Title [pParse] precursors in .ms2 files should also be rectified
Priority feature Status processing
Superseder Nosy List Yudong, ctarn
Assigned To ctarn Keywords pParse, pXtract

Created on 2020-11-27.10:27:05 by Yudong, last changed by ctarn.

File name Uploaded Type Edit Remove
Question for pParse.pdf Yudong, 2020-11-27.10:27:05 application/pdf
msg2 (view) Author: ctarn Date: 2020-11-27.19:12:35
Hi Yudong. Thanks for reaching out.

The monoisotopic m/z data in .ms2 files are extracted from .raw file by pXtract without 
any rectification (currently). The rectified precursors are saved as .mgf and .pf2 
files. Please check the precursors in the .mgf file.

In addition, indeed, the algorithm currently works better on short peptides than long 
peptides. You can try other models embedded in pParse which target to different 

In the next release, pParse will be able to export precursor-rectified .ms1/.ms2 files 
msg1 (view) Author: Yudong Date: 2020-11-27.10:27:05
For short peptides, the extraction of monoisotopic m/z works well by pParse. but I 
find that it fails to extract the monoisotopic m/z for longer peptides. please see 
the attachment.
Date User Action Args
2020-11-30 15:59:00ctarnsettitle: The extraction of monoisotopic m/z -> [pParse] precursors in .ms2 files should also be rectified
priority: notice -> feature
2020-11-27 19:12:36ctarnsetstatus: unread -> processing
keyword: + pParse, pXtract
assignedto: ctarn
messages: + msg2
nosy: + ctarn
2020-11-27 10:27:06Yudongcreate