Open Mass Spec Database
The Human metabolome database (HMDB) contains many MS/MS and NMR spectra for human metabolites. You can acquire the spectra from the downloads section. The HMDB includes external identifiers for each compound. This includes the PubChem Compound IDs that are given on the NCBI database. There are 2 265 compounds with LC-MS/MS spectra in the HMDB.

The excellent MS-DIAL software package also comes with extensive positive and negative ion mode LC-MS/MS and GC-MS/MS spectral libraries in flat text format; that's also worth a look.  

A lot of the raw spectral data is restricted due to multi party agreements (NIST, chemspider).