Fig. 2: Comparison of DDA, discovery DIA and library DIA-based maps.

All maps were acquired with 100 min LC gradients. Source data are provided as a Source Data file. a Topology of organellar maps in PCA space. Coloured dots correspond to organellar marker proteins. For comparability a single PCA was performed across all three experiments and the comparative experiments displayed in Fig. 4. PCs 1 and 3 provide the best visual separation of non-nuclear compartments, as PC2 (30% variability) is dominated by nuclear proteins. b Left panel: Number of proteins identified or profiled in at least 1 or in all 3 out of 3 replicate maps. Right panel: Overlap of profiled proteins between acquisition modes. c Performance of support vector machine compartment classification. The same 839 marker proteins were used for all three maps. The numbers of markers used for training (70%) and testing (30%) are indicated for each compartment. F1 scores are the harmonic mean of recall (true positives / [true positives + false negatives]) and precision (true positives / [true positives + false positives]) based on the test set. Error bars show the standard deviation of 20 sub-samples from the test set. d Number of organellar assignments, by confidence class - (I) very high, (II) high, (III) medium, (IV) low (see Methods). The 839 marker proteins are not included. e Normalized profile scatter within stable protein complexes. Only non-redundant complexes with at least five subunits quantified across all datasets were included. Each point represents the average normalized distance to the median complex profile in one map replicate. Horizontal lines indicate the median from n = 57 quantifications across 3 biological replicates. f Inter-replicate scatter, for the 2656 proteins profiled across all conditions and replicates. X-axis shows the average absolute distance of replicates to the corresponding average protein profile. The lines and numbers indicate the 70th percentile. Lower scatter reflects higher map reproducibility (X-axis cut at 0.2; <1% of profiles not shown).