I got 5000+ identified proteins from MaxQuant and computed 180+ differential proteins. Then I annotated all identified proteins using EggNog-emapper and constructed a TERM2GENE object: Below shows the first ten lines. This object contains 5387 unique proteins and 810320 GO terms.

goid protein
1   GO:0000166  O94851
2   GO:0001947  O94851
3   GO:0002009  O94851
4   GO:0003007  O94851
5   GO:0003143  O94851
6   GO:0003674  O94851
7   GO:0003779  O94851
8   GO:0003824  O94851
9   GO:0004497  O94851
10  GO:0005488  O94851

And I have a vector of differential proteins, named "diffpros":

[1] "Q92841" "Q9BTV4" "P37198" "Q9P2N5" "Q9BXW7" "Q53H12" "Q96G74" "Q8IYB3" "Q8NCN5"
 [10] "P53367" "P19838" "Q00169" "Q9HBM1" "Q9Y676" "Q02750" "Q14318" "O95994" "Q9NVZ3"
 [19] "Q6WCQ1" "Q96GD4" "Q96S52" "O00764" "Q53GS7" "Q4G0J3" "Q15121" "Q9UJ68" "P82932"
 [28] "P58107" "Q8IZT6" "P04040" "O15270" "Q16540" "O14949" "Q9NWT6" "P13473" "Q96RS0"
 [37] "Q9UHA3" "P62380" "Q99569" "Q8TD30" "Q9UL18" "Q9P0U4" "Q5VZM2" "Q9H9Y2" "P11274"
 [46] "Q96AQ8" "Q8TDB6" "Q9BR61" "O76054" "Q8N9N8" "Q9UNN8" "Q9NXC5" "P48382" "P42858"
 [55] "Q86Y79" "Q96CB8" "Q8WUW1" "P48509" "Q9NVS2" "O15120" "Q9UBP0" "P35611" "Q9P2E3"
 [64] "P49757" "Q93096" "O00308" "P34810" "A0JLT2" "Q9UIL1" "Q8IVL6" "Q6P2I3" "Q8WXA3"
 [73] "Q9UJX6" "Q9Y3C0" "Q7Z7E8" "Q9H1A3" "P82094" "Q5MNZ6" "P31327" "Q8TB22" "Q96AA3"
 [82] "O00213" "Q9NPL8" "Q15629" "Q9BVC4" "Q7Z4F1" "Q6ZRS2" "Q16656" "P33527" "P08582"
 [91] "P48200" "O95249" "Q9NUL7" "Q96F44" "O60921" "Q96CW5" "Q6PGN9" "P19256" "Q9UP95"
[100] "Q8N2G8" "Q9BVK8" "Q5ST30" "Q9UHN6" "Q9UGN5" "O43299" "Q9NR77" "O00418" "P15529"
[109] "P54803" "Q9NRL2" "P35908" "O00566" "Q9UI12" "Q9NP77" "Q53GS9" "Q96N67" "Q14651"
[118] "Q96EV2" "Q9H330" "P09601" "Q15349" "Q86XI2" "P05412" "Q9UL25" "Q9NTX5" "Q9H0W8"
[127] "P26572" "O75940" "Q13443" "Q6NSJ5" "O00255" "Q5VV42" "O76071" "Q8N4C8" "P49662"
[136] "O75157" "P49841" "Q92804" "P24386" "Q9BT73" "Q96P47" "Q14691" "Q96RU2" "Q9BRT9"
[145] "Q9Y6K9" "Q9HB07" "Q9BWH2" "P06454" "Q9HCN8" "Q9UHR4" "O95628" "O60294" "Q8N1G0"
[154] "P51580" "Q9UL03" "Q587I9" "P62072" "Q6EEV4" "Q96BW5" "Q8WUA4" "Q99996" "Q9H7C9"
[163] "Q709C8" "Q9BRT2" "Q9H6H4" "Q92845" "O75037" "Q8NBN7" "Q9NXV2" "Q9UEG4" "Q12962"
[172] "O14772" "Q5EBL4" "P17813" "P56937" "Q9NWX6" "Q8N5I9" "Q6ZWJ1" "Q5HYA8" "Q14938"
[181] "Q5JPI9"

This is my code running enricher():

ego <- enricher(
  diffpros,
  TERM2GENE = term2pro
)

I do not add "universe" here because I found it would automatically take all proteins in TERM2GENE as the universe. No enriched terms were produced.

ID Description GeneRatio  BgRatio      pvalue  p.adjust    qvalue
GO:0034452 GO:0034452  GO:0034452     3/180  10/5387 0.003701603 0.9128235 0.9128235
GO:0045724 GO:0045724  GO:0045724     3/180  10/5387 0.003701603 0.9128235 0.9128235
GO:0016021 GO:0016021  GO:0016021    27/180 476/5387 0.004084516 0.9128235 0.9128235
GO:0001833 GO:0001833  GO:0001833     3/180  11/5387 0.004965590 0.9128235 0.9128235
GO:1902855 GO:1902855  GO:1902855     3/180  11/5387 0.004965590 0.9128235 0.9128235
GO:0007568 GO:0007568  GO:0007568    19/180 307/5387 0.006447999 0.9128235 0.9128235
                                                                                                                                                                                                 geneID
GO:0034452                                                                                                                                                                         P53367/P42858/P49841
GO:0045724                                                                                                                                                                         P42858/Q92845/Q5HYA8
GO:0016021 Q9BTV4/Q53H12/Q00169/Q14318/Q96S52/P13473/Q96AQ8/Q9UNN8/P48509/P49757/P34810/Q15629/Q7Z4F1/P33527/O95249/P19256/Q9UP95/Q9UHN6/Q9NR77/P15529/Q9H330/P26572/Q13443/Q6NSJ5/Q9BWH2/Q99996/P17813
GO:0001833                                                                                                                                                                         Q86XI2/Q14691/Q9BRT9
GO:1902855                                                                                                                                                                         P42858/Q92845/Q5HYA8
GO:0007568                                                         P37198/Q02750/Q96GD4/Q9UJ68/P04040/Q5VZM2/P42858/Q9Y3C0/P48200/O60921/P35908/Q9UI12/Q15349/P05412/P26572/O00255/P49841/P17813/Q14938
           Count
GO:0034452     3
GO:0045724     3
GO:0016021    27
GO:0001833     3
GO:1902855     3
GO:0007568    19

I gave it some other tries. For example, I kept only the GO terms with "BP" ontology in my TERM2GENE object and tried to enrich BP GO terms. No terms enriched.

Are there really no enriched terms?? Or is it because the number of identified proteins is too small? There are some p-values smaller than 0.05 but padj are really large.

I want some enriched results...