Table II

Twenty-five most highly downregulated microsomal proteins between low (PC3M) and high (PC3M-LN4) metastatic prostate cancer cells, as determined by SILAC

Protein nameGenBank acc. no.aSILAC ratiob
Predicted osteoblast protein76617140.35 (1)
Adenylyl cyclase-associated protein54535950.34 ± 0.06 (6)
Chain A, crystal structure of human phosphoglucose isomerase144886800.34 ± 0.04 (5)
Heat shock 27 kDa protein 145045170.33 ± 0.06 (3)
Acidic (leucine-rich) nuclear phosphoprotein 32 family, member A54538800.30 ± 0.05 (3)
DEAD-box protein 3 (helicase-like protein 2) (HLP2) (DEAD-box, X isoform)30236280.29 (1)
Membrane component, chromosome 11, surface marker 1201274880.29 (1)
Template activating factor-I, splice form α21362580.29 ± 0.03 (4)
Ubiquitin (high molecular mass conjugates)1366700.29 (1)
α-Actinin 1 (α-actinin cytoskeletal isoform)1129590.25 ± 0.05 (12)
Annexin III48266430.25 ± 0.05 (4)
Protein kinase, cAMP-dependent, catalytic, α45060550.24 (1)
Oxidized protein hydrolase71446480.23 (1)
BRCA2 and CDKN1A-interacting protein isoform BCCIPα77065810.22 ± 0.04 (3)
Transglutaminase 247592280.22 (1)
Protein kinase, cAMP-dependent, regulatory, type I, α45060630.21 ± 0.05 (3)
Nucleobindin 1200702280.18 (1)
Nonhistone chromosomal protein HMG-14788130.17 ± 0.09 (8)
Synaptojanin 2A253610670.15 (1)
Aldehyde dehydrogenase 1A345020410.14 ± 0.04 (7)
Chain A, crystal structure of the human co-chaperone P2392570730.14 ± 0.09 (2)
Similar to 60S ribosomal protein L14205551640.13 (1)
Lipocalin 1 precursor45049630.11 ± 0.01 (2)
Aminopeptidase N (AA 1 - 967)286780.06 ± 0.01 (2)
Eukaryotic translation initiation factor 2B, subunit 2 β, 39 kDa76570580.05 (1)
  • a GenBank accession number.

  • b SILAC ratio refers to fold increase in protein expression, as described in “Experimental Procedures,” with number of lysine-containing peptides quantified from each protein shown in parentheses.