Issue 2: [pParse] precursors in .ms2 files should also be rectified - pFind Forum

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.

Files
File name	Uploaded	Type	Edit	Remove
Question for pParse.pdf	Yudong, 2020-11-27.10:27:05	application/pdf

Messages
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 purposes. In the next release, pParse will be able to export precursor-rectified .ms1/.ms2 files directly.
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.

History
Date	User	Action	Args
2020-11-30 15:59:00	ctarn	set	title: The extraction of monoisotopic m/z -> [pParse] precursors in .ms2 files should also be rectified priority: notice -> feature
2020-11-27 19:12:36	ctarn	set	status: unread -> processing keyword: + pParse, pXtract assignedto: ctarn messages: + msg2 nosy: + ctarn
2020-11-27 10:27:06	Yudong	create