How to differentiate Doppler shift from star emission

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I have seen people talking about measuring Doppler shift of stars to know how fast they are receding from us. But if I measured say a particular frequency f, how do I know whether this is shifted frequency or just the emission?
 
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Spectral lines are always at the same frequency at the point of emission. Compare it with the received frequency of these lines to get the redshift (expansion of the universe + Doppler effect + gravitational redshift).
 
You do not measure only single frequency but some broader part of the spectrum. You can then identify one or more characteristic lines based on their profiles and their relative distances in the spectrum. Once you got that, you know the redshift.
 
It's a pattern recognition problem. Different elements give off certain patterns of lines. So you're looking for that pattern, shifted from its normal position.

For instance sodium has a very characteristic close-together pair of lines, at 589.0 nm and 589.6 nm.
http://hyperphysics.phy-astr.gsu.edu/hbase/quantum/sodium.html

If you can find a pair with the right separation at some shifted wavelength, that tells you simultaneously that you're probably seeing sodium and also how much the shift is.

Hydrogen is by far the most abundant element, so I think that's the one that they typically match against first. And it wouldn't be based on just two lines, but a whole spectrum of lines. If you can find the spectra from multiple elements shifted by the same amount, that obviously confirms you've correctly identified the pattern and the amount of shift.
 
For example, the Hydrogen spectrum looks like this:
20130819-123457.jpg

If you see bright lines in your spectrum in this pattern, but shifted to the left or right of the spectrum, you can tell that you are seeing Hydrogen lines Doppler shifted.
( As a side note: Since the surface of a star is made up of particles which are traveling at random directions with respect to you and at some average speed depending on the surface temp of the star, this produces a smearing out or "broadening" of the spectral lines, since the light from each of these moving particles adds its own component to the overall Doppler shift. The greater the average velocity of these particles, the broader the lines. Since this average velocity depends on star temp, the width of the lines can give us a way of measuring the star's temperature.)
 

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Janus said:
Since this average velocity depends on star temp, the width of the lines can give us a way of measuring the star's temperature.)
Just looking at the overall spectrum is much easier.
The rotation of the star also contributes to the width of the lines, it can be used to estimate the rotation axis of stars.