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Please include the following statement when referencing the CPTAC Assay Portal
We would like to acknowledge the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal (assays.cancer.gov) for developing assays and establishing criteria for the assays described in this publication.

APOB

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
APOB N/A
Sequence Length (AA) Molecular Weight (Da)
4563 515605
Protein Name
Apolipoprotein B-100
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MDPPRPALLA LLALPALLLL LLAGARAEEE MLENVSLVCP KDATRFKHLR
60 70 80 90 100
KYTYNYEAES SSGVPGTADS RSATRINCKV ELEVPQLCSF ILKTSQCTLK
110 120 130 140 150
EVYGFNPEGK ALLKKTKNSE EFAAAMSRYE LKLAIPEGKQ VFLYPEKDEP
160 170 180 190 200
TYILNIKRGI ISALLVPPET EEAKQVLFLD TVYGNCSTHF TVKTRKGNVA
210 220 230 240 250
TEISTERDLG QCDRFKPIRT GISPLALIKG MTRPLSTLIS SSQSCQYTLD
260 270 280 290 300
AKRKHVAEAI CKEQHLFLPF SYKNKYGMVA QVTQTLKLED TPKINSRFFG
310 320 330 340 350
EGTKKMGLAF ESTKSTSPPK QAEAVLKTLQ ELKKLTISEQ NIQRANLFNK
360 370 380 390 400
LVTELRGLSD EAVTSLLPQL IEVSSPITLQ ALVQCGQPQC STHILQWLKR
410 420 430 440 450
VHANPLLIDV VTYLVALIPE PSAQQLREIF NMARDQRSRA TLYALSHAVN
460 470 480 490 500
NYHKTNPTGT QELLDIANYL MEQIQDDCTG DEDYTYLILR VIGNMGQTME
510 520 530 540 550
QLTPELKSSI LKCVQSTKPS LMIQKAAIQA LRKMEPKDKD QEVLLQTFLD
560 570 580 590 600
DASPGDKRLA AYLMLMRSPS QADINKIVQI LPWEQNEQVK NFVASHIANI
610 620 630 640 650
LNSEELDIQD LKKLVKEALK ESQLPTVMDF RKFSRNYQLY KSVSLPSLDP
660 670 680 690 700
ASAKIEGNLI FDPNNYLPKE SMLKTTLTAF GFASADLIEI GLEGKGFEPT
710 720 730 740 750
LEALFGKQGF FPDSVNKALY WVNGQVPDGV SKVLVDHFGY TKDDKHEQDM
760 770 780 790 800
VNGIMLSVEK LIKDLKSKEV PEARAYLRIL GEELGFASLH DLQLLGKLLL
810 820 830 840 850
MGARTLQGIP QMIGEVIRKG SKNDFFLHYI FMENAFELPT GAGLQLQISS
860 870 880 890 900
SGVIAPGAKA GVKLEVANMQ AELVAKPSVS VEFVTNMGII IPDFARSGVQ
910 920 930 940 950
MNTNFFHESG LEAHVALKAG KLKFIIPSPK RPVKLLSGGN TLHLVSTTKT
960 970 980 990 1000
EVIPPLIENR QSWSVCKQVF PGLNYCTSGA YSNASSTDSA SYYPLTGDTR
1010 1020 1030 1040 1050
LELELRPTGE IEQYSVSATY ELQREDRALV DTLKFVTQAE GAKQTEATMT
1060 1070 1080 1090 1100
FKYNRQSMTL SSEVQIPDFD VDLGTILRVN DESTEGKTSY RLTLDIQNKK
1110 1120 1130 1140 1150
ITEVALMGHL SCDTKEERKI KGVISIPRLQ AEARSEILAH WSPAKLLLQM
1160 1170 1180 1190 1200
DSSATAYGST VSKRVAWHYD EEKIEFEWNT GTNVDTKKMT SNFPVDLSDY
1210 1220 1230 1240 1250
PKSLHMYANR LLDHRVPQTD MTFRHVGSKL IVAMSSWLQK ASGSLPYTQT
1260 1270 1280 1290 1300
LQDHLNSLKE FNLQNMGLPD FHIPENLFLK SDGRVKYTLN KNSLKIEIPL
1310 1320 1330 1340 1350
PFGGKSSRDL KMLETVRTPA LHFKSVGFHL PSREFQVPTF TIPKLYQLQV
1360 1370 1380 1390 1400
PLLGVLDLST NVYSNLYNWS ASYSGGNTST DHFSLRARYH MKADSVVDLL
1410 1420 1430 1440 1450
SYNVQGSGET TYDHKNTFTL SYDGSLRHKF LDSNIKFSHV EKLGNNPVSK
1460 1470 1480 1490 1500
GLLIFDASSS WGPQMSASVH LDSKKKQHLF VKEVKIDGQF RVSSFYAKGT
1510 1520 1530 1540 1550
