Format

Send to

Choose Destination
See comment in PubMed Commons below
Mol Cell Proteomics. 2013 Jun;12(6):1735-40. doi: 10.1074/mcp.O112.025940. Epub 2013 Feb 26.

SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra.

Author information

1
Departments of Neurobiology, Harvard Medical School, Boston, Massachusetts 02119, USA. Oliver.Serang@Childrens.Harvard.edu

Abstract

The past 15 years have seen significant progress in LC-MS/MS peptide sequencing, including the advent of successful de novo and database search methods; however, analysis of glycopeptide and, more generally, glycoconjugate spectra remains a much more open problem, and much annotation is still performed manually. This is partly because glycans, unlike peptides, need not be linear chains and are instead described by trees. In this study, we introduce SweetSEQer, an extremely simple open source tool for identifying potential glycopeptide MS/MS spectra. We evaluate SweetSEQer on manually curated glycoconjugate spectra and on negative controls, and we demonstrate high quality filtering that can be easily improved for specific applications. We also demonstrate a high overlap between peaks annotated by experts and peaks annotated by SweetSEQer, as well as demonstrate inferred glycan graphs consistent with canonical glycan tree motifs. This study presents a novel tool for annotating spectra and producing glycan graphs from LC-MS/MS spectra. The tool is evaluated and shown to perform similarly to an expert on manually curated data.

PMID:
23443135
PMCID:
PMC3675827
DOI:
10.1074/mcp.O112.025940
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center