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.