Table S1. Sample Details for Each Proteomic Experiment

Sample

Media

Yeast Strain

Purification

YDPM File Nameb

A

YP-Lactate

W303

DG

yplDG1_matY

B

YP-Lactate

W303

DG

yplDG1_memY

C

YP-Lactate

W303

DG

yplDG2_memY

D

YP-Lactate

W303

DG

yplDG3_memY

1

YP-Lactate

W303

FFE

ypl01_memY

ypl01_memY_FT

ypl01_matY

ypl01_matY_FT

2

YP-Lactate

W303

FFE

ypl02_memY

ypl02_memY_FT

ypl02_matY

ypl02_matY_FT

4

YP-Dextrose

W303

FFE

ypd04_memY

ypd04_matY

5, 10, 11a

SC-Lactate

S1001

FFE

scl01_memY

scl01_memY_FT

scl01_matY

scl01_matY_FT

7, 12a

SC-Dextrose

S1001

FFE

scd01_memY

scd01_memY_FT

scd01_matY

scd01_matY_FT

13

YP-Dextrose

W303

FFE

ypd13_memY

ypd13_matY

14

YP-Lactate

W303

FFE

ypl14_memY

ypl14_matY

15

YP-Lactate

W303

FFE

ypl15_memY

ypl15_matY

 

aIn rows with multiple samples, more than one culture was grown under the same conditions (same media, same strain), but mitochondria were purified separately. Due to low protein yield, corresponding fractions were joined for MS analysis.

bDatasets produced by MS: filenames ending with FT were derived from FTICR analysis, all others from LC/MS/MS. Filenames containing ³mem² designate analysis of the mitochondrial membrane fraction; ³mat,² of the mitochondrial matrix fraction. The datasets and more information about them are available at http://www-deletion.stanford.edu/YDPM/YDPM_index.html.

YP, yeast peptone; SC, synthetic complete; DG, differential centrifugation by Nycodenz density gradient; FFE, free-flow electrophoresis.

DOI: 10.1371/journal.pbio.0020160.t001