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Reinders J, et al.  (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54

Abstract: Proteomic analyses of different subcellular compartments, so-called organellar proteomics, facilitate the understanding of cellular functions on a molecular level. In this work, various orthogonal multidimensional separation techniques both on the protein and on the peptide level are compared with regard to the number of identified proteins as well as the classes of proteins accessible by the respective methodology. The most complete overview was achieved by a combination of such orthogonal techniques as shown by the analysis of the yeast mitochondrial proteome. A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS, 1D-SDS-PAGE combined with nano-LC-MS/MS and 2D-PAGE with subsequent MALDI-mass fingerprinting. Our PROMITO approach identified the 749 proteins, which were found in the largest previous study on the yeast mitochondrial proteome, and additionally 102 proteins including 42 open reading frames with unknown function, providing the basis for a more detailed elucidation of mitochondrial processes. Comparison of the different approaches emphasizes a bias of 2D-PAGE against proteins with very high isoelectric points as well as large and hydrophobic proteins, which can be accessed more appropriately by the other methods. While 2D-PAGE has advantages in the possible separation of protein isoforms and quantitative differential profiling, 1D-SDS-PAGE with nano-LC-MS/MS and multidimensional LC-MS/MS are better suited for efficient protein identification as they are less biased against distinct classes of proteins. Thus, comprehensive proteome analyses can only be realized by a combination of such orthogonal approaches, leading to the largest dataset available for the mitochondrial proteome of yeast.

