Skip to main content

Table 3 Vesicular trafficking-related proteins identified by dMS and SC.

From: A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development

     Stage II (55 mm) vs. early stage II (35 mm) Stage III (80 mm) vs. Stage II (55 mm)
     dMS SC dMS SC
Gene Family Annotation iCitrus ID Blast Hit TAIR ID Peptides Ratio Bayes
Factor
Fold Change Direction* Peptides Ratio Bayes
Factor
Fold Change Direction*
Rab RABA1a/ARA2 5282 AT1G06400 3 0.03 -- -- -- 2 2.85 -- -- --
  RABA1d/Rab11B 50939 AT4G18800 7 0.025 1.34 1.52 0 -- -- 0.95 1.53 0
  RABA1f 23943 AT5G60860 5 0.11 465 31.9 -1 -- -- 0.8 1.2 0
  RABA2a/Rab11C 33548 AT1G09630 6 0.72 63362 23 -1 2 7.43 31.8 4.5 1
  RABA2b 27900 AT1G07410 3 0.026 3302 28 -1 -- -- -- -- --
  RABB1b/Rab2C 28361 AT4G35860 -- -- -- -- -- 3 33.41 -- -- --
  RABB1c 57271 AT4G17170 5 0.11 72 3.2 -1 4 28.6 1555 5.02 1
  RABD1/FP8 44137 AT3G11730 3 0.33 395 17.8 -1 --   0.9 1.45 0
  RABD2a/Rab1b 22194 AT1G02130 3 0.07 1472 24 -1 2 31.24 62.5 5.00 1
  RABD2b/Rab1A 21238 AT5G47200 2 0.04 -- -- -- -- -- -- -- --
  RABE1a/Rab8 55887 AT3G53610 3 0.03 54.9 3.6 -1 -- -- 1.04 1.5 0
  RABE1e/Rab8E 58806 AT3G09900 2 0.04 -- -- -- -- -- -- -- --
  RABE1c/Rab8/ARA-3 21701 AT3G46060 4 1.06 8.8 1.8 0 2 3.48 0.82 1.2 0
  RABG3d 44916 AT1G52280 2 0.01 -- -- -- -- -- -- -- --
  RABG3f/Rab7B 30351 AT3G18820 3 0.006 0.8 1.3 0 2 6.94 2.16 1.79 0
  RABH1b/Rab6A 53105 AT2G44610 5 0.07 478 18.3 -1 -- -- 0.75 1.2 0
  RABH1e 30604 AT5G10260 2 0.05 -- -- -- -- -- -- -- --
Arf ARLA1c 26509 AT3G49870 3 0.79 0.58 1.13 0 2 4.49 1.07 1.67 0
  ARFA1e 422 AT3G62290 3 0.13 -- -- -- 3 26.62 -- -- --
  ARFA1f 22081 AT1G10630 5 0.15 -- -- -- 6 19.71 -- -- --
  SAR1c 34375 AT4G02080 -- -- -- -- -- 3 4.91 -- -- --
Ran STL2P/SEC12P-Like 54385 AT2G01470 -- -- 2319 5.37 1 -- -- 0.67 1.04 0
  RANBP1 42600 AT5G58590 5 0.5 3.4 2.8 0 7 129.80 0.6 1.98 0
  RANBP1b 2905 AT2G30060 -- -- 1.3 4.2 0 5 130.08 280 22.3 1
  RAN3 57970 AT5G55190 2 0.87 0.64 1.82 0 7 20.25 3.7 1.67 0
Rho GP3/ROP4 29311 AT1G75840 2 0.28 -- -- 0 -- -- -- -- --
GDI GDI1 34016 AT2G44100 -- -- 1.58 2.18 0 3 5.00 0.73 1.13 0
  GDI2-like 876 AT5G09550 -- -- -- -- -- 2 3.11 -- -- --
VAMP/R-SNAREs SEC22 58654 AT1G11890 2 0.20 26.9 13.6 -1 -- -- 1.06 1.46 0
  VAP27-1 54676 AT3G60600 2 0.77 -- -- -- -- -- -- -- --
  VAMP713 23669 AT5G11150 2 1.41 -- -- -- -- -- -- -- --
Qa-SNAREs SYP132 (syntaxin 132) 12539 AT5G08080 -- -- 3 6.2 0 2 3.21 1.25 1.65 0
  VAM3 (syntaxin 22) 37248 AT5G46860 -- -- 1.35 1.86 0 -- -- 4.5 2.3 0
Qb-SNAREs VTI11 24253 AT5G39510 2 0.05 0.65 1.37 0 -- -- 0.5 1.2 0
Qc-SNAREs SYP71 (SYNTAXIN) 27696 AT3G09740 -- -- 2.17 4.34 0 -- -- -- -- --
  ALPHA-SNAP2 2375 AT3G56190 -- -- 1.00 1.00 0 -- -- 6.41 7.6 0
ESCRT III SNF7.1 35782 AT4G29160 4 1.31 4.88 2.99 0 7 597.36 106 5.5 1
Dynamin ADL6 (dynamin-like protein 6) 36589 AT1G10290 -- -- -- -- -- 2 6.63 -- -- --
others SEC61 35474 AT1G29310 3 0.10 171.70 17.65 -1 -- -- 1.00 1.4 0
  SEC14 30056 AT1G72160 5 3.42 37.17 13.65 1 16 12.92 4.8 1.5 0
  PATL2 35474 AT1G22530 3 0.104 170.5 17.65 -1 3 6.83 1.04 1.43 0
  SCAMP 34675 AT1G32050 3 1.70 1.50 1.55 0 2 4.11 0.74 1.18 0
  SC3 (secretory carrier 3) 30772 AT1G61250 2 0.98 2.9 6.12 0 -- -- 1.00 1.02 0
  SYT1 45523 AT2G20990 4 8.7 0.3 1.5 0 4 2.64 1.2 1.6 0
  COP-I coatomer, B-COPα 29871 AT2G21390 2 0.4 0.6 1.22 0 3 11.47 1.31 1.73 0
  RTNLB3 reticulon 42672 AT1G64090 2 0.53 2.1 3.7 0 2 2.31 0.72 1.48 0
  RTNLB5 reticulon 13580 AT2G46170 -- -- 0.97 1.02 0 -- -- 4.35 2.97 0
  RTNLB6 reticulon 22293 AT3G10260 -- -- 1.24 1.4 0 2 36.56 187.81 5.76 1
  clathrin heavy chain 57153 AT3G08530 -- -- 83.92 13.36 -1 -- -- 0.76 1.17 0
  clathrin heavy chain 60690 AT3G08530 2 0.05 63.7 13.65 -1 -- -- 46.45 10.98 -1
  Clathrin light chain 51128 AT2G20760 2 119 2300591 11.55 1 2 1.8 0.8 1.2 0
  Clathrin light chain 21278 AT3G51890 2 118 1511 6.2 1 -- -- 1.63 1.57 0
  myosin heavy chain 38388 AT4G31340 -- -- 0.6 1.00 0 -- -- 0.75 1.3 0
  myosin heavy chain 37311 AT1G06530 3 0.02 156 16 -1 -- -- 1.1 1.4 0
  1. * The column "direction" under spectral counting measurement represent expression direction, 1 = up-regulated, 0 = no change, -1 = down-regulated.
  2. Proteins identified by dMS were considered to be upregulated when expression fold > 2, not changed when 0.5 < fold < 2 and down-regulated when fold change was < 2. For SC Bayes factor of > 10 was used for significance difference.