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MSP430FR5994: Issue with ADC values

Part Number: MSP430FR5994

Hello Everyone, 

I have an issue with my ADC values being incorrect when the PWM starts. I am working on a project that needs that I take ADC values for several parameters. Before the PWM thats drives my buck converter starts, the ADC values being read (after converting it to the actual quantity value) is quite correct with  multimeter values, but once the PWM starts, the variation between the actual quantity value and the microcontroller values is about 1.5V - 2V for the voltage values I am measuring and I need the accuracy to be about 0.01V - 0.05V. I am using MSP430FR5994 launchpad. I have tried some few options to resolve this which includes

1.) Adding a 0.1uf Filter Capacitor placed directly at the ADC input on the launchpad

2.) I have tried to increase the ADC sampling time to 128 and 256 cycles but finally settled for 64 cycles as it gave me better result than the others

3.)  One of the ADC measurement involve using an op-amp for voltage measurement, tried to replace it with a voltage divider (quite better with voltage divider than op-amp but not satisfactory).

4.) Since using a launchpad, I used the same 3.3V biasing circuit for my circuit to power the launchpad (disconnected the 3.3V jumper to the ez-fet), adc measurement improved but not satisfactory

5.) all unused ADC pins have been connected to ground also.

With all the points above tried already, the ADC values variation still stands between 1V and 1.5V. I will appreciate any help regarding this. 

Thanks

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