P28834Idh1 (isocitrate dehydrogenase 1 alpha-4-beta-4 subunit)8.997.8039.340402822

P14843Aro3 (DAHP synthase)7.047.1041.540312921

P25294Sis1 (HSP40 family chaperone)9.898.6019.132473820

P17505Mdh1 (mitochondrial malate dehydrogenase)8.507.1035.735243319

P06168Ilv5 (acetohydroxyacid reductoisomerase)9.106.9544.445232118

P50095Imd3 (IMP dehydrogenase homolog)7.047.3056.955263317

P07251Atp1 (mitochondrial FiF0-ATPase alpha subunit)9.107.2058.660173316

P15992Hsp26 (heat shock protein 26)5.315.2023.930484115

P40150Ssb2 (heat shock protein 70 isoforms)5.405.3066.649 (frg)92114

P00925Eno2 (enolase 2)5.705.7046.921 (frg)141813

P00817Ipp1 (inorganic pyrophosphatase)5.365.2031.834333312

P41277Gpp1 (DL–glycerol-3-phosphatase)6.106.0030.432342311

P32905Rps0a (40S ribosomal protein S0-A)4.704.9027.938192110

P22203Vma4 (Vacuolar ATPase Vi domain subunit E)5.305.1026.52820149

P10591Ssa1 (heat shock protein 70 isoforms)5.005.007027 (frg)19238

P06169Pdc1p (Pyruvate decarboxylase isozyme1)5.805.2061.631 (frg)19227

P07259Ura2p (Carbamyl phosphate synthase)5.605.3056.15214216

P15705Sti1p (stress induced protein)5.405.3066.3607235

P06633His7p (Imidazole glycerol phosphate synthase)5.305.3061678234

Q05905YLR301w (Hypothetical ORF)5.105.1027.52926303

P40106Gpp2 (DL-glycerol-3-phosphatase)5.305.3027.93428302

P47143Ado1p (Putative adensoine kinase)5.005.0036.44016191

SwissProt Accession No

Top ranking protein

in MS-Fit searchdPredExpPredExp

Matched peptide coverage (%)b

No. of matching peptides (%)a

Spot. No.

Molecular mass (kDa)c pIc

TABLE S1. Proteins induced by 300mM citric acid, pH 3.5, were identified by peptide mass fingerprinting

41

Table S1. (cont…)

aThe number of tryptic peptides assigned to the protein divided by the total number of tryptic pepides predicted for the protein expressed as a percentagebThe number of amino acids in the matched peptides divided by the total number of amino acids in the predicted protein sequence expressed as a percentagecTheoretical PI and molecular weights were obtained from the protein entry in the MIPS database (http://mips.gsf.de/cgi-bin/proj/yeast)dThe programme MS-Fit (URL: http://prospector.uscf.edu/ucsfhtml3.2/msfit.htm) was used to search the SwissProt database for proteins with calculated tryptic peptide masses that matched the measured experimentally-derived masses eThe term ‘frg’ in brackets indictaes that the protein detected was a proteolytic cleavage fragment

42

P38720Gnd1p (6-phosphogluconate dehydrogenase)6.194.853.925 (frg)c273328

P38879Egd2 (GAL4 DNA-binding enhancer protein 2)4.804.8018.7292712B

P14540Fba1 (aldolase)5.516.0039.629 (frg)e142126

Q04322Ydr533cp (hypothetical protein)5.266.0025.726562427

P28272Ura1 (dihydroorotate dehydrogenase)5.805.9034.835261725

Q46654Rps0b (40S ribosomal protein S0-B)4.694.9028323142A

P32473Pdb1 (beta subunit of pyruvate dehydrogenase)5.235.0040.335342224

P29311Bmh1(Brain modulosignalin homolog)4.804.9030.131191623

SwissProt Accession No

Top ranking protein

in MS-Fit searchdPredExpPredExp

Matched peptide coverage (%)b

No. of matching peptides (%)a

Spot. No.

Molecular mass (kDa)c PIc

P00812Car1 (arginase)5.385.503641272629

TABLE S4. Proteins whose expression is affected by HOG1 identified by peptide mass fingerprinting

48

aThe number of tryptic peptides assigned to the protein divided by the total number of tryptic pepides predicted for the protein expressed as a percentage

bThe number of amino acids in the matched peptides divided by the total number of amino acids in the predicted protein sequence expressed as a percentage

cTheoretical PI and molecular weights were obtained from the protein entry in the MIPS database (http://mips.gsf.de/cgi-bin/proj/yeast)

dThe programme MS-Fit (URL: http://prospector.uscf.edu/ucsfhtml3.2/msfit.htm) was used to search the SwissProt database for proteins with calculated tryptic peptide masses

that matched the measured experimentally-derived masses

eThe term ‘frg’ in brackets indictaes that the protein detected was a proteolytic cleavage fragment