MassQL Patterns
This page includes common patterns that you might want to query for in mass spec data
Query Mass Spectrometry Data¶
MS1 precursor ion/s based on monoisotopic mass with absolute mass error¶
Finding MS1 peak at m/z 256.1696 with a 0.01 m/z tolerance.
QUERY scaninfo(MS1DATA) WHERE
MS1MZ=256.1696:TOLERANCEMZ=0.01
MS1 precursor ion/s based on monoisotopic mass with relative mass error¶
Finding MS1 peak at m/z 256.1696 with a 5.0 ppm tolerance.
QUERY scaninfo(MS1DATA) WHERE
MS1MZ=256.1696:TOLERANCEPPM=5
MS1 precursor ion/s based on monoisotopic mass and isotope mass with relative mass error¶
Finding MS1 peak at m/z 256.1696
Finding MS1 peak at m/z 258.1656 with a 5.0 PPM tolerance.
*example: monoisotopic mass + 1.996 for 34S
QUERY scaninfo(MS1DATA) WHERE
MS1MZ=256.1696 AND
MS1MZ=258.1656:TOLERANCEPPM=5
MS1 precursor ion/s with 34S isotope pattern¶
Finding MS1 peak at m/z X.
Finding MS1 peak at m/z X+1.996 with a 5.0 PPM tolerance.
QUERY scaninfo(MS1DATA) WHERE
MS1MZ=X AND
MS1MZ=X+1.996:TOLERANCEPPM=5
MS2 spectrum with product ion with absolute mass error¶
Finding MS2 peak at m/z 167.0857 with a 0.01 m/z tolerance.
QUERY scaninfo(MS2DATA) WHERE
MS2PROD=167.0857:TOLERANCEMZ=0.01
MS2 spectrum with product ion with relative mass error¶
Finding MS2 peak at m/z 167.0857 with a 5.0 ppm tolerance.
QUERY scaninfo(MS2DATA) WHERE
MS2PROD=167.0857:TOLERANCEPPM=5
MS2 spectrum with a neutral loss and product ion with relative mass error¶
Finding MS2 neutral loss peak at m/z 176.0321.
Finding MS2 peak at m/z 85.02915 a 5.0 PPM tolerance.
QUERY scaninfo(MS2DATA) WHERE
MS2NL=176.0321 AND
MS2PROD=85.02915:TOLERANCEPPM=5
MS1 scan associated with MS2 spectrum containing a product ion with absolute mass error¶
Finding MS1 scan associated with MS2 spectrum - relevant to data-dependent acquisition experiments
QUERY MS1DATA WHERE
MS2PROD=167.0857:TOLERANCEPPM=5
Query Liquid/Gas Chromatography - Mass Spectrometry Data¶
Total ion chromatogram¶
Returning the summed scan information on MS1.
QUERY scansum(MS1DATA)
Extracted ion chromatogram¶
QUERY scansum(MS1DATA) FILTER
MS1MZ=256.1696:TOLERANCEPPM=5
MS2 spectra with a given MS1 isotopic pattern¶
If you're looking for molecules with an isotopic pattern and want to get the MS2 spectra associated with it, we have a pretty easy way to do this.
Since you're looking for a variable m/z denoted as X, once you find it, simply enforce the MS2 precursor m/z to also be X.
Note
This will cause isotopic patterns that lack MS2 to be dropped
Here is a quick example of a query
QUERY scaninfo(MS2DATA) WHERE
MS1MZ=X AND
MS1MZ=X+1 AND
MS2PREC=X
Dynamic Shapes With Mobility¶
If you're looking for certain mobility of molecules that is dependent upon the m/z of the molecule, you can start including variables in the mobility range function.
QUERY scaninfo(MS2DATA) WHERE MS2PREC=X AND MOBILITY=range(min=X*0.0011+0.5-0.1, max=X*0.0011+0.5+0.1