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. Author manuscript; available in PMC: 2015 Jun 9.
Published in final edited form as: J Am Soc Mass Spectrom. 2012 Aug 16;23(10):1707–1715. doi: 10.1007/s13361-012-0424-9

Table 2.

MassMatrix comparison of negative mode NETD and UVPD and positive mode CID LC-MS/MS experiments.

Protein % Sequence Unique Peptides
NETD UVPD CID NETD UVPD CID
BSA 51 58 70 26 33 51
αS1-casein 35 43 32 9 (4/1)* 12 (4/1)* 9 (2/1)*
αS2-casein 38 32 31 6 (4/4)* 9 (4/4)* 12 (3/2)*
β-lactoglobulin A 64 56 48 7 8 11
β-casein 15 24 25 2 (1/1)* 6 (1/1)* 6 (2/1)*
Lysozyme C 24 43 81 2 4 10
Ribonuclease A 13 42 52 1 3 5
*

unique peptides (phosphopeptides/phosphorylation sites)