TOTNSAF, UNIQNSAF, ADJNSAF

[Jimmy]

Damian,

Can you explain what these three columns are:  TOTNSAF, UNIQNSAF, ADJNSAF

I see values 22.27, 38.19, and 32.15 for TOTNSAF, UNIQNSAF, and ADJNSAF, respectively.  It's a little odd seeing the TOT (total?) number less than the UNIQ (unique?) value so my intuitive interpretation of these column headers must be wrong.  Thanks.

[Damian]

Hi,

TOTNSAF stand for NSAF computed using all of the spectral counts (the total) for a given protein.

UNIQNSAF provides the NSAF for a protein using only spectra associated with peptides that are unique to that protein. So in TPP terms, if the peptide's weight (wt) is below 0.9 it is not considered to be unique to the protein.

ADJNSAF gives you the NSAF for a protein using the adjusted spectral count for that protein. The original paper describes out adjusted spectral counts are computed and a figure with a simple example is available here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113614/figure/F2/

Intuitively you are correct. It does sound strange to see TOT lower than UNIQ. This occurs because the final step for computing NSAF is to divide the length-adjusted spectral counts by the sum of the column (TOT, UNIQ, ADJ).

The column sum for TOT would be larger since all spectral evidence is being used here. The column sum for UNIQ will be a smaller value because fewer spectra are being counted. After the division is performed UNIQNSAF can be larger than TOTNSAF.

Let me know if this helps,
Damian

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