Actually i am trying to find upregulated proteins using limma package which is very straight forward 

The problem is that I cannot find a logic behind of it. As an example 

This is the data obtained from Mass spectrometery

In R format 

df<- structure(list(X = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 7L
), .Label = c("P1", "P2", "P3", "P4", "P5", "P6", "P8", "Q7"), class = "factor"), 
    Control_1 = c(27.2, 62.2, 4.5, 33.6, 1202.9, 1012.3, 36, 
    4.6), Control_2 = c(34.9, 74.5, 3.3, 58.3, 795.3, 1307.3, 
    46.1, 8.4), Treated_1 = c(1871, 1258.1, 437.6, 2854.6, 922.7, 
    1545.4, 1564.9, 174.3), Treated_2 = c(1710.7, 1485.8, 207.7, 
    2580.8, 1489.1, 2236, 1633.2, 206.1)), .Names = c("X", "Control_1", 
"Control_2", "Treated_1", "Treated_2"), class = "data.frame", row.names = c(NA, 
-8L))

When I do the Limma, with a design like below 

design <- model.matrix(~c(rep(1,2),rep(0,2)))

I get the following 

in R format 

df2<- structure(list(X = structure(c(1L, 2L, 3L, 4L, 5L, 6L, 8L, 7L
), .Label = c("P1", "P2", "P3", "P4", "P5", "P6", "P8", "Q7"), class = "factor"), 
    Fold.Change = c(-1759.8, -1303.6, -318.75, -2671.75, -206.8, 
    -730.9, -1558, -183.7), AveExper = c(910.95, 720.15, 163.275, 
    1381.825, 1102.5, 1525.25, 820.05, 98.35), t = c(-25.59881, 
    -13.353164, -3.238507, -22.70456, -0.6925649, -2.274524, 
    -52.42197, -13.04355), p_value = c(0.000247059, 0.001443824, 
    0.05467982, 0.000342436, 0.5428383, 0.1161553, 3.50056e-05, 
    0.001538154), adj.p_value = c(0.005736091, 0.012069176, 0.1084498, 
    0.005981734, 0.5772197, 0.183387, 0.002334204, 0.01238259
    ), B = c(-4.133516, -4.141755, -4.280436, -4.134362, -4.683112, 
    -4.374939, -4.131131, -4.142291)), .Names = c("X", "Fold.Change", 
"AveExper", "t", "p_value", "adj.p_value", "B"), class = "data.frame", row.names = c(NA, 
-8L))

I know that I should log2 the value at the beginning but it is strange to me that a fold change be minus so it will all be down regulated proteins ? 

Any comment is appreciated 

From the data you show at the top, all proteins are down-regulated because the intensities in your controls are lower than in your treatment, hence negative log2 fold-changes.

If it is the negative values that confuse you, it is because down-regulation (i.e fold-changes between 0 and 1) become negative in log space (-Inf to 0), while up-regulation (i.e. fold-changes between 1 and +Inf) are positive in log space (0 to +Inf).

Hope this helps.