. 2015 Feb 19;14(9):2357–2374. doi: 10.1074/mcp.M114.047050

Table I. List of 34 proteins for which MRM-MS assays were developed and the heavy-isotope labeled internal standard (SIS) peptides used.^a Peptides annotated with an asterisk (96 of 115) were detected at all sites used throughout the data analysis.

SwProt	Protein description	Synthetic internal standard ¹³C/N¹⁵ peptides^b	E coli expressed L/H protein^c
P09972	Fructose-bisphosphate aldolase C	ALQASALNAWR, AEVNGLAAQGK, ELSDIALR, TPSALAILENANVLAR, QVLFSADDR*	+/+
P04083	Annexin A1	ALYEAGER, GTDVNVFNTILTTR, GVDEATIIDILTK, AAYLQETGKPLDETLK, TPAQFDADELR	+/+
P09525	Annexin A4	VLVSLSAGGR, GLGTDEDAIISVLAYR, DEGNYLDDALVR, GLGTDDNTLIR, GAGTDEGCLIEILASR*	+/+
P20073	Annexin A7	LYQAGEGR, SEIDLVQIK, GAGTDDSTLVR, EFSGYVESGLK, GFGTDEQAIVDVVANR	+/+
Q53G71	Calreticulin variant (Fragment)	QIDNPDYK, GLQTSQDAR, FYALSASFEPFSNK, EQFLDGDGWTSR*, GQTLVVQFTVK	+/+
O00299	Chloride intracellular channel protein 1	LHIVQVVCK, YLSNAYAR, IEEFLEAVLCPPR, GVTFNVTTVDTK, GFTIPEAFR*	+/+
P15311	Ezrin	IQVWHAEHR, EDEVEEWQHR, SGYLSSER, IALLEEAR, SQEQLAAELAEYTAK*	+/+
Q16658	Fascin	YLTAEAFGFK, FLIVAHDDGR, YLAPSGPSGTLK, VTGTLDANR, LSCFAQTVSPAEK*	+/+
P02792	Ferritin light chain	LGGPEAGLGEYLFER (R6), KPAEDEWGK (K6)	+/+
P39748	Flap endonuclease 1	HLTASEAK, WSEPNEEELIK, SIEEIVR, QLQQAQAAGAEQEVEK, LIADVAPSAIR	+/+
P09211	Glutathione S-transferase P	FQDGDLTLYQSNTILR, YISLIYTNYEAGK, EEVVTVETWQEGSLK, PPYTVVYFPVR, ASCLYGQLPK*	+/+
Q04760	Lactoylglutathione lyase	FSLYFLAYEDK, SLDFYTR, IAWALSR, GFGHIGIAVPDVYSACK, FEELGVK*	+/+
P62993	Growth factor receptor-bound protein 2	FNSLNELVDYHR, FGNDVQHFK, NYVTPVNR, ATADDELSFK, ESESAPGDFSLSVK*	+/+
P04792	Heat shock protein beta-1	LFDQAFGLPR, AQLGGPEAAK, VSLDVNHFAPDELTVK, DGVVEITGK, QLSSGVSEIR*	+/+
Q14116	Interleukin-18	EDELGDR, SDIIFFQR, TIFIISMYK, ISTLSCENK, GMAVTISVK	+/+
P09382	Galectin-1	DGGAWGTEQR, DSNNLCLHFNPR, FNAHGDANTIVCNSK, SFVLNLGK, LPDGYEFK*	+/+
O00151	PDZ and LIM domain protein 1	CGTGIVGVFVK, GCTDNLTLTVAR, VAASIGNAQK, VWSPLVTEEGK, DFEQPLAISR	+/+
P32119	Peroxiredoxin-2	GLFIIDGK, TDEGIAYR, LSEDYGVLK, ATAVVDGAFK	+/+
Q13162	Peroxiredoxin-4	DYGVYLEDSGHTLR, LVQAFQYTDK, IPLLSDLTHQISK, QITLNDLPVGR	+/+
P23297	Protein S100-A1	ELLQTELSGFLDAQK (L6)	+/+
P29034	Protein S100-A2	ELPSFVGEK* (K6), YSCQEGDK (K6)	+/+
P04271	Protein S100-B	AMVALIDVFHQYSGR* (R6), ELINNELSHFLEEIK (K6)	+/+
P54727	UV excision repair protein RAD23 homB	EQVIAALR, IDIDPEETVK, ILNDDTALK*	+/+
O76070	Gamma-synuclein	EQANAVSEAVVSSVNTVATK, EGVVGAVEK, ENVVQSVTSVAEK, TVEEAENIAVTSGVVR*	+/+
P09493	Tropomyosin alpha-1 chain	HIAEDADR, LVIIESDLER, SIDDLEDELYAQK, QLEDELVSLQK*	+/+
O00762	Ubiquitin-conjugating enzyme E2 C	YLQETYSK, WSALYDVR, LSLEFPSGYPYNAPTVK, DPAATSVAAAR, GISAFPESDNLFK*	+/+
P63279	SUMO-conjugating enzyme UBC9	DHPFGFVAVPTK, GTPWEGGLFK, DDYPSSPPK*, DWRPAITIK	+/+
P00974	Pancreatic trypsin inhibitor	AGLCQTFVYGGCR (V5)	+/−^d
P41160	Leptin	INDISHTQSVSAK	+/−^e
P68082	Myoglobin	LFTGHPETLEK	+/−^e
P02687	Myelin basic protein	YLASASTMDHAR (R6), HGFLPR (R6)	+/−^e
P07288	Prostate-specific antigen	LSEPAELTDAVK, IVGGWECEK (V5)	+/−^e
P00433	Peroxidase C1A	SSDLVALSGGHTFGK	+/−^e
P02741	C-reactive protein	GYSIFSYATK, ESDTSYVSLK	+/−^e

^a MRM-MS assays were constructed and run for a total of 365 peptides: 125 peptides were unlabeled and derived from synthesis as well as digestion of the light versions of all of the proteins shown. Another 125 peptides were chemically synthesized heavy-labeled versions, and another 115 peptides derived by digestion from the 27 uniformly heavy-labeled proteins.

^b Chemically synthesized ¹³C/N¹⁵-labeled peptides used as internal standards; labeled amino acids are indicated in bold. These peptides are labeled on the C-terminal Lys as K8 (¹³C₆, ¹⁵N₂) or C-terminal Arg as R10 (¹³C₆, ¹⁵N₄) unless otherwise noted. Exceptions include peptides from ferritin, protein S100-A2, protein S100-B, and myelin basic protein that were labeled with K6 (¹³C₆) Lys or R6 (¹³C₆) Arg. Protein S100-A1 was labeled at an internal Leu, L6 (¹³C₆). Prostate-specific antigen and pancreatic trypsin inhibitor were labeled at an internal Val, V5 (¹³C₅).

^c Twenty-seven proteins expressed in E. coli in both natural isotope abundance and uniformly N15-labeled (U-N15) forms. A total of 115 U¹⁵N-labeled peptides derived from the heavy labeled proteins were monitored.

^d Commercially available unlabeled protein.

^e Commercially available unlabeled proteins used as controls (5).

Table I. List of 34 proteins for which MRM-MS assays were developed and the heavy-isotope labeled internal standard (SIS) peptides used.a Peptides annotated with an asterisk (96 of 115) were detected at all sites used throughout the data analysis.

Table I. List of 34 proteins for which MRM-MS assays were developed and the heavy-isotope labeled internal standard (SIS) peptides used.^a Peptides annotated with an asterisk (96 of 115) were detected at all sites used throughout the data analysis.