Error with PDtoMSstatsFormat function

[Sam Siljee]

Hi all,

I'm looking at using MSstats for my PhD project, and am having some trouble importing my pilot proteomics data from Proteome Discoverer (2.4).

When I run the `PDtoMSstatsFormat` function, I get the output:

Error in `[.data.table`(pd_input, , pd_cols, with = FALSE) :
column(s) not found: ProteinGroupAccessions, PrecursorArea

My input data is the PSMs table exported as a tsv file, I suspect there's some thing I'm doing wrong in PD to end up without protein group accessions and precursor area columns.

Alternatively, it could be the fact that I'm comparing one biological replicate run with two different acquisition methods. (label-free quantification).

Sorry if I didn't word the question clearly, I'm still learning!

Many thanks!

Sam

[Priyam Jani]

Hi Sam, I think you have to manually rename those two column headers before importing to MSStats. There is another thread here where it was discussed.

[Sam Siljee]

Thank you for that!

I've solved that problem using `mutate` to add a column "ProteinGroupAccessions" from the original column "Master.Protein.Accessions", however I could not find a corresponding column for PrecursorArea.

I've subsequently solved this by running a search in PD with all raw files and LFQ (as opposed to running each separately), which gave the column "Precursor.Abundance".

Now however I run into the problem where I get a long list of "returning -InfWarning: no non-missing arguments to max;" errors, and then

"INFO  [2022-12-20 09:03:57] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
INFO  [2022-12-20 09:03:57] ** Features with one or two measurements across runs are removed.
INFO  [2022-12-20 09:03:57] ** Run annotation merged with quantification data.
INFO  [2022-12-20 09:03:57] ** Features with one or two measurements across runs are removed.
INFO  [2022-12-20 09:03:57] ** Fractionation handled.
Error in setnames(x, value) :
  Can't assign 4 names to a 0 column data.table"

Is there someone who's also had this problem?

Thanks!

Sam

[Sam Siljee]

I have a theory that it;s due to the fact I've only got two runs in my data set, and that they get filtered out because there will alway be less than three observations.

Sam

[Mateusz Staniak]

Hi Sam,

I'll look for other possible causes and update the converter to handle alternative column names, but if having only two runs is the problem, you can turn off that filtering step using the "removeFewMeasurements" parameter.

Kind regards

Mateusz

[Sam Siljee]

Thank you Mateusz, I really appreciate your help!

I've tried adding the argument "removeFewMeasurements = FALSE" how I get the same error.

I've also tried with another trial dataset from five runs, with the same results.

I've attached some of the trial dataset.

SessionInfo

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_New Zealand.utf8  LC_CTYPE=English_New Zealand.utf8    LC_MONETARY=English_New Zealand.utf8
[4] LC_NUMERIC=C                         LC_TIME=English_New Zealand.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] forcats_0.5.2   stringr_1.5.0   dplyr_1.0.10    purrr_0.3.5     readr_2.1.3     tidyr_1.2.1    
 [7] tibble_3.1.8    ggplot2_3.4.0   tidyverse_1.3.2 MSstats_4.4.1

Best regards,

Sam

[Sam Siljee]

As an update to this, I've updated a bunch of the other packages, and it's now working as it should.

Perhaps I was having problems with the dependencies? Either way, I'm happy it's fixed!

Sam