PRM traces for deteccon of target pepcdes in all samples. Part I. PD-1, PD-L1, PD-L2 (PRM with stable isotope dilucon). Part II. IDO1, LAG3, HAVCR2 (TIM-3),.
Morales-Betanzos et al.
Supplemental Dataset 2 PRM traces for detec:on of target pep:des in all samples Part I. PD-1, PD-L1, PD-L2 (PRM with stable isotope dilu:on) Part II. IDO1, LAG3, HAVCR2 (TIM-3), C10orf54 (VISTA), CD40 (PRM with labeled reference pep:de normaliza:on)
Part I. Quan+ta+on of PD-1, PDL1, and PD-L2 by PRM with stable isotope dilu+on
PD1 PD-1 was quan:fied via the proteotypic pep:de LAAFPEDR. PRM transi:ons traces for the endogenous LAAFPEDR pep:de and the (13C15N standard for each sample are shown in the following 3 pages.
B1
B2
B4
B5
B8
B9
B10
B11
B7
Standard
Endogenous
Standard
Endogenous
PD1 endogenous= LAAFPEDR standard = LAAFPEDR (C13 N15)
B13
B14
B12
B17
B20
B21
Standard
Endogenous
Standard
Endogenous
PD1 endogenous= LAAFPEDR standard = LAAFPEDR (C13 N15)
B22
B23
B24
B25
B26
Standard
Endogenous
PD1 endogenous= LAAFPEDR standard = LAAFPEDR (C13 N15) B28
B29
PD-L1 PD-L1 was quan:fied via the proteotypic pep:des LQDAGVYR and VNAPYNK. PRM transi:ons traces for the endogenous LQDAGVYR and VNAPYNK pep:des and the 13C15N standard for each sample are shown in the following 3 pages.
B1
B2
B4
B5
B7
B8
B9
B10
B11
B13
Standard
Endogenous
Standard
Endogenous
PDL1 endogenous= LQDAGVYR standard = LQDAGVYR (C13 N15)
B14
B12
B17
B20
B21
Standard
Endogenous
Standard
Endogenous
PDL1 endogenous= LQDAGVYR standard = LQDAGVYR (C13 N15)
B22
B23
B24
B25
B26
Standard
Endogenous
PDL1 endogenous= LQDAGVYR standard = LQDAGVYR (C13 N15) B28
B29
B1
B2
B4
B5
B7
B8
B9
B10
B11
B13
Standard
Endogenous
Standard
Endogenous
PDL1 endogenous= VNAPYNK standard = VNAPYNK(C13 N15)
B14
B12
B17
B20
B21
Standard
Endogenous
Standard
Endogenous
PDL1 endogenous= VNAPYNK standard = VNAPYNK(C13 N15)
B22
B23
B24
B25
B26
Standard
Endogenous
PDL1 endogenous= VNAPYNK standard = VNAPYNK(C13 N15) B28
B29
PD-L2 PD-L2 was quan:fied via the proteotypic pep:de TPEGLYQVTSVLR. PRM transi:ons traces for the endogenous TPEGLYQVTSVLR pep:de and the (13C15N standard for each sample are shown in the following 3 pages.
B1
B2
B4
B5
B8
B9
B10
B11
B7
Standard
Endogenous
Standard
Endogenous
PDL2 endogenous= TPEGLYQVTSVLR standard = TPEGLYQVTSVLR (C13 N15)
B13
B14
B12
B17
B20
B21
Standard
Endogenous
Standard
Endogenous
PDL2 endogenous= TPEGLYQVTSVLR standard = TPEGLYQVTSVLR (C13 N15)
B22
B23
B24
B25
B26
Standard
Endogenous
PDL2 endogenous= TPEGLYQVTSVLR standard = TPEGLYQVTSVLR (C13 N15) B28
B29
Part II. Rela+ve quan+ta+on of IDO1, LAG3, HAVCR2 (TIM-3), C10orf54 (VISTA) and CD40 by the labeled reference pep+de (LRP) method 1. IDO1 YILIPASQQPK; reference standard CD4-ILGNQGSFLTK (C13 N15) 2. LAG3 LPAGVGTR; reference standard PDL1-LQDAGVYR (C13 N15) 3. HAVCR2 (TIM-3) LANDLR; reference standard PDL1-VNAPYNK (C13 N15) 4. C10orf54 (VISTA) HPLSYVAQR; reference standard CD3G- WNLGSNAK (C13 N15) 5. CD40 YCDPNLGLR; reference standard PD1-LAAFPEDR (C13 N15)
IDO1 melanoma endogenous
YILIPASQQPK
synthe+c standard YILIPASQQPK
YILIPASQQPK A representa:ve PRM transi:ons trace for the pep:de YILIPASQQPK is shown at leb, along with that for a synthe:c standard (unlabeled) YILIPASQQPK pep:de. For quan:ta:on by the LRP method the summed transi:ons for YILIPASQQPK were normalized to the summed transi:ons for the CD4 pep:de ILGNQGSFLTK (13C15N), which eluted in the same bRPLC frac:on. See traces for each sample on the following 3 pages.
