Table 1 Signature peptides for organelle markers and three case study proteins and their corresponding MRM methods.

From: Development of a UPLC-MRM-based targeted proteomic method to profile subcellular organelle marker proteins from human liver tissues

Protein

Signature peptidea

Start–endb

Average mass MH+ (Da)c

MRM (m/z)d

Cone (V)

CEf (eV)

Precursor ion

Product ione

β2M

IQVYSR

27–32

765.9

383.45

425.21

32

16

524.28

12

652.34

14

IQVYS(R)

775.9

388.42

435.26

16

534.27

12

662.34

14

FcRn

LFLEAFK

97–103

868.1

434.54

365.22

20

18

607.35

12

754.41

16

LFLEA(F)K

878.1

439.54

375.22

18

617.35

12

764.41

16

CYP3A4

EVTNFLR

244–250

879.0

440.10

650.40

40

10

EVTN(F)LR

889.0

445.10

660.40

HSC70

ITITNDK

501–507

804.92

402.73

477.20

40

16

590.30

12

691.40

14

ITITND(K)

812.92

406.90

485.43

16

598.61

12

699.70

14

FEELNADLFR

302–311

1254.39

627.30

435.30

40

28

735.40

24

848.50

20

FEELNADLF(R)

1264.39

632.67

445.50

28

745.73

24

858.90

20

LAMP1

VWVQAFK

357–363

878.07

439.54

592.35

30

14

778.42

16

VWVQA(F)K

888.07

444.54

602.35

14

788.42

16

AFSVNIFK

349–356

926.11

463.56

294.18

30

22

707.41

14

AFSVNI(F)K

936.11

468.56

304.18

22

717.41

14

TVESITDIR

138–146

1034.16

517.58

704.39

30

18

833.44

14

TVESITDI(R)

1044.16

522.58

714.39

18

843.44

14

HSP60

LSDGVAVLK

397–405

902.09

451.27

260.20

40

12

430.30

13

701.42

14

LSDGVAVL(K)

910.09

455.48

268.31

12

438.62

13

709.73

14

VTDALNATR

421–429

961.07

480.76

461.25

40

16

645.37

16

760.39

16

VTDALNAT(R)

971.07

486.03

471.48

16

655.66

16

770.78

16

GRP78

LTPEEIER

533–540

987.10

493.76

546.29

40

18

675.33

22

772.38

18

LTPEEIE(R)

997.10

499.03

556.56

18

685.67

22

782.79

18

ITITNDQNR

524–532

1075.17

537.78

646.29

40

16

747.34

18

860.42

18

ITITNDQN(R)

1085.17

543.10

656.63

16

757.72

18

870.83

18

Rab7

ATIGADFLTK

39–48

1037.21

519.11

432.74

40

14

751.40

18

ATIGADFLT(K)

1045.21

523.11

436.74

14

759.40

18

VIILGDSGVGK

11–21

1058.27

529.64

619.30

40

16

845.47

16

VIILGDSGVG(K)

1066.27

533.64

627.30

16

853.47

16

Rab5

LVLLGESAVGK

23–33

1086.32

543.67

437.26

42

14

647.34

16

LVLLGESAVG(K)

1094.32

547.67

441.26

14

655.34

16

Histone H3.1

YRPGTVALR

42–50

1033.23

517.12

320.17

42

22

713.43

22

YRPGTVAL(R)

1043.23

522.12

320.17

22

723.43

22

  1. aStable isotope-labeled amino acid residues are included in parentheses.
  2. bStart and end residue positions of peptides in the corresponding full-length protein.
  3. cTheoretical average mass of mono-protonated molecular ion.
  4. dAll precursor ions have a charge state of + 2, and all product ions used as the quantification trace have a charge state of + 1.
  5. eBolded product ions were used as the quantification trace during MRM.
  6. fCE = Collision Energy.
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