Table 1.
Assessment of published endoplasmic reticulum proteomics datasets
| Organelle | Tissue/cells | Species | ER purification | Mass spectrometry | Proteins detected | Reference |
|---|---|---|---|---|---|---|
| NE | Neuroblastoma N2a cells | Mouse | NE preparation (Triton-X-100 treatment) | 2D-BAC gels, MALDI MS | 148 | Dreger et al. (2001) |
| NE | Liver | Mouse | Substractive proteomics (NE fraction-MM fraction) | MudPIT, LCQ-Deca ion-trap MS, Tandem MS | 566 | Schirmer et al. (2003) |
| NE | Liver | Rat | Nuclear pore complex fraction (enriched in nucleoporins) | 1D gels, MALDI-QqTOF MS, Tandem MS | 94 | Cronshaw et al. (2002) |
| NE | Saccharomyces cerevisiae | Yeast | Purified nuclear pore complex | HPLC, 1D gels, MALDI-TOF MS, Tandem MS | 174 | Rout et al. (2000) |
| ERa | Liver | Ratb | Membrane proteins | 1D and 2D gels, MALDI-TOF MS | 68 (1D) 39 (2D) |
Galeva and Altermann (2002) |
| ERa | Liver | Hamsterc | Tenfold enrichmentj (calnexin marker, IB) | 2D gels, MALDI-Q-TOF MS | 39 | Morand et al. (2005) |
| ERd | Liver | Mouse | PCP-fraction co-sedimenting with calnexin | LC, linear ion-trap Fourier transform MS, Tandem MS | 229 | Foster et al. (2006) |
| RER | Saccharomyces cerevisiae | Yeast | Purified ribosomes | Multidimensional LC, LCQ ion-trap MS, Tandem MS | 95 | Link et al. (1999) |
| RER | Liver | Mouse | 75% RMe, luminal proteins | 2D gels, MALDI-TOF MS, Tandem MS | 141 | Knoblach et al. (2003) |
| RER | Pancreas | Dog | Ribosome-associated membrane protein | Blue Native gels, LCQ ion- trap MS, Tandem MS | 30 | Shibatani et al. (2005) |
| RER | Liver | Rat | 4.0-fold enrichment j (G6Pase enzyme assay) 77% RMe, f | 1D gels, LC, QTOF-2 MS, Tandem MS | 787 | Gilchrist et al. (2006) |
| SER | Liver | Rat | 4.5-fold enrichment j (G6Pase enzyme assay) 58% SMe, 39% RMe, g | 1D gels, LC, QTOF-2 MS, Tandem MS | 998 | Gilchrist et al. (2006) |
| ERGICh | HepG2 cellsi | Human | 110-fold enrichmentj (ERGIC-53 marker, IB) | 1D gels, LC, Tandem MS | 24 | Breuza et al. (2004) |
| ER-Golgi derived vesiclesd | Liver | Mouse | PCP-fraction co-sedimenting with p115 | LC, linear ion-trap Fourier transform MS, Tandem MS | 220 | Foster et al. (2006) |
BAC 16-benzyldimethyl-n-hexadecyl ammonium chloride, ERGIC ER-golgi intermediate compartment, G6Pase glucose-6-phosphatase, HPLC high pressure liquid chromatography, IB immuno-blot, LC liquid chromatography, MALDI matrix-assisted laser desorbtion ionization, MM microsomal membrane, MS mass spectrometry, MudPIT Multidimensional protein identification technology, PCP protein correlation profiling, RM rough microsomes, SM smooth microsomes, TOF time of flight
aTotal microsomes (containing both rough and smooth ER membrane derivatives)
bUntreated and phenobarbital treated rats
cModel of insulin resistance and metabolic dislipidemia fructose-fed animal
dFractions obtained by rate-zonal centrifugation of the postnuclear supernatant
eMorphometric characterization by electron microscopy
fPresence of ≥11 ribosomal particles/vesicle
gPresence of 1–4 ribosomal particles/vesicle
hImmuno-affinity purified ERGIC membranes
iCells were treated with brefeldinA to accumulate cycling proteins in the ERGIC
jEnrichment over homogenate