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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Two Questions: About Fragment.info Column in Ver. 1.9 & Meaning of MS2.Scan #1286

Open dong-gi-jang opened 2 days ago

dong-gi-jang commented 2 days ago

Dear DiaNN Team,

Thank you for developing such an amazing tool.

I have two questions:

1) In version 1.8.x, the report.tsv file included a Fragment.info column (e.g., b6^1/427.23 ...). However, I couldn’t find this column in either report.tsv or report.parquet files in version 1.9.x. Could you kindly let me know where I might find this information in the latest version?

2) I understand that the MS2.Scan column in report.tsv does not correspond to the absolute index in the .raw file. If I were to map this value back to the .raw file, does it represent the apex of the feature, or does it refer to some specific scan?

Best regards, Dong-Gi

vdemichev commented 2 days ago

Hi Dong-Gi,

  1. Please use --export-quant in the new DIA-NN, it will then save fragment info, also in a lot more convenient format.
  2. Yes, it's some internal index. For matching to the raw data please use RT.

Best, Vadim

ds2268 commented 8 hours ago

@vdemichev: regarding the MS2.Scan. My understanding was that MS2.Scan is the count of the MS2 scans and should be easily mapped to mzml with such regard by basically just counting ms level = 2 in mzml (at least for thermo files). Is my understanding correct?