Table 1 Performance comparison of directDIA and LFQ-DDA on the spike-in metaproteome samples.

From: Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

 

directDIA

LFQ-DDA (PEAKS)

Proteome coverage

Quantified proteins per runa

18,268 ± 24

10,229 ± 13

Quantified peptides per runa

70,272 ± 203

47,137 ± 95

Reproducible proteinsb

17,960

9925

Reproducible peptidesb

69,045

44,657

Species-specific proteinsb,c

1514

863

Species-specific peptidesb,c

5899

2970

Data completeness

Protein full/sparse ratiod

91% (17,031/18,712)

84% (9077/10,774)

Peptide full/sparse ratiod

88% (63,407/72,374)

75% (38,542/51,384)

Quantification precision

Protein CVe

9.1% to 9.6%

9.3% to 9.7%

Peptide CVe

12.3% to 13.1%

8.4% to 8.8%

Quantification accuracy

FC errorf

−0.21 to +0.51

−0.09 to +2.02

FC relative errorg

−20% to +15%

−22% to +40%

Outperforming frequencyh

11

7

  1. amean ± standard deviation.
  2. bshared in at least 2/3 replicate runs in each sample group.
  3. cuniquely belonging to one of the 6 spiked species.
  4. dratio of proteins or peptides detected in all the runs (“full”) to those detected in at least one runs (“sparse”).
  5. ecoefficient of variation (CV) in median values within each sample group.
  6. fmedian fold change (FC) − theoretical value.
  7. g(median FC − theoretical value)/theoretical value.
  8. hnumber of comparisons where the measured median FC values were closer to the theoretical values than the other quantification strategy.
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