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Retention time

Figure 2 Related peptide ions are clustered across the entire study. High confidence matching is achieved, independent of small variations in mass and retention time detected. Each symbol represents a detected ion in one sample, plotted at the observed mass-to-charge ratio and chromatographic retention time.

database. For human plasma studies, the human International Protein Index (IPI; European Bioinformatics Institute) is searched. For samples not of human origin, other public databases may be used, depending on the species. The search results are parsed based on peptide and protein score thresholds that are determined by setting an acceptable false-positive rate of identification calculated by searching a randomized database [35].

In addition, we have developed novel software that adds a differential abundance correlation filter to mass and retention-time fingerprinting [virtual mass spectrometry (VMS)]. Protein identification using mass and retentiontime fingerprinting alone suffers from the high level of mass redundancy for peptides from complex species. VMS incorporates the protein identification and peptide expression resolver (PIPER) filter, which requires all peptides pointing to the same protein to share the same relative intensity across all samples, a logical requirement for association. Application of the PIPER filter to the identified peptides results in false-positive protein identification rates below 5% [36]. This method provides for the identification of proteins where the peptide ions can be detected but are not sufficiently intense to provide an interpretable MS/MS fragmentation pattern [37] . In addition to adding new protein identifications, VMS can also be used to supplement LC-MS/MS by

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