Proteomics

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GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment

ABSTRACT: This study shows the efficacy of a new tandem mass spectrometry peak finding software, GAGfinder. GAGfinder works by iterating through all potential fragments of a given precursor composition and comparing a theoretical isotopic distribution to the peak heights found in a tandem mass spectrum. We used ten synthetic heparan sulfate oligosaccharide to test the effectiveness of the method and compare GAGfinder's performance to that of an averagine-based algorithm.

INSTRUMENT(S): solariX

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: John Hogan  

LAB HEAD: Joseph Zaia

PROVIDER: PXD009101 | Pride | 2018-04-09

REPOSITORIES: Pride

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20120421_Hex7_5uM_5IPA_0.5NH4OH_402.55_acc1.0s_EED20eV_0.5s_1.73A_100scans_000001.mzML Mzml
20120427_Arixtra_5uM_5IPA_0.5NH4OH_250.15_acc4.0s_EED20eV_0.5s_1.63A_lens-19.0V_100scans_000001.mzML Mzml
20130108_Boons034-_NETD_000001.mzML Mzml
20130110_Hex65-_NETD_000001.mzML Mzml
20130308_dp158-_NETD_000001.mzML Mzml
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Publications

Software for Peak Finding and Elemental Composition Assignment for Glycosaminoglycan Tandem Mass Spectra.

Hogan John D JD   Klein Joshua A JA   Wu Jiandong J   Chopra Pradeep P   Boons Geert-Jan GJ   Carvalho Luis L   Lin Cheng C   Zaia Joseph J  

Molecular & cellular proteomics : MCP 20180403 7

Glycosaminoglycans (GAGs) covalently linked to proteoglycans (PGs) are characterized by repeating disaccharide units and variable sulfation patterns along the chain. GAG length and sulfation patterns impact disease etiology, cellular signaling, and structural support for cells. We and others have demonstrated the usefulness of tandem mass spectrometry (MS<sup>2</sup>) for assigning the structures of GAG saccharides; however, manual interpretation of tandem mass spectra is time-consuming, so comp  ...[more]

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