Table II Summary of peptide identification from MS/MS spectra for selected ocean datasets
BSt45 (90,072 spectra)CS51 (100,588 spectra)
PSMs (%)Unique peptidePSMs (%)Unique peptide
Reads based7795 (8.6%)295815,167 (15.1%)5652
Contigs based (S*)1892 (2.10%)8176526 (6.49%)2442
Graph2Pro (S*)12,728 (14.1%)454226,576 (26.4%)9932
Contigs based (M*)8631 (9.6%)336717,427 (17.3%)6388
Graph2Pro (M*)15,172 (16.8%)585729,072 (28.9%)11,463
Graph2Pro (M*) + Var2Pep15,913 (17.7%)624031,145 (31.0%)12,380
  • Note: S* represents SOAPdenovo2, M* represents MegaHit, PSM stands for peptide spectrum match. Bst stands for Bering strait, and CS stands for Chukchi sea. Graph2Pro (S*) and Graph2Pro (M*) represent using assembly graph from SOAPdenovo2 (S*) and MegaHit (M*) as the reference in Graph2Pro, respectively. In all cases, FDR (false discovery rate) was estimated using a target-decoy search approach, and a cutoff of 1% at spectrum level was applied. This table only shows the results for two datasets. See Fig. 2 and supplementary Data File S1 for results of all data sets.