Mds

Figure 5 Sample groups distinguished by differentially expressed peptides. Multidimensional scaling analysis was performed using the intensity values for 4089 differentially expressed peptide ions from 24 samples. Separation along three axes of variance (MDS1 to MDS3) is shown, where each sphere represents a patient sample. The groups are identified by the colors indicated. (See insert for color reproduction of the figure. )

set (first 24 samples) to determine the identity of the blinded sample test set. None of the individual peptide ions could discriminate the three groups very well. However, sets of five or 10 peptides were much more effective, as shown in the receiver operating characteristic (ROC) plots in Figure 6 . In the case of multiple peptide analysis, peptides were chosen randomly from the population of differentially expressed peptides in order to provide multiple examples of the range of discrimination possible. The AUC required to fully discriminate groups is a value of 1. This was most frequently achieved as the panel size increased from one to 10 proteins (Figure 6, right panels).

To better understand the biology underlying the differentially expressed peptides, their parent proteins were identified. This was accomplished by LC-MS/MS and VMS to identify groups of peptides representing a single protein. This result was further filtered by requiring that the relative intensity of a minimum of three peptide ions be well correlated across all samples. Approximately 200 proteins met these and other strict confidence criteria. Half of these proteins distinguished either breast cancer or ovarian cancer from the other two conditions. The remaining half of the proteins distinguished cancer (breast or ovarian) from normal healthy subjects. These results suggest that circulating blood proteins provide a rich source of high-quality

1 -peptide panel (1000 peptides)

5-peptide panel

(1000 random combinations)

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10-peptide panel

(1000 random combinations)

* Starting with random sets of 890 peptides, the median AUC panels of size 5 is under 0.4.

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False Positive
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Project Management Made Easy

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