iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections

Table 2

Number of proteins commonly quantified with pairs of software packages.

Software packages	Number of quantified proteins; HAdV-B3-infected cells	Number of quantified proteins; HAdV-C5-infected cells
ProgenesisF-T2PQ versus Progenesis LC-MS	438	438
ProgenesisF-T2PQ versus ProgenesisF-T3PQ	347	347
ProteinPilot versus ProgenesisF-T2PQ	406	410
ProteinPilot versus Progenesis LC-MS	569	564
ScaffoldQ+ versus ProgenesisF-T2PQ	396	394
ScaffoldQ+ versus Progenesis LC-MS	535	532
ScaffoldQ+ versus ProteinPilot	1,267	1,263