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. Author manuscript; available in PMC: 2010 Jan 14.
Published in final edited form as: Methods. 2006 Oct;40(2):135–142. doi: 10.1016/j.ymeth.2006.05.026

Table 2.

Proteins of lower abundance that have high plus-minus ratios1.

Individual MudPIT Runs3
MudPIT #1 MudPIT #2 MudPIT #3 MudPIT #4 Combined Data5
Protein PS2 plus minus plus minus plus minus plus minus plus minus ratio6
YBR016W N 0 0 5 0 18 0 4 0 4.9 0 24.6
PSR2 N 0 0 8 0 9 0 16 0 4.9 0 24.4
RPS10A/B FP 0 0 9 0 12 0 10 0 4.8 0 24.2
YGL108C FP 2 0 27 0 0 0 0 0 4.4 0 21.9
YPL236C N 3 0 6 0 4 0 4 0 4.4 0 22.0
YBR014C N 3 0 10 0 0 0 5 0 4.1 0 20.4
SEC63 FP 3 0 6 0 0 0 8 0 4.1 0 20.3
SAM3 N 2 0 4 0 3 0 9 0 3.8 0 19.2
ADR1 FP 0 0 20 0 5 0 5 0 3.8 0 19.1
RHO2
N
0
0
5
0
9
0
9
0
3.6 0 18.2
Total Spec Counts4 3148 5897 24132 3836 11645 4240 18803 12945
1

Spectral count data for the ten proteins ranking between 52 and 61 from the 70 top-ranking proteins (see "Selection of Candidate Palmitoyl-Protein").

2

Palmitoylation Status (PS) is indicated: new palmitoyl-proteins (N) and non-palmitoylated false-positive proteins (FP).

3

For each protein, raw spectral counts from the MudPIT runs of the four paired plus- and minus-hydroxylamine samples are shown.

4

Total spectral counts from each MudPIT run.

5

Raw spectral counts from each MudPIT were normalized (individual spectral count values were divided by the total spectral count number from that run and then multiplied by 10,000). Then, the four normalized values were averaged. To avoid division by zero, a value of 0.2 was substituted for those proteins having an averaged, normalized minus-hydroxylamine sample spectral count value of zero.

6

The ratio of averaged, normalized plus-hydroxylamine sample spectral counts to averaged, normalized minus-hydroxylamine sample spectral counts.