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Table 3 Identification and quantification of methanol metabolic enzymes and control proteins in peroxisomal preparations (Pex) and homogenates (Hom) of P. pastoris grown on methanol. MASCOT scores indicate identification of the respective proteins in the samples while peak areas of the identified peptides were used for quantification. To normalize the dataset, average ratios of the summarized peak areas of Aox1 peptides of peroxisomal samples vs homogenates were set to 1, and all ratios were calculated in relation to this. Peroxisomal proteins serve as positive control, while methanol dissimilation, pentose phosphate pathway (PPP), and glycolysis-related enzymes are negative controls localized to the cytosol

From: Systems-level organization of yeast methylotrophic lifestyle

Short name Function/localization Description MASCOT Score Pex1 MASCOT Score Pex2 MASCOT Score Hom1 MASCOT Score Hom2 ratio peak area Pex/Hom
AOX1 Methanol assimilation Alcohol oxidase 1 1542.8 1157.2 1021.4 1061 1.00
DAS1 Methanol assimilation Dihydroxyacetone synthase 1 1918.9 1503 971.2 970.4 14.79
DAS2 Methanol assimilation Dihydroxyacetone synthase 2 1797.9 1473.2 986.3 961.1 7.10
DAK2 Methanol assimilation Dihydroxyacetone kinase 226.9 0 666.2 550.4 0.26
FBA1-2 Methanol assimilation Fructose-bisphosphate aldolase 464.8 185.7 287 291.5 0.96
FBP1 Methanol assimilation Fructose-1,6-bisphosphatase 623.8 419.8 585 576.8 2.42
SHB17 Methanol assimilation Sedoheptulose-1,7-bisphosphatase 357.4 314 191 145.2 3.05
RKI1-2 Methanol assimilation Ribose-5-phosphate ketol-isomerase 217.1 0 0 139.8 2.97
TAL1-2 Methanol assimilation Transaldolase 374.3 279.8 0 0 > > 1
CTA1 Peroxisomal protein Catalase 907.3 434.4 414.3 304.3 1.26
PEX3 Peroxisomal protein Peroxisomal biogenesis factor 119.2 109.9 0 0 > > 1
PEX5 Peroxisomal protein Peroxisomal targeting signal 1 receptor 86.1 62.5 127.8 36.3 1.09
PEX11 Peroxisomal protein Peroxisomal membrane protein 523.4 262.1 221.5 151.8 4.26
PEX14 Peroxisomal protein Peroxisomal membrane protein 145.2 103.7 0 0 > > 1
PMP20 Peroxisomal protein Peroxiredoxin 536 437.3 260.7 274.2 1.49
PMP47 Peroxisomal protein Peroxisomal membrane protein 539.5 345.7 165.9 162.5 8.02
FLD Methanol dissimilation Formaldehyde dehydrogenase 0 0 577.9 424.4 0.00
FGH1 Methanol dissimilation S-formylglutathione hydrolase 0 0 455.4 432.4 0.00
FDH1 Methanol dissimilation Formate dehydrogenase 491.1 303.5 910.5 856.7 0.12
TAL1-1 PPP Transaldolase 220.2 0 376.7 206.5 0.38
TKL1 PPP Transketolase 0 0 85 166 0.00
ZWF1 PPP Glucose-6-phosphate 1-dehydrogenase 0 0 0 46.7 0.00
GND2 PPP 6-phosphogluconate dehydrogenase 247.1 66.6 626.8 522.9 0.26
FBA1-1 Glycolysis Fructose-bisphosphate aldolase 0 0 347.3 379.1 0.00
HXK1 Glycolysis Hexokinase 0 0 100.6 195.6 0.00
TDH3 Glycolysis Glyceraldehyde-3-phosphate dehydrogenase 0 0 629.6 705.5 0.00
PGK1 Glycolysis Phosphoglycerate kinase 0 0 372.1 224.3 0.00
GPM1 Glycolysis Phosphoglycerate mutase 0 0 121.7 108.4 0.00