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Table 2 Protein-level identifications obtained over three search databases.

From: Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

  

JGI Genes

All modelsa

(87,287)

JGI Genes

Filtered modelsb (11,200)

DSM proteins

(14,165)

Gel01–12% SDS (partial) 8 bands

APS hits

638

42

40

 

Mascot hits(1)c

461

38

36

 

Mascot hits(2)d

448

38

36

Gel02–15% SDS (partial) 33 bands

APS hits

1443

109

111

 

Mascot hits(1)c

1062

102

102

 

Mascot hits(2)d

1047

102

102

Gel03–10% SDS (full) 110 bands

APS hits

2349

153

156

 

Mascot hits(1)c

1572

146

140

 

Mascot hits(2)d

1572

146

139

  1. aSearches performed against 87,287 protein sequences translated from 87,287 predicted gene models, cluster at 8709 loci on the genome.
  2. aSearches performed against the 11,200 "best" gene models, based on homology to known proteins, from the full 87,287 set. Note, some clusters have more than one "best" model, and some have none, hence there are more "best" models than clusters.
  3. cProtein hits are reported with 1 or more peptide identification with significant Mascot scores (p < 0.05)
  4. dProtein hits are reported with 1 or more peptide identification with significant scores using the Mascot MudPit Score.
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BMC Genomics

ISSN: 1471-2164

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