Nyquist Maximum data rate formula for PCM
The first document (from mason.gmu.edu) gives a confusing explanation of the formulas. The second document is what's the standard way of referring to the channel capacity

Now the two formulas are:


$C = 2B ~\log_2(M) ~~~~~~~~~~~~,~~~\text{Nyquist}$
$C = B ~\log_2(1 + \text{SNR}) ~~~,~~~\text{Shannon-Hartley}$


Eventhough the first formula, (referred to as Nyquist in the first document), is assumed to yield channel capacity (of a noiseless! channel which is infinite) it's actually giving the necessary minimum data bit-rate to represent an analog message signal of bandwidth $B$ Hz, and quantized to $M$ levels ($\log_2(M)$ bits) using a PCM representation. According to the Nyquist sampling theorem, the minimum allowed sampling rate would be $2B$ Hz, hence there will be $2B$ samples per second each quantized to $M$ levels, yielding a total of $ D = 2B ~ \log_2(M)$ bits per second data rate to represent the analog message signal. Hence it's not channel capacity, it's the minimum necessary bitrate to represent an anlog signal using $M$-bit PCM technique. 

The second formula is what we call: maximum channel (reliable) transmission capacity in bits per second rates, or Channel-Capacity in short, over a more realistic noisy channel (such as telephone wires, all sorts of RF channels, and also the fiber optic or satellite links by modeling them with the inherent noise floors). It gives you the maximum achievable rate of information (or data) transmission through a channel of bandwith $B$ Hertz, by using a modulation scheme with the given SNR (ratio of transmitted signal power to the channel noise power). 

Note that despite being treated in communications sections, PCM is not a data transmission format but a data representation format. Analog data is converted to digital by samlping and quantizaiton through an ADC of $N$-bit quantization at a sampling rate of $F_s$ samples per second. The resulting sampled-quantized data is practically represented in binary digital system for processing and transmission. In such a case every $N$-bit quantized sample of the message signal is laid out as $N$ consecutive binary digits (bits) to represent a single PCM sample of message data. When it comes to transmission, those bits can be transmitted one by one as is done by using BPSK or in groups of M-bits as is done by 8-QAM (where 8 PCM bits are transmitted at once by a single 8-QAM transmission symbol).