Why are none of the proteins I export being found in my pathways analysis?
Pathways tools are useful for putting your protein alterations into context, identifying statistical trends in which biochemical pathways are associated with the changes you detect.
Of course, it is important that the pathways tool has access to information relevant to the species and pathways in which your alterations have been detected. Many pathways tools do support a wide range of databases. For example, P02768) are acceptable, but not all formats may be. The accession you obtain is entirely determined by the database searched; since Progenesis QI for proteomics is compatible with a range of external databases, it will accept various accessions, and it is important for pathway analysis that compatible formats are used.
It is also possible to convert your accessions in some cases, using tools such as Uniprot mapping, BridgeDb, Biomart (and incidentally, MetaboAnalyst for metabolites if linking to metabolomics data as well).
Finally, it is of course possible that there are no significant alterations in pathways derived from your data (meaning pathway results are not returned); however, if your entries are not being matched to entities in the databases (for example, as described in Section 3.2.1 of the IMPaLA tutorial), then one of the above possibilities is the likely cause.
- Kamburov et al., 2011: "Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA". Bioinformatics 27: 2917-8.