Table 2. Number of proteins after combining the PFM- and PSM-derived protein probabilities.

For each of the datasets investigated, we display the number of proteins at q < 0.01 inferred using the fragmentation spectra (second column), as well as the number of unique peptides matched to a fragmentation spectra (third column) and the number of unique peptides matched to MS1-features (fourth column) mapping to these proteins. Similarly, the fifth column gives the number of proteins at q < 0.01 after incorporating the peptide-feature matches, while the following two columns give the number of peptides matched to fragmentation spectra and MS1-features mapping to these proteins. The last two columns give the number and percentage of additional proteins obtained when including the peptide-feature matches (PFM). Here PSM stands for peptide-spectrum match.

	PSM proteins			PSM+PFM proteins
Dataset	#proteins	PSM peptidesa	PFM peptidesb	#proteins	PSM peptidesa	PFM peptidesb	Additional proteins	Increase
yeast-01	996	5,370	1,231	1,054	5,481	1,438	58	5.8%
yeast-02	972	5,291	1,159	1,044	5,417	1,391	72	7.4%
yeast-03	967	5,170	1,198	1,031	5,276	1,415	64	6.6%
human-01	1,614	9,736	3,198	1,704	9,878	3,580	90	5.6%
human-02	1,622	9,752	3,362	1,715	9,896	3,821	93	5.7%
human-03	1,714	9,255	3,437	1,806	9,370	3,937	92	5.4%

^aUnique peptides matched to fragmentation spectra with posterior error probability < 1.0.

^bUnique peptides matched to MS1-features.