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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.