Disagreement between Adjusted Precursor Mass and Proteoform

[James Fulcher]

Hello,

             I've recently noticed what I believe is a potential bug in the TopPIC output. My interpretation has been that "Adjusted Precursor Mass"  is equivalent to the theoretical monoisotopic mass of an identified proteoform (the exception to this rule are proteoforms with unknown mass shifts). I've noticed, however, that the adjusted precursor mass is 1 Da different for two proteoforms that only differ in the localization of an acetyl group. See below for a selected example:



I noticed that `#unexpected modifications` is different between the two, though it isn't clear to me why that would result in different masses. Any thoughts?

Bests,
James

[liuxia...@gmail.com]

Hi, James, 

The two identifications are different. The second was reported by database search and its precursor mass matched the preoteoform with an N-terminal acetylation. The first one contained an unexpected mass shift of +43 Da in database search identification and the PTM was further localized in which +/- 1 Da error was allowed. 

The two identifications may be from the same proteoform. The deconvolution tool may have reported a precursor mass with a +1 Da error for the first spectrum. If the precursor mass for the spectrum is correct, then the +1 Da error allowed in localization is the reason for the problem. 

Best, 

Xiaowen 

[James Fulcher]

Hi Xiaowen,

            Thanks - that makes sense. 

- James