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mwang87 / MassQueryLanguage

The Mass Spec Query Language (MassQL) is a domain specific language meant to be a succinct way to express a query in a mass spectrometry centric fashion.
https://mwang87.github.io/MassQueryLanguage_Documentation/
MIT License
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MS1 precursor ion/s with 34S isotope pattern #213

Open Mattesimone opened 2 years ago

Mattesimone commented 2 years ago

Hi,

I run massql tool (Commandline) to search for sulfur-containing signals with the following query: QUERY scaninfo(MS1DATA) WHERE MS1MZ=X AND MS1MZ=X+1.996:TOLERANCEPPM=2 I'm attaching the unexpected output in which the difference between mz_lower and mz_upper mz is always 20.

Then I execute the same MassQL query against my data at GNPS but the job failed: ID=be0a38f7bdd2472da1f5cd5b4d58bdfc Screenshot 2022-03-18 at 14 37 41

Thanks in advance for help

Matteo

mwang87 commented 2 years ago

Yes, your job just took too long on GNPS so it was killed. The mz_upper and mz_lower, are by definition above and below the "comment" which is the value of the X you found. Its mostly been used to make rendering much easier, though likely it should probably belong in an accompanying script rather than main MassQL.

To make it run faster, I'd recommend setting minimum peak intensity thresholds for your X peak. 

QUERY scaninfo(MS1DATA) WHERE MS1MZ=X:INTENSITYPERCENT=5 AND 
MS1MZ=X+1.996:TOLERANCEPPM=2
Mattesimone commented 1 year ago

Hey Ming,

thank you so much for helping me to understand better Mass Query Language output by querying MS1DATA. I like Mass Query Language (great job). Thank you for your suggestion.

Matteo

On 18 Mar 2022, at 18:40, Ming Wang @.***> wrote:

Yes, your job just took too long on GNPS so it was killed. The mz_upper and mz_lower, are by definition above and below the "comment" which is the value of the X you found. Its mostly been used to make rendering much easier, though likely it should probably belong in an accompanying script rather than main MassQL.

To make it run faster, I'd recommend setting minimum peak intensity thresholds for your X peak.

QUERY scaninfo(MS1DATA) WHERE MS1MZ=X:INTENSITYPERCENT=5 AND MS1MZ=X+1.996:TOLERANCEPPM=2 — Reply to this email directly, view it on GitHub https://github.com/mwang87/MassQueryLanguage/issues/213#issuecomment-1072643433, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANR3TR76NQ7JTYRQ54YGXVDVAS52FANCNFSM5RB4PKIA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.

mwang87 commented 1 year ago

Awesome! Good luck with it and feel free to ask questions and contribute.