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. Author manuscript; available in PMC: 2010 Sep 1.
Published in final edited form as: J Proteome Res. 2009 Sep;8(9):4243–4251. doi: 10.1021/pr900298b

Table 1.

An Excerpt of the Tabulated Data on Which the Spectral Correlation Analyses Are Baseda

experimental-QQQ library-ion trap
protein peptide prec m/z prod m/z fragment sample AUC rank
order		 relative
intensity		 rank
match		 intensity rank
order		 relative
intensity
YDR388W GNVEEQTDALTITHFK 901.95 532.30 y4 Low-pI yeast 498649 1 100.0 0 7843 2 78.4
YDR388W GNVEEQTDALTITHFK 901.95 746.30 y6 Low-pI yeast 367296 2 73.7 0 10000 1 100.0
YDR388W GNVEEQTDALTITHFK 901.95 1045.30 y9 Low-pI yeast 217902 3 43.7 0 5764 5 57.6
YDR388W GNVEEQTDALTITHFK 901.95 1146.50 y10 Low-pI yeast 217631 4 43.6 0 7309 3 73.1
YDR388W GNVEEQTDALTITHFK 901.95 930.50 y8 Low-pI yeast 187535 5 37.6 0 7176 4 71.8
YDR388W GNVEEQTDALTITHFK 901.95 859.50 y7 Low-pI yeast 102327 6 20.5 1 4822 6 48.2
YDL084W TAVFYGGTPISK 620.83 659.37 y7 High-pI yeast 18063116 1 100.0 1 10000 1 100.0
YDL084W TAVFYGGTPISK 620.83 822.44 y8 High-pI yeast 15182154 2 84.1 1 8438 2 84.4
YDL084W TAVFYGGTPISK 620.83 969.51 y9 High-pI yeast 10944881 3 60.6 1 7734 3 77.3
YDL084W TAVFYGGTPISK 620.83 444.28 y4 High-pI yeast 8930639 4 49.4 1 5256 4 52.6
YDL084W TAVFYGGTPISK 620.83 1068.58 y10 High-pI yeast 2302069 5 12.7 1 2153 5 21.5
YDL084W TAVFYGGTPISK 620.83 545.33 y5 High-pI yeast 1008182 6 5.6 1 1216 6 12.2
Q29443 NYELLC[160]GDNTR 677.81 722.29 y6 18 Mix 164326 1 100.0 1 10000 1 100.0
Q29443 NYELLC[160]GDNTR 677.81 835.37 y7 18 Mix 135696 2 82.6 1 6119 2 61.2
Q29443 NYELLC[160]GDNTR 677.81 562.26 y5 18 Mix 63110 3 38.4 1 5157 3 51.6
Q29443 NYELLC[160]GDNTR 677.81 948.46 y8 18 Mix 41916 4 25.5 1 3704 4 37.0
Q29443 NYELLC[160]GDNTR 677.81 505.23 y4 18 Mix 5325 5 3.2 0 946 6 9.5
Q29443 NYELLC[160]GDNTR 677.81 1077.50 y9 18 Mix 3093 6 1.9 0 3392 5 33.9
a

This data includes the MRMer-calculated AUC value for each triple quadrupole-targeted transition and the corresponding spectral library-derived peak intensity. The resulting rank orders and relative intensities are also included, along with basic information about each transition (e.g., protein, peptide sequence, m/z values, etc.). The full data set, which includes all data from all three samples, is provided in Supplemental Table 2.