Error in eval(bysub, x, parent.frame()) : object 'Run' not found

[Jared Churko]

Hi,

When trying to use the  PDtoMSstatsTMTFormat function, I get the following error:

INFO [2025-04-10 15:25:08] ** Raw data from ProteomeDiscoverer imported successfully. INFO [2025-04-10 15:25:09] ** Raw data from ProteomeDiscoverer cleaned successfully. INFO [2025-04-10 15:25:10] ** Using provided annotation. INFO [2025-04-10 15:25:10] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'. INFO [2025-04-10 15:25:10] ** The following options are used: - Features will be defined by the columns: PeptideSequence, PrecursorCharge - Shared peptides will be removed. - Proteins with single feature will not be removed. - Features with less than 3 measurements within each run will be removed. Error in eval(bysub, x, parent.frame()) : object 'Run' not found

However both files do have a run column defined.

I am using Proteome discoverer 3.2.0.450 and MSstatTMT 2.6.1

Please see the abbreviated annotation and input files attached. 

library(MSstatsTMT)

raw.pd<- read.csv("Pkp2mutTMT_ResultsAbrev_PSMs.csv", header = T)

annotation <- read.csv("PKP2_PD_Annotations3.csv", header = T)

input.pd <- PDtoMSstatsTMTFormat(input = raw.pd,
                                  annotation = annotation,
                                  which.proteinid = "Master.Protein.Accessions",
                                  useNumProteinsColumn = TRUE)

[Anthony Wu]

Hi Jared,

Could you upgrade MSstatsTMT to the latest version on bioconductor (2.14.1).  And then for the PD input file, the run column should be named `SpectrumFile`.  I believe that is the default of PD, but please let me know otherwise and we can prioritize updating the PD converter to enable using a different name for the run column.

Tony

[Jared Churko]

Thanks Tony, 

Updating MSstatsTMT and replacing the "File ID" column name with  "SpectrumFile" name worked.