YGLSCQRDPN TGRLNGESNL RFNSSYLQGT NQITGRYEDG TLSLTSTSDL
1560 1570 1580 1590 1600
QSGIIKNTAS LKYENYELTL KSDTNGKYKN FATSNKMDMT FSKQNALLRS
1610 1620 1630 1640 1650
EYQADYESLR FFSLLSGSLN SHGLELNADI LGTDKINSGA HKATLRIGQD
1660 1670 1680 1690 1700
GISTSATTNL KCSLLVLENE LNAELGLSGA SMKLTTNGRF REHNAKFSLD
1710 1720 1730 1740 1750
GKAALTELSL GSAYQAMILG VDSKNIFNFK VSQEGLKLSN DMMGSYAEMK
1760 1770 1780 1790 1800
FDHTNSLNIA GLSLDFSSKL DNIYSSDKFY KQTVNLQLQP YSLVTTLNSD
1810 1820 1830 1840 1850
LKYNALDLTN NGKLRLEPLK LHVAGNLKGA YQNNEIKHIY AISSAALSAS
1860 1870 1880 1890 1900
YKADTVAKVQ GVEFSHRLNT DIAGLASAID MSTNYNSDSL HFSNVFRSVM
1910 1920 1930 1940 1950
APFTMTIDAH TNGNGKLALW GEHTGQLYSK FLLKAEPLAF TFSHDYKGST
1960 1970 1980 1990 2000
SHHLVSRKSI SAALEHKVSA LLTPAEQTGT WKLKTQFNNN EYSQDLDAYN
2010 2020 2030 2040 2050
TKDKIGVELT GRTLADLTLL DSPIKVPLLL SEPINIIDAL EMRDAVEKPQ
2060 2070 2080 2090 2100
EFTIVAFVKY DKNQDVHSIN LPFFETLQEY FERNRQTIIV VLENVQRNLK
2110 2120 2130 2140 2150
HINIDQFVRK YRAALGKLPQ QANDYLNSFN WERQVSHAKE KLTALTKKYR
2160 2170 2180 2190 2200
ITENDIQIAL DDAKINFNEK LSQLQTYMIQ FDQYIKDSYD LHDLKIAIAN
2210 2220 2230 2240 2250
IIDEIIEKLK SLDEHYHIRV NLVKTIHDLH LFIENIDFNK SGSSTASWIQ
2260 2270 2280 2290 2300
NVDTKYQIRI QIQEKLQQLK RHIQNIDIQH LAGKLKQHIE AIDVRVLLDQ
2310 2320 2330 2340 2350
LGTTISFERI NDILEHVKHF VINLIGDFEV AEKINAFRAK VHELIERYEV
2360 2370 2380 2390 2400
DQQIQVLMDK LVELAHQYKL KETIQKLSNV LQQVKIKDYF EKLVGFIDDA
2410 2420 2430 2440 2450
VKKLNELSFK TFIEDVNKFL DMLIKKLKSF DYHQFVDETN DKIREVTQRL
2460 2470 2480 2490 2500
NGEIQALELP QKAEALKLFL EETKATVAVY LESLQDTKIT LIINWLQEAL
2510 2520 2530 2540 2550
SSASLAHMKA KFRETLEDTR DRMYQMDIQQ ELQRYLSLVG QVYSTLVTYI
2560 2570 2580 2590 2600
SDWWTLAAKN LTDFAEQYSI QDWAKRMKAL VEQGFTVPEI KTILGTMPAF
2610 2620 2630 2640 2650
EVSLQALQKA TFQTPDFIVP LTDLRIPSVQ INFKDLKNIK IPSRFSTPEF
2660 2670 2680 2690 2700
TILNTFHIPS FTIDFVEMKV KIIRTIDQML NSELQWPVPD IYLRDLKVED
2710 2720 2730 2740 2750
IPLARITLPD FRLPEIAIPE FIIPTLNLND FQVPDLHIPE FQLPHISHTI
2760 2770 2780 2790 2800
EVPTFGKLYS ILKIQSPLFT LDANADIGNG TTSANEAGIA ASITAKGESK
2810 2820 2830 2840 2850
LEVLNFDFQA NAQLSNPKIN PLALKESVKF SSKYLRTEHG SEMLFFGNAI
2860 2870 2880 2890 2900
EGKSNTVASL HTEKNTLELS NGVIVKINNQ LTLDSNTKYF HKLNIPKLDF
2910 2920 2930 2940 2950
SSQADLRNEI KTLLKAGHIA WTSSGKGSWK WACPRFSDEG THESQISFTI
2960 2970 2980 2990 3000
EGPLTSFGLS NKINSKHLRV NQNLVYESGS LNFSKLEIQS QVDSQHVGHS
3010 3020 3030 3040 3050
VLTAKGMALF GEGKAEFTGR HDAHLNGKVI GTLKNSLFFS AQPFEITAST
3060 3070 3080 3090 3100
NNEGNLKVRF PLRLTGKIDF LNNYALFLSP SAQQASWQVS ARFNQYKYNQ
3110 3120 3130 3140 3150
NFSAGNNENI MEAHVGINGE ANLDFLNIPL TIPEMRLPYT IITTPPLKDF
3160 3170 3180 3190 3200
SLWEKTGLKE FLKTTKQSFD LSVKAQYKKN KHRHSITNPL AVLCEFISQS
3210 3220 3230 3240 3250
IKSFDRHFEK NRNNALDFVT KSYNETKIKF DKYKAEKSHD ELPRTFQIPG
3260 3270 3280 3290 3300
YTVPVVNVEV SPFTIEMSAF GYVFPKAVSