report.gg_matrix.tsv vs report.tsv

[AnirudhKashyap511]

What does it mean if the report.tsv file has data but report.gg_matrix.tsv has no data, could the timsTOF file be corrupted, which means that I need to run the data and diann again or does it mean somethign else. Also, wanted to know how changing the DIANN versions would change protein abundance if it changes at all?

Thank you so much!

[vdemichev]

Hi,

Possible reasons: no FASTA provided, no genes passed q-value filtering. How does the log look like?

could the timsTOF file be corrupted

No.

how changing the DIANN versions would change protein abundance

Protein abundance is not comparable between versions.

Best,
Vadim

[vdemichev]

no genes passed q-value filtering

Likely this

[AnirudhKashyap511]

Thank you for your prompt reply, I had another question if you dont mind. I was trying to understand my data and PG.Quantity PG.Normalised PG.MaxLFQ Genes.Quantity Genes.Normalised Genes.MaxLFQ Genes.MaxLFQ.Unique
all showed similar values so was wondering what that could mean?

[vdemichev]

all showed similar values

That's fine. Can even be identical if there's a single run & single precursor matching the protein.

[AnirudhKashyap511]

Thanks! Makes sense, just had one last question. How is protein abundance calculated? Is Ms1Area being summed? I tried it it doesnt match.

[vdemichev]

Based on Precursor.Normalised, using MaxLFQ (Legacy) or QuantUMS (QuantUMS mode)