B1
B2
B4
B5
B8
B9
B10
B11
B7
Standard Ref
Endogenous
Standard Ref
Endogenous
IDO1 endogenous= YILIPASQQPK reference standard = CD4-ILGNQGSFLTK (C13 N15)
B13
B14
B12
B17
B20
B21
Standard Ref
Endogenous
Standard Ref
Endogenous
IDO1 endogenous= YILIPASQQPK reference standard = CD4-ILGNQGSFLTK (C13 N15)
B22
B23
B24
B25
B26
Standard Ref
Endogenous
IDO1 endogenous= YILIPASQQPK reference standard = CD4-ILGNQGSFLTK (C13 N15) B28
B29
LAG3 melanoma endogenous
LPAGVGTR
synthe+c standard LPAGVGTR
LPAGVGTR
A representa:ve PRM transi:ons trace for the pep:de LPAGVGTR is shown at leb, along with that for a synthe:c standard (unlabeled) LPAGVGTR pep:de. For quan:ta:on by the LRP method the summed transi:ons for LPAGVGTR were normalized to the summed transi:ons for the PD-L1 pep:de LQDAGVYR (13C15N), which eluted in the same bRPLC frac:on. See traces for each sample on the following 3 pages.
B1
B2
B4
B5
B7
B8
B9
B10
B11
B13
Standard Ref
Endogenous
Standard Ref
Endogenous
LAG3 endogenous= LPAGVGTR reference standard = PDL1-LQDAGVYR (C13 N15)
B14
B12
B17
B20
B21
Standard Ref
Endogenous
Standard Ref
Endogenous
LAG3 endogenous= LPAGVGTR reference standard = PDL1-LQDAGVYR (C13 N15)
B22
B23
B24
B25
B26
Standard Ref
Endogenous
LAG3 endogenous= LPAGVGTR reference standard = PDL1-LQDAGVYR (C13 N15) B28
B29
HAVCR2 (TIM-3) LANDLR melanoma endogenous LANDLR
synthe+c standard LANDLR
A representa:ve PRM transi:ons trace for the pep:de LANDLR is shown at leb, along with that for a synthe:c standard (unlabeled) LANDLR pep:de. For quan:ta:on by the LRP method the summed transi:ons for LANDLR were normalized to the summed transi:ons for the PD-L1 pep:de VNAPYNK (13C15N), which eluted in the same bRPLC frac:on. See traces for each sample on the following 3 pages.
B1
B2
B4
B5
B8
B9
B10
B11
B7
Standard Ref
Endogenous
Standard Ref
Endogenous
HAVCR2 (TIM-3) endogenous= LANDLR reference standard = PDL1-VNAPYNK (C13 N15)
B13
B14
B12
B17
B20
B21
Standard Ref
Endogenous
Standard Ref
Endogenous
HAVCR2 (TIM-3) endogenous= LANDLR reference standard = PDL1-VNAPYNK (C13 N15)
A representa:ve PRM transi:ons trace for the pep:de HPLSYVAQR is shown at leb, along with that for a synthe:c standard (unlabeled) HPLSYVAQR pep:de. For quan:ta:on by the LRP method the summed transi:ons for HPLSYVAQR were normalized to the summed transi:ons for the CD3G pep:de WNLGSNAK (13C15N), which eluted in the same bRPLC frac:on. See traces for each sample on the following 3 pages.
YC[+57]DPNLGLR A representa:ve PRM transi:ons trace for the pep:de YC[+57]DPNLGLR is shown at leb, along with that for a synthe:c standard (unlabeled) YC[+57]DPNLGLR pep:de. For quan:ta:on by the LRP method the summed transi:ons for YC[+57]DPNLGLR were normalized to the summed transi:ons for the PD-1 pep:de LAAFPEDR (13C15N), which eluted in the same bRPLC frac:on. See traces for each sample on the following 3 pages.
B1
B2
B4
B5
B8
B9
B10
B11
B7
Standard Ref
Endogenous
Standard Ref
Endogenous
CD40 endogenous= YC[+57]DPNLGLR reference standard = PD1-LAAFPEDR (C13 N15)
B13
B14
B12
B17
B20
B21
Standard Ref
Endogenous
Standard Ref
Endogenous
CD40 endogenous= YC[+57]DPNLGLR reference standard = PD1-LAAFPEDR (C13 N15)
B22
B23
B24
B25
B26
Standard Ref
Endogenous
CD40 endogenous= YC[+57]DPNLGLR reference standard = PD1-LAAFPEDR (C13 N15) B28
