Dear ProteoAnalyst team,
I am using the ProteoAnalyst web platform and have encountered an issue where the differential abundance analysis runs successfully, but the downloaded DEG/DEP results do not include protein/gene identifiers. The output contains statistics such as fold change and p values, but no ProteinID, GeneID, Symbol, or feature name.
I uploaded a protein intensity matrix with features as rows and samples as columns. The first column was labelled ProteinID.
Example data matrix:
ProteinID 8_AD_H1 17_AD_H2 23_AD_H3 28_AD_H4
MED19 45737.12891 53634.57813 53561.89844 45152.41016
FAM234B 23750.01367 36863.00781 26307.13672 25078.14258
VPS37C 27736.82617 25725.53711 25767.83594 21270.30469
Separate metadata file:
#NAME Group
8_AD_H1 AD_OE_h
17_AD_H2 AD_OE_h
23_AD_H3 AD_OE_h
28_AD_H4 AD_OE_h
The full dataset contains approximately 7,000 protein/gene-level features and 31 samples across multiple experimental groups.
Steps leading to issue
Uploaded the protein intensity matrix and separate metadata file.
Confirmed that sample groups were recognised correctly.
Performed preprocessing:
Opened the differential abundance analysis module.
Selected Group as the comparison variable.
Ran the comparison siAD_n versus siNeg_n.
Downloaded the DEG/DEP results using the available download button.
Observed issue
The downloaded DEG/DEP result contains statistical columns, but no feature identifier column.
Example of downloaded output:
logFC FoldChange P.Value adj.P.Val
…
Expected output
ProteinID logFC FoldChange P.Value adj.P.Val
Thank you for the help