Fengchao

> But I think nativeID is specifically intended and useful for mapping across different tools, and for remaining valid when files are filtered or subsetted. It's why I started putting...

For Thermo data, the `spectrumNativeID` is already in the pepXML file. For the others that require changing the scan indexing, I am trying to get it done before the next...

Hi @chambm , I added the Waters and other vendor's support. Here are the `pepXML` and `_calibrated.mzML` files generated by the MSFragger: [010208_ecoli_003-dda2_calibrated.zip](https://github.com/user-attachments/files/17298722/010208_ecoli_003-dda2_calibrated.zip). Basically, I used the approach we discussed...

Hi Anler, Thanks for the bug report. Could you share `20170311_QEh1_LC2_FaMaChCh_SA_HLApI_3912-BAM_1_R1.raw` and `2024-05-23-decoys-contam-Noncoding_ref.fasta.fas` with us? I need the files to figure out the cause of the error. Here is the...

Hi Anler, Thanks for sharing the file. The error was because there were MS2 peaks with unreasonable large m/z. I have added a filter to remove those peaks since it...

Hi Scott, I think I need to clarify some technical details first. When enabling IonQuant for the LFQ-related analysis, the MSstats.csv file is generated by IonQuant, and the format can...

Yes, MSstatsPTM can be used for both TMT and LFQ data. I think I can make IonQuant LFQ support it in the future. Best, Fengchao

We have made FragPipe fully support MSstatsPTM for DDA LFQ and DIA LFQ. Contact us if you want to try the pre-released version. Best, Fengchao

The error was from DIA-Umpire. @guoci can you take a look? Thanks, Fengchao

Hi @nicolasgrinberg , The error is not about DIA+. It was thrown by DIA-Umpire (as the new title I have changed), which is before MSFragger starts. We are waiting for...