Table I. Pearson's linear correlation analysis for the NadjSPC values across the three biological replicates for each of the five sample types. Within each comparison, 0–0 pairs were removed to avoid artificial increase of the correlation values. For each pair is listed: the correlation coefficient, the p value in paranthesis, and the number of proteins in brackets.

Avg (NadjSPC) >0 (i.e. all detected proteins)
Sample	REP(1,2)	REP(2,3)	REP(1,3)
WB	0.911046 (0.000000) [1456]	0.935535 (0.000000) [1577]	0.915923 (0.000000) [1755]
BC	0.973189 (0.000000) [1026]	0.975794 (0.000000) [930]	0.968234 (0.000000) [1137]
Bu1	0.942316 (0.000000) [737]	0.949920 (0.000000) [650]	0.966941 (0.000000) [785]
Bu2	0.950022 (0.000000) [519]	0.956288 (0.000000) [521]	0.973451 (0.000000) [553]
BR	0.907301 (0.000000) [1156]	0.946602 (0.000000) [1236]	0.870057 (0.000000) [1408]
Avg (NadjSPC) > = 0.01
Sample	REP(1,2)	REP(2,3)	REP(1,3)
WB	0.901750 (0.000362) [10]	0.968338 (0.000004) [10]	0.927791 (0.000109) [10]
BC	0.994483 (0.000000) [11]	0.996094 (0.000000) [11]	0.995430 (0.000000) [11]
Bu1	0.989705 (0.000000) [15]	0.990646 (0.000000) [15]	0.991988 (0.000000) [15]
Bu2	0.982754 (0.000000) [18]	0.990855 (0.000000) [18]	0.984292 (0.000000) [18]
BR	0.933994 (0.000001) [14]	0.952317 (0.000000) [14]	0.863387 (0.000069) [14]
Avg (NadjSPC) > = 0.001 and <0.01
Sample	REP(1,2)	REP(2,3)	REP(1,3)
WB	0.676583 (0.000000) [190]	0.807994 (0.000000) [190]	0.722070 (0.000000) [190]
BC	0.651988 (0.000000) [185]	0.693290 (0.000000) [185]	0.495089 (0.000000) [185]
Bu1	0.743508 (0.000000) [178]	0.521708 (0.000000) [178]	0.557247 (0.000000) [178]
Bu2	0.779909 (0.000000) [170]	0.675159 (0.000000) [170]	0.674097 (0.000000) [170]
BR	0.558248 (0.000000) [188]	0.835215 (0.000000) [188]	0.619625 (0.000000) [188]
Avg (NadjSPC) > = 0.0001 and <0.001
Sample	REP(1,2)	REP(2,3)	REP(1,3)
WB	0.211049 (0.000000) [821]	0.312124 (0.000000) [811]	0.370317 (0.000000) [835]
BC	0.159327 (0.000240) [527]	0.315368 (0.000000) [473]	0.137764 (0.001402) [535]
Bu1	0.121923 (0.023725) [344]	0.178438 (0.001819) [303]	0.014824 (0.783194) [347]
Bu2	0.195202 (0.003078) [228]	0.123246 (0.068064) [220]	0.071228 (0.286327) [226]
BR	0.099402 (0.011413) [647]	0.388469 (0.000000) [614]	0.135713 (0.000445) [666]
Avg (NadjSPC) > = 0.00001 and <0.0001
Sample	REP(1,2)	REP(2,3)	REP(1,3)
WB	−0.606859 (0.000000) [435]	−0.362424 (0.000000) [525]	−0.558647 (0.000000) [679]
BC	−0.499333 (0.000000) [301]	−0.392403 (0.000000) [227]	−0.495410 (0.000000) [374]
Bu1	−0.547358 (0.000000) [197]	−0.540131 (0.000000) [129]	−0.566530 (0.000000) [221]
Bu2	−0.679944 (0.000000) [103]	−0.350547 (0.000141) [113]	−0.447838 (0.000000) [139]
BR	−0.591225 (0.000000) [304]	−0.379592 (0.000000) [372]	−0.539781 (0.000000) [495]