Proteome Discoverer V3.1, removal of Spectrum File column

[lyons89]

My group has recently updated PD from 2.5 to 3.1 and I discovered that the 'Spectrum File' column is missing from the PSMs tab. I reached out to Thermo support and they have confirmed that they removed the 'Spectrum File' column. I wanted to update the MSstats team since the 'Spectrum File' column is required for MSstats and MSstatsTMT packages. I'm hoping that changing out Spectrum File for File ID will do the trick.

For anyone else who needs a quick fix for this, I found a workaround by downloading the Input Files data from PD3.1, which contains the File Name column, and then joining it with the PSMs data using the File ID column. Next, use the base function basename to extract the Spectrum File name from the File Name column.

[mstaniak]

thanks for letting us know, we will update our converters accordingly

[tonywu1999]

Next Step:

• Add run_column parameter to MSstats and TMT converters to enable use of FileID.

[mstaniak]

I pushed these changes to Bioc, please close once they're reflected in MSstats(TMT)