A theoretical spectrum of b-ions from Ubl-modified target peptide, without y-ions from Ubl-modified target peptide and b-ions from Ubl.
Figure 2
Figure 2
The flow chart of the proposed algorithm.
Figure 3
Figure 3
The process of mass shift path finding. (a) Equivalent mass differences are clustered as mass shift classes and evaluated. (b) Qualified mass shift classes are connected into mass shift sets and evaluated to find the mass shift paths. Fragmented Ubl produces various mass shifts while most of non-peptide PTMs produce only one mass shift.
Figure 4
Figure 4
The Human Ub/Ubl sequences with digestion pattern by trypsin. Bold: no miscleavage, italic or bold with underline: 1 miscleavage, full polypeptide sequences: 2 miscleavages.
Figure 5
Figure 5
Peak matching on Mass Spectrum ID 58395 from HUPO BPP Experiment #1735 (a) No PTM: BPP annotation (b) Ub on 15K: Analysis result by Mascot considering GlyGly (Ub) as a variable modification (c) Ub on 4K: Analysis result by the proposed method which is matched with Ubiprot annotation
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Eng Jimmy K, M A L, Yates John R III. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. JASMS. 1994;5:976–989. - PubMed
    1. Yates JR, Eng JK, McCormack aL. Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases. Analytical chemistry. 1995;67(18):3202–3210. doi: 10.1021/ac00114a016. - DOI - PubMed
    1. Yates JR, Eng JK, McCormack aL, Schieltz D. Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Analytical chemistry. 1995;67(8):1426–1436. doi: 10.1021/ac00104a020. - DOI - PubMed
    1. MacLean B, Eng JK, Beavis RC, McIntosh M. General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics. 2006;22(22):2830–2832. doi: 10.1093/bioinformatics/btl379. - DOI - PubMed
    1. Ahrné E, Müller M, Lisacek F. Unrestricted identification of modified proteins using MS/MS. Proteomics. 2010;10(4):671–686. doi: 10.1002/pmic.200900502. - DOI - PubMed

Publication types

LinkOut - more resources