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Table 1 Search output produced by searching MS sequence data of various peptides against curated databases (CD) and the public databases, MSDB, NCBInr, and PBR

From: Fit-for-purpose curated database application in mass spectrometry-based targeted protein identification and validation

Project Sample source Sample preparation Targeted protein Database: Top hit
     Score Peptide number Score Peptide number
1a Sheeppox virus SDS-PAGE gel band Unknown band (104 kD) MSDB: lumpy disease virus protein PBR: sheeppox virus protein
859 51 1039 80
2b Human In-solution digest tau, transcript variant 2 (40.27 kD) NCBInr: PNS specific tau, 78.8 kD CD: tau, transcript variant 2, 40.27 kD
465 29 (17)¶ 1615 34 (27)
3b Sheep-hamster (chimera) SDS-PAGE gel band Sheep-hamster chimeric PrP NCBInr: PrP in Dpc Micelles CD: sheep-hamster chimeric PrP
4987 1(1) 3857 9(8)
4b E. coli In-solution digest Flagellin H37 NCBInr: bacterial flagellin (E. coli) CD: H37, gi|30059966|
18862 31(26) 29742 33(31)
  1. aA QSTAR system was used to test the samples and Mascot database search with 0.4 kD peptide mass tolerance, 0.4 kD MS/MS tolerance, two missed tryptic cleavages, possible methionine oxidation, and all cysteine residues as carboxamidomethyl-cysteine due to alkylation with iodoacetamide.
  2. bAn Orbitrap system was used with 30 ppm peptide mass tolerance, 0.5 kD MS/MS tolerance, and two missed tryptic cleavage for all database searches. Oxidation on methionine and deamidation on glutamine and asparagines were chosen as possible modifications.
  3. ¶Numbers without brackets denote total specific peptide match numbers while numbers in brackets denote significant specific peptide match numbers as per the Mascot search engine.