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Not able to see MS2

We have a Shimadzu LC MSMS QQQ system. Now from the Labsolution software it was exported to MzML. Now after that I have loaded in the MS Dial. But system not able to detect MS2. Also, the library is reporting the results as 'w/o ms2'. I am confused. Please help.

Re: Not able to see MS2

Reply #1
Hello,

(a) Can you first select/ check "MS2 assigned" instead of "suggested" and see if int he Ion Table you see any hits/ spectra? If not then the datasets does not have any MS/MS spectra, or your search criteria are too stringent etc.

(b) "w/o Name" is based on precursor ion / MS1 hits alone with a certain mass window, but less confidence hits and I would typically bother not considering them for any downstream analysis. 

(b) Its mostly likely that the files do not have MS/MS data in them, or lost during conversion process to mzML etc.
Also, can you please share the RAW unprocessed file from the vendor and the converted mzML file through Google Drive etc. for us/ me  (email: bbmisraccb@gmail.com) to look at the file and see whats going on.

Without that its difficult to suggest from pictures alone!

Thanks,
Biswa

 

Re: Not able to see MS2

Reply #2
Plus also,:

[A]  see here for a relevant response from Hiroshi san on converting data out from Shimadzu software: http://www.metabolomics-forum.com/index.php?topic=1605.0  (to make sure you got the .mzML out in "Centroid" mode!)

Whats "w/o MS2 NAME" here: http://www.metabolomics-forum.com/index.php?topic=1580.msg4749#msg4749

Exactly. See the FAQ site.
http://prime.psc.riken.jp/compms/msdial/faq.html
What is the 'w/o' tag of identification results?
1. This program first tries to find a metabolite candidate from a MSP file by means of MS/MS similarity, accurate mass, isotope ratio, and retention time. A metabolite getting 'highest score' in the metabolite candidates is annotated. Note that this score is the total score from retention time similarity, isotope ratio similarity, accurate mass similarity, and MS/MS similarity.
2. But if the 'highest score' is less than user-defined identification cut off, 'non-MS/MS based identification' is performed. That is, this program next tries to find a metabolite candidate by means of accurate mass, isotope ratio, and retention time. Then, a metabolite getting 'highest score' in candidates is annotated. Note that this score is the total score from retention time, isotope ratio, and accurate mass. This result will be shown as 'w/o MS2:***'.
3. If any compounds are not found from the above two criteria, the result will be 'unknown'.


Hope these two points above help you!

Thanks,
Biswa










Thanks!

Re: Not able to see MS2

Reply #3
Dear Anish

Maybe, because your instrument is QqQ, you should set 0.2 Da for ms1/ms2 tolerance in the data collection tab parameter setting.
Did you do this?

Hiroshi

Re: Not able to see MS2

Reply #4
Hi,
Yes I did this. But Local Shimadzu people are telling in a single run it cannot accommodate both the runs i.e. MS1 and MS2. So in the file, only MS1 is coming, not the MS2

Re: Not able to see MS2

Reply #5
w/o MS2 tag means that the peak was annotated without ms2 information. Therefore, the tag will be appeared even though your data does not have MS2 spectral information.

Hiroshi

Re: Not able to see MS2

Reply #6
Thank you, but the issue is my LC MS MS system of Shimadzu is not able to write both MS1 and MS2 in the file. I asked the application support, but he is not able to help me on that

Re: Not able to see MS2

Reply #7
Oh...I will ask Shimadzu persons to help you (because I am Japanese.:D
Please send me your private address.

Thanks

Hiroshi