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Figure S1. Sensitivity of the spectral library search with different values of n, the number of most intense peaks retained. The number of correct SSMs are plotted against the FDR predicted by PeptideProphet for the new SpectraST discriminant function (the logarithm of the expectation value, obtained from the rank-based dot product) for Dataset 1 and Dataset 2. For Dataset 2, a randomly chosen subset of 8 LC-MS runs was used to speed up the optimization.

Figure S2. The number of correct SSMs using different combinations of U and V when the FDR is controlled at 1%. For Dataset 2, a randomly chosen subset of 8 LC-MS runs was used to speed up the optimization.

Figure S3. The histogram of the search space (the number of candidate library spectra matched) for all query spectra in Dataset 1 and Dataset 2.

Figure S4a. One of 6 replicate SSMs of IINEPTAAAIAYGLDKK (charge 3+). Original SpectraST also found 4 out of 6 of these SSMs as top identifications with high dot products, but did not pass the FDR threshold due to very large dot bias penalty.

Figure S4b. One of 6 replicate SSMs of GIPEFWLTVFK (charge 2+). Original SpectraST also found all 6 of these SSMs as top identifications with high dot products, but did not pass the FDR threshold due to very large dot bias penalty.

Figure S4c. One of 3 replicate SSMs of AGAEVVK (charge 1+). Original SpectraST also found all 3 SSMs as top identifications but the delta scores were not high enough to pass the FDR threshold.

Figure S4d. One of 16 replicate SSMs of DGNASGTTLLEALDC160ILPPTRPTDKPLR (charge 4+). Original SpectraST also found 15 of these SSMs as top identifications but the delta scores were not high enough to pass the FDR threshold.

Figure S4e. One of 4 replicate SSMs of ENPSATLEDLEKPGVDEEPQHVLLR (charge 3+). Original SpectraST also found all 4 SSMs as top identifications but the dot products were not high enough to pass the FDR threshold.

Table S1. A list of different combinations of U and V used in this study. Combination A means that there is no restriction on the m/z locations of the 50 retained peaks.

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