Table 4.

Results for filtering of non-peptide masses.

		Arabidopsis t.	Rhodopirelulla b.	Mus musculus
1	Identification no PR filtering	423	1009	872
2	Identification with PR filtering	432	1017	894
3	Change in identification (Percent)	2.13	0.79	2.52
4	Total nr. of samples*	818	1169	1709
5	Nr. samples with PBMS increase	240	622	724
6	Nr. samples with no change of PBMS	571	542	982
7	Nr. samples with PBMS decrease	7	5	3
8	Percent increase of PBMS score	29.34	53.21	42.36
9	Percent decrease of PBMS score	0.86	0.43	0.18

Columns: Arabidopsis t., Rhodopirelulla b., Mus musculus – peptide mass fingerprint datasets (cf. Methods). Row 1 – number of samples with a significant PBMS score prior to filtering of non-peptide peak masses. Row 2 – number of samples with a significant PBMS score for peak-lists with non-peptide removed. Row 3 – relative change of the identification rate (Row 2 – Row 1)/Row1 100. Row 4 – Total number of samples which produced a PBMS score. Row 5 -number of samples for which an increase of the PBMS score due to non peptide peak filtering was observed. Row 6 – number of samples for which no change of the PBMS score due to non-peptide peak filtering was observed. Row 7 – number of samples for which a decrease of the PBMS score due to non-peptide peak filtering was observed. Row 8–9 – relative increase and decrease of the PBMS score, respectively.