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30 synthetic peptide fragments of proteins from the human microbiota

ABSTRACT: The peptides shown in Table 2 and Supplementary Table S3 were found in MS/MS spectra search against the HuMiProt90 database and validated several times — both in silico and by comparison with the spectra of synthetic peptides. The in silico approach included machine learning used by Scaffold 4 software to validate identifications based on the target-decoy approach (FDR 0.56% by PSM), as well as filtering homologous sequences among known human proteins, taking into account possible single amino acid polymorphism. The key stage of validation was the production of 30 synthetic peptides identified as fragments of proteins from the human microbiota. Identification, de novo or by searching against databases, cannot serve as the ultimate stage of investigation because it contains some deliberately incorrect identifications. Figure 2B demonstrates an example of spectrum comparison for a sequence identified in the plasma/serum and a synthetic peptide. Similar pairs of spectra for all 30 peptides are shown in Supplementary Figures S1. The correlation between the mass spectra of blood plasma/serum samples and the spectra of synthetic peptides is not less than 0.7 (for 23 peptides, the correlation is more than 0.8).

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Bacteria

SUBMITTER: Georgij Arapidi

LAB HEAD: Georgij Pavlovich Arapidi

PROVIDER: PXD027675 | Pride | 2024-06-14

REPOSITORIES: pride

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Dataset's files

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			Action	DRS
	30_Bactria_peptides_15_2_Condensed.sf3	Other
	30_Bactria_peptides_validated_20210105_TnRev.fasta	Fasta
	P513_20170709_synth_pep_mix_1_of_6_5-40_60min_7uLinj_1.wiff	Wiff
	P513_20170709_synth_pep_mix_1_of_6_5-40_60min_7uLinj_1.wiff.scan	Wiff
	P513_MGFPeaklist.dat	Other

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