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What are the methods for PTMScan® mass spectrometry?

The methods for the LC and MS are shown below:
 

 ParameterSetting
Sample prepIP sample resuspension volume20 uL
 Sample volume per injection4 uL
 Resuspension buffer5% acetonitrile/0.1% trifluoroacetic acid
   
ChromatographyColumn dimensions100 um ID x 45 cm long
 Stationary phaseSepax GP C18, 1.8um, 120A
 Solvent A0.125% formic acid in water
 Solvent B0.125% formic acid in acetonitrile
 Flow rate275 nL/min
 Gradient0 min - 3% B, 1 min - 6% B, 91 min - 38% B, 141 min - 100% B, 142 min - 3%B, 154 min (end) - 3% B
   
Mass SpectrometryInstrument modelThermo Fusion Lumos
 MS1 detector / resolving powerOrbitrap / 120000
 MS1 scan range300-1500 m/z
 DDA mode3s cycle time
 Isolation width1.6 m/z
 Fragmentation modeHCD
 MS2 detector / resolving powerOrbitrap / 60000
   
Database SearchSearch PlatformComet
 DatabaseMouse SwissProt
 Precursor match tolerance(+/-)50 ppm
 Product ion match tolerance(+/-) 0.02 Da
 Post-search filter on precursor mass(+/-) 5 ppm
 FDR cutoff5%

These parameters can also be found in the “Methods Overview” tab on the example data Excel files.
 

Last updated: September 12, 2024

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