Status: Published Type: Journal Article PubMed ID: 16823961

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AAC1 AAC3 AAT1 ABF2 ACC1 ACH1 ACK1 ACN9 ACO1 ACO2
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BEM2 BIR1 BMS1 BNA3 BNA4 BPH1 CAB5 CAF4 CAN1 CAT2
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CCM1 CCP1 CEM1 CFT1 CHA1 CHD1 CIN8 CIR1 CIR2 CIT1
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CIT2 CIT3 COA1 COA3 COB COG7 COQ1 COQ10 COQ2 COQ3
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COQ5 COQ6 COQ8 COQ9 COR1 COS111 COS7 COT1 COX1 COX10
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COX11 COX12 COX13 COX14 COX15 COX16 COX17 COX2 COX20 COX3
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COX4 COX5A COX5B COX6 COX7 COX8 COX9 CPR1 CPR3 CRC1
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CRD1 CSF1 CSR1 CTF18 CTP1 CUE1 CYB2 CYC1 CYC2 CYC3
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CYC7 CYM1 CYR1 CYS4 CYT1 CYT2 DBP2 DCS1 DIC1 DIS3
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DLD1 DLD2 DNF1 DNM1 DOA4 DOC1 DOP1 DPM1 DSS1 DUG1
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ECM10 ECM16 ECM19 ECM31 ECM33 EFR3 EHD3 EHT1 EIS1 ELG1
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EMI5 EMP65 ENA2 ERG6 ERP1 ERP6 ERV1 ESP1 ETR1 FAA1
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FAA2 FAB1 FAS1 FAS2 FAT3 FAU1 FCJ1 FIS1 FKS1 FKS3
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FLC3 FLX1 FMC1 FMP10 FMP16 FMP21 FMP23 FMP25 FMP27 FMP30
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FMP32 FMP33 FMP37 FMP40 FMP41 FMP43 FMP45 FMP46 FMP48 FMP52
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FMT1 FOL1 FPR1 FRD1 FRE5 FSF1 FUM1 FUN12 FUN14 FUN30
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FUS2 FUS3 FZO1 GAS1 GCD7 GCN1 GCV1 GCV2 GCV3 GDB1
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#251 - 260 )
GDH2 GDH3 GDS1 GEM1 GEP3 GEP4 GEP5 GEP7 GET1 GGC1
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GIP3 GIS1 GLE1 GLO4 GLR1 GLT1 GND1 GNP1 GOR1 GPA2
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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GPD2 GPI18 GPM1 GRS1 GRX2 GRX5 GSY1 GTF1 GTT1 GTT2
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GUT2 GYL1 GYP1 HAL9 HEM1 HEM14 HEM15 HER1 HER2 HFA1
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Topics Genes linked to topics (#291 - 300 )
HFD1 HMI1 HNT2 HOL1 HSC82 HSF1 HSP10 HSP60 HSP78 HTD2
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#301 - 310 )
HXT10 HXT14 HXT6 HXT7 HYP2 IBA57 ICL2 ICP55 IDH1 IDH2
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Topics Genes linked to topics (#311 - 320 )
IDP1 IDP3 IFM1 ILV1 ILV2 ILV3 ILV5 ILV6 IMA1 IMG1
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Topics Genes linked to topics (#321 - 330 )
IMG2 IML2 IMO32 IMP1 INH1 IRA1 IRA2 IRC20 IRS4 ISA2
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ISD11 ISM1 ISU1 JAC1 JEN1 JJJ1 KAR5 KGD1 KGD2 KHA1
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KIP2 KOG1 LAG2 LAP3 LAS1 LAT1 LDB16 LEU4 LEU5 LEU9
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Topics Genes linked to topics (#351 - 360 )
LIP2 LIP5 LOS1 LPD1 LRG1 LSC1 LSC2 LSP1 LYP1 LYS12
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LYS20 LYS4 MAE1 MAM33 MAS1 MAS2 MBA1 MBF1 MCR1 MCT1
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MCX1 MDH1 MDJ1 MDL1 MDL2 MDM12 MDM30 MDM34 MDM38 MDN1
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MDS3 MDV1 MEC1 MEF1 MEF2 MET13 MET3 MGE1 MGM1 MGM101
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MGR1 MGR3 MHR1 MIA40 MIP1 MIR1 MIS1 MLH1 MLP2 MMF1
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MMM1 MMR1 MMT1 MMT2 MNP1 MOD5 MOS1 MOS2 MOT1 MPA43
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Topics Genes linked to topics (#411 - 420 )
MPM1 MRE11 MRF1 MRH1 MRH4 MRP1 MRP13 MRP17 MRP2 MRP20
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Topics Genes linked to topics (#421 - 430 )
MRP21 MRP4 MRP49 MRP51 MRP7 MRPL1 MRPL10 MRPL11 MRPL13 MRPL15
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MRPL16 MRPL17 MRPL19 MRPL20 MRPL22 MRPL23 MRPL24 MRPL25 MRPL27 MRPL28
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Topics Genes linked to topics (#441 - 450 )
MRPL3 MRPL32 MRPL33 MRPL35 MRPL36 MRPL37 MRPL38 MRPL39 MRPL4 MRPL40
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Topics Genes linked to topics (#451 - 460 )
MRPL44 MRPL49 MRPL50 MRPL51 MRPL6 MRPL7 MRPL8 MRPL9 MRPS12 MRPS16
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MRPS17 MRPS18 MRPS28 MRPS35 MRPS5 MRPS8 MRPS9 MRS1 MRS2 MRS4
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Topics Genes linked to topics (#471 - 480 )
MSB1 MSC1 MSC6 MSD1 MSE1 MSF1 MSH1 MSK1 MSM1 MSP1
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MSR1 MSS1 MSS116 MSS18 MSS51 MST1 MSW1 MSY1 MTF1 MTF2
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Topics Genes linked to topics (#491 - 500 )
MTG1 MYO4 MZM1 NAM2 NAM9 NAT1 NAT2 NCA2 NCE102 NCP1
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Topics Genes linked to topics (#501 - 510 )
NDE1 NDE2 NDI1 NEM1 NEW1 NFS1 NFU1 NGL1 NIF3 NIT3
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NOC2 NOP14 NSR1 NTG1 NUC1 NUM1 NUP2 NUT1 OAC1 OAF3
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Topics Genes linked to topics (#521 - 530 )
OCT1 ODC1 ODC2 OLI1 OM14 OM45 OMS1 OPI3 OPY1 OSM1
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Topics Genes linked to topics (#531 - 540 )
OXA1 OYE2 PAM16 PAM17 PAM18 PBP1 PDA1 PDB1 PDH1 PDR18
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Topics Genes linked to topics (#541 - 550 )
PDR5 PDX1 PEP4 PET100 PET111 PET112 PET117 PET122 PET123 PET127
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Topics Genes linked to topics (#551 - 560 )
PET130 PET191 PET309 PET494 PET54 PET8 PET9 PGC1 PGK1 PHB1
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Topics Genes linked to topics (#561 - 570 )
PHB2 PHO88 PHR1 PIB2 PIC2 PIF1 PIL1 PIM1 PIS1 PKP1
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Topics Genes linked to topics (#571 - 580 )
PKP2 PMA1 PMA2 PNG1 PNT1 POL1 POM152 POR1 POR2 POS5
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Topics Genes linked to topics (#581 - 590 )
PPA2 PPM2 PPT2 PRD1 PRP19 PRP31 PRP43 PRX1 PSD1 PSK2
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#591 - 600 )
PSP1 PST2 PTC5 PTC7 PTH1 PTH2 PTP1 PUT1 PUT2 QCR10
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#601 - 610 )
QCR2 QCR6 QCR7 QCR8 QCR9 QRI7 RAD23 RAD50 RAT1 RAX2
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#611 - 620 )
RCF1 RCF2 RDL1 RDL2 REX2 RHO1 RIM1 RIM2 RIP1 RMA1
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Topics Genes linked to topics (#621 - 630 )
RMD9 RNR3 ROT2 RPB2 RPL40B RPM2 RPO21 RPO41 RPS18A RPS18B
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#631 - 640 )
RPS24A RRF1 RRG1 RRG9 RSM10 RSM18 RSM19 RSM22 RSM23 RSM24
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#641 - 650 )
RSM25 RSM26 RSM27 RSM28 RSM7 RSP5 RTC2 RTN1 SAC1 SAL1
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#651 - 660 )
SAM35 SAM37 SAM50 SAP185 SAP4 SCL1 SCM4 SCO1 SCO2 SDH1
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#661 - 670 )
SDH2 SDH3 SDH4 SEC4 SEC63 SEN2 SEN34 SEN54 SFA1 SFC1
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#671 - 680 )
SHH4 SHM1 SHY1 SIR3 SLM1 SLM5 SLS1 SMC2 SMC6 SMF2
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#681 - 690 )
SMK1 SNF1 SNL1 SNQ2 SOD1 SOD2 SOV1 SPC105 SPF1 SPG1
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#691 - 700 )
SPP382 SPT5 SPT6 SPT7 SSC1 SSQ1 STF1 STT4 SUC2 SUR7
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Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#701 - 710 )
SUV3 SWC3 SYG1 SYH1 SYM1 SYT1 TAO3 TAZ1 TBS1 TCB1
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Topics Genes linked to topics (#711 - 720 )
TCB3 TCD1 TCD2 TCM62 TDA5 TDH3 TEF4 TEL1 TES1 TFA1
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Topics Genes linked to topics (#721 - 730 )
TFC3 THS1 TIF4631 TIM10 TIM11 TIM12 TIM13 TIM17 TIM18 TIM21
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Topics Genes linked to topics (#731 - 740 )
TIM22 TIM23 TIM44 TIM50 TIM54 TIM8 TIM9 TNA1 TOF2 TOM20
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Topics Genes linked to topics (#741 - 750 )
TOM22 TOM40 TOM5 TOM6 TOM7 TOM70 TOM71 TOP2 TOR2 TOS4
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Topics Genes linked to topics (#751 - 760 )
TPS2 TRR2 TRX3 TSC13 TTI1 TUF1 UFD4 UGO1 ULS1 URA2
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#761 - 770 )
UTP10 VAR1 VAS1 VMR1 VMS1 VPS13 VPS15 VPS21 VPS54 VPS68
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#771 - 780 )
VPS73 VRG4 WAR1 WWM1 XDJ1 YAT1 YBL059W YBL095W YCK1 YCP4
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#781 - 790 )
YDL027C YDL086W YDL119C YDL157C YDR061W YDR341C YDR381C-A YEL067C YER038W-A YER076C
Additional Literature blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#791 - 800 )
YER181C YFH1 YGR012W YGR021W YGR266W YHB1 YHM2 YHR080C YIL077C YIM1
Additional Literature blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#801 - 810 )
YIR024C YJL045W YJL070C YJL113W YJL133C-A YJL171C YJR003C YJR039W YJR085C YJR098C
Additional Literature blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#811 - 820 )
YKL070W YKR023W YKR070W YKT6 YLF2 YLH47 YLR001C YLR253W YLR290C YLR419W
Additional Literature blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#821 - 830 )
YMC1 YMC2 YME1 YME2 YML133C YML6 YMR221C YMR31 YNK1 YNL144C
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#831 - 840 )
YNL195C YNL200C YNL208W YNL320W YNR040W YOR020W-A YOR022C YPL109C YPR011C YPR097W
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#841 - 850 )
YPR098C YPT1 YRF1-7 YRO2 YSA1 YSC83 YTA12 ZEO1 ZIM17 ZRG8
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Cellular Location blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Primary Literature blue ball blue ball

Topics Genes linked to topics (#851 )
ZUO1
Additional Literature blue ball
Cellular Location blue ball

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