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Analysis of O-glycoproteomics data with MS-Decipher, MetaMorpheus, MSFragger-Glyco and Mascot

ABSTRACT: We presented a user-friendly proteomic database search platform, MS-Decipher, for the identification of peptides from MS data. Two scoring schemes, rank score and hyperscore, could be used for peptide spectra matching. FDR controlling strategies could be used after searching, and it was found that MS-Decipher performs well compared to traditional database searching software. In addition, a special search mode, O-search, is presented to search O-glycopeptides for the O-glycoproteomics analysis. Data and result files in several formats could be used in searching and validation. Dataset of tryptic peptides from serum were used to evaluate the performance of our software in analysis of O-glycoproteomics . The searches using the same parameters were also performed by other commonly used software, like MetaMorpheus, MSFragger-Glyco and Mascot, to compare the performance.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Mingliang Ye

PROVIDER: PXD027004 | JPOST Repository | Thu Jan 13 00:00:00 GMT 2022

REPOSITORIES: jPOST

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			Action	DRS
	LLY_HF_OGP_A_1.mgf	Mgf
	LLY_HF_OGP_A_10.mgf	Mgf
	LLY_HF_OGP_A_15.mgf	Mgf
	LLY_HF_OGP_A_16.mgf	Mgf
	LLY_HF_OGP_A_17.mgf	Mgf

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TEST file for jpost repository

Project description:We presented a user-friendly proteomic database search platform, MS-Decipher, for the identification of peptides from MS data. Two scoring schemes, rank score and hyperscore, could be used for peptide spectra matching. FDR controlling strategies could be used after searching, and it was found that MS-Decipher performs well compared to traditional database searching software. In addition, a special search mode, O-search, is presented to search O-glycopeptides for the O-glycoproteomics analysis. Data and result files in several formats could be used in searching and validation. Dataset of tryptic peptides from serum were used to evaluate the performance of our software. The searches using the same parameters were also performed by other commonly used software, like Mascot, SEQUEST, MS Amanda 2.0 and MS-GF+, to compare the performance.

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Project description:Reanalysis of submissions PXD005411, PXD005413, PXD005412, PXD005553, PXD005555, PXD005565 and PXD019937 using Glyco-Decipher. Identification results of peptide-spectrum matches supporting Glyco-Decipher manuscript (Glyco-Decipher: glycan database-independent peptide matching enables discovery of new glycans and in-depth characterization of site-specific N-glycosylation). Recently, several elegant bioinformatics tools have been developed to identify glycopeptides from tandem mass spectra for site-specific glycoproteomics studies. These glycan database-dependent tools have substantially improved glycoproteomics analysis but fail to identify glycopeptides with unexpected glycans. We present a platform called Glyco-Decipher to interpret the glycoproteomics data of N-linked glycopeptides. It adopts a glycan database-independent peptide matching scheme that allows the unbiased profiling of glycans and the discovery of new glycans linked with modifications. Reanalysis of several large-scale datasets showed that Glyco-Decipher outperformed the open search method in glycan blind searching and the popular glycan database-dependent software tools in glycopeptide identification. Our glycan database-independent search also revealed that modified glycans are responsible for a large fraction of unassigned glycopeptide spectra in shotgun glycoproteomics.

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