Good questions and worth explaining for those new to the field.
X!Tandem is a program which to assign peptide sequences ("ID"s) to ms/ms
spectra. We call this type of program a "search engine" (for "peptide
ID search engine" or similar). Other programs in this class are OMSSA,
Sequest, Mascot, and others. Each of these programs can be run on its
own, and outputs a score for each "assigned" peptide. This score
reflects the search engine's estimation of how likely or confident that
assignment is (I use those terms not necessarily as true stats meanings
here.)
So now you have input of peptide IDs and "scores". The TPP tools (Pep
and Prot Prophet) do two major things of interest. One, they take the
variously-derrived scores, compute additional information not
necessarily accounted by the search engine (asking such questions as
"how reasonable is this sequence, given its terminii, length,
hydrophobicity, and so on), and combine these numbers to arrive at a
statistically valid p value. Two, the TPP tools do this for many
supported search engines, which allows the possibility of comparing the
peptide assignments to other results, i.e. in a publication context.
(For a more complex approach to the last point, look at the TPP's
InterProphet tool.)
Regarding FDR, I will leave that to someone else to answer in detail.
Hope this helps,
Natalie
On 3/10/10 8:46 PM, Amit Kumar Yadav wrote:
Dear All,
I was just browsing the gpm site and reading about tandem. It says
that peptideprophet and proteinprophet need not be used with X!Tandem.
Can someone explain (in simple terms please) how TPP uses tandem
result data to assign probabilities?
Another naive question is about calculation of FDR from X!Tandem
results? How should it be done?
For reference-
Quoting from http://www.thegpm.org/TANDEM/index.html "Unlike
some... ... Therefore, separate assembly and statistical analysis
software, e.g. PeptideProphet and ProteinProphet, do not need to be
used."
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