Table I

Selection of proteins found to be unique in ESCs or enriched in ESCs compared with differentiated ESCs according to the peptide ratios determined by FT-ICR-MS/MS

Dilution ratios used for Western blotting and immunofluorescent labeling with antibodies recognizing these selected proteins are indicated. Ab, antibody.

Gene symbolPeptide ratioa [ESC peptidesb]Antibody (source/Ref.)HostAntibody dilution
HumanMouseWestern blotImmunofluorescence
ACTB1.30 [65]1.09 [72]Anti-actin, pan Ab-5 (Labvision catalog no. MS-1295-P1ABX)Mouse1:2,000N.A.c
CACYBP1.29 [9]4.50 [18]Anti-CACYBP/SIP (28)Rabbit1:1,0001:300
CCT81.53 [23]2.43 [34]THC-2 (29)Rabbit1:1,0001:200
CSTF2TUnique [4]Unique [4]Anti-CstF-64, 3A7 (30)Mouse1:501:50
DDX52.38 [19]2.38 [32]Anti-p68 (31)Rabbit1:5001:300
HSPD11.65 [51]2.55 [56]Anti-Hsp60 (32)Mouse1:1,0001:300
KIAA0368 (ECM29)Unique [10]N.I.dAnti-ECM29-1 (33)RabbitN.A.1:50
KIAA0368 (ECM29)Unique [10]N.I.Anti-ECM29-3 (33)Rabbit1:1,000N.A.
KPNA23.00 [9]9.00 [18]Anti-importin, karyopherin-α/Rch-1 (34)Mouse1:1,0001:200
MCM4Unique [18]Unique [10]Anti-MCM4, C-terminal region (35)Rabbit1:1,0001:200
MSH6Unique [15]12.50 [25]Anti-MSH6, G70220-150 (36)Mouse1:5001:200
MTHFD12.55 [28]3.86 [27]Anti-DCS, trifunctional (37)Rabbit1:1,0001:200
NLN4.00 [4]N.I.Anti-EP24.16, neurolysin; gift from A. S. Heimann, Proteimax (38)Rabbit1:1,0001:200
POU5F1N.I.Unique [2]Anti-Oct3/4, C-10 (Santa Cruz Biotechnology catalog no. sc-5279)Mouse1:2001:200
POU5F1N.I.Unique [2]Anti-POU5F1, Oct4 (Sigma catalog no. P0873)Rabbit1:2001:200
PPM1GUnique [5]8.00 [8]Anti-FIN13, Ab no. 630 (39)Rabbit1:501:200
RANBP2Unique [12]Unique [7]Anti-RANBP2 (40)Goat1:1,0001:300
RPS4X1.70 [34]19.50 [39]Anti-S4X (41)Rabbit1:501:50
TOP2AUnique [20]10.00 [30]Anti-topoisomerase IIα, 3F6 (42)Mouse1:2501:30
USP9XUnique [9]Unique [7]Anti-FAM (43)Rabbit1:8001:100
UTF1N.I.Unique [3]Anti-UTF1 (44)RabbitN.A.1:20
  • a Number of unique peptides identified in ESCs divided by the number of unique peptides identified in Dif-ESCs.

  • b Number of unique peptides identified in ESCs.

  • c N.A., not applicable.

  • d N.I., not identified.