DIANN converter: Cannot detect PeptideModifiedSequence in input columns

[She1111]

DIANN converter: Cannot detect PeptideModifiedSequence in input columns

[mstaniak]

is this column present in the input?

[She1111]

is this column present in the input?

Yes. Because the file is too large to upload, here is screen shot of the file.

[mstaniak]

please try changing "Modified.Sequence" to "Peptide.Modified.Sequence".
Is this a default column name? What version of DIA-NN did you use? I might need to add an option for this, example data I used had a different name for this column.

[She1111]

please try changing "Modified.Sequence" to "Peptide.Modified.Sequence". Is this a default column name? What version of DIA-NN did you use? I might need to add an option for this, example data I used had a different name for this column.

Yes it is the default column name. I used DIA-NN 1.8.1.

I run this code but it returns a error:

report_TrP <- fread("C:/Learning/0-Data/report.tsv")
annot_TrP <- read.csv("C:/Learning/0-Data/annotation.csv")
colnames(report_TrP)[14] <- "Peptide.Modified.Sequence"
report_TrP <- DIANNtoMSstatsFormat(report_TrP, annotation = annot_TrP)

INFO  [2023-07-18 17:52:20] ** Raw data from DIANN imported successfully.
Error in `[.data.table`(dn_input, , req_cols, with = FALSE) : 
  column(s) not found: ModifiedSequence

[She1111]

And I also try to change "Modified.Sequence" to "ModifiedSequence", it also cannot detect PeptideModifiedSequence.

It is strange that it could detect PeptideModifiedSequence but could not detect FragmentIon when I used DIANNtoMSstatsFormat on around 1st July with the same data.

[mstaniak]

My bad, ModifiedSequence should be the column name, we change that to PeptideModifiedSequence internally.

Currently, this warning only affects oxidation filtering. You can do it manually if needed. Currently, our internal oxidation filter uses a wrong column name. I will update MSstats package to fix this, other than that everything should be OK.
I'm closing this issue, please re-open if needed. Also please let me know if you have other problems with the converter.

[mstaniak]

Requires MSstats update

[mstaniak]

Thanks for reporting the issue btw!

[She1111]

Thank you so much for your quick reply! :) Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Mateusz Staniak ***@***.***> Sent: Tuesday, July 18, 2023 8:04:01 PM To: Vitek-Lab/MSstatsConvert ***@***.***> Cc: Yajie Zhang ***@***.***>; Author ***@***.***> Subject: Re: [Vitek-Lab/MSstatsConvert] DIANN converter: Cannot detect PeptideModifiedSequence in input columns (Issue #80) Thanks for reporting the issue btw! — Reply to this email directly, view it on GitHub<#80 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A7EYJKEJWPSKHARZCU5NK3LXQ3FZDANCNFSM6AAAAAA2OSWOWA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[She1111]

Hi,

I have two lists of data that have been converted from the same DIA-NN file but at different times. One was done on 2nd July, and the other on 19th July. They are different. Which one is the reliable one?

Thanks in advance!

Best regards,
Shel
MSstats_log_2023_07_02_20_42_53.114015_previous.log
MSstats_log_2023_07_18_18_27_27.259128_latest.log

[mstaniak]

Current version. In the past the converter aggregated fragment ion information prematurely.

[She1111]

Current version. In the past the converter aggregated fragment ion information prematurely.

THANK YOU so much for your quickly reply and help! I am going to use the latest one for further MSstats analysis.

Cheers,
Shel

[She1111]

Hi,

I notice that DIANNtoMSstatsFormat will select Protein.Names in DIA-NN output file as ProteinName automatically which can not match with the information of proteins from Uniprot when I use MSstatsLiP package. Is it feasible to add an option for selecting presented columns? Or is it more convenient to just rename the column name in RAW datafile?

Thanks in advance!

Cheers,
Shel

[mstaniak]

For now, please rename the column. I will add that option in a few days, thanks for letting me know