Question #1:
gi|16128924|
gi|90111643|
gi|16128170|
gi|16131219|
gi|145698290|
gi|16128008|
gi|16128109|
gi|16128396|
gi|16131300|
gi|16131385|

Question #2:
gi|16128924|
gi|16131300|
gi|90111528|
gi|16129452|
gi|90111643|
gi|16131218|
gi|16131600|
gi|16128699|
gi|16128703|
gi|16131476|
NOTE: Use accession numbers when identifying proteins, there are many copies of "predicted protein", but only one of "gi|16129875|"

Question #3: Three: (gi|16128924|, gi|90111643|, gi|16131300|)
Question #4: No. The total number of unique proteins is 17, not 20, so we are not doubling our identifications out of the top 10 proteins in each fraction. Conceptually, this is because that although we are adding an additional dimension to our analysis with SCX, there is still insufficient peak capacity to isolate every peptide in the sample. Furthermore, identifying new peptides does not mean new proteins are identified. For example, doubling our peptide identifications does not double our protein identifications if the new peptides match to proteins already identified by the previous peptides.
Question #5: 16%
Question #6: 15%
Question #7: One (LVLEVQQQLGGGIVR)
Question #8: The additional dimension increased our peak capacity, enabling us to identify more unique peptides. This gives greater protein sequence coverage, increasing our confidence in protein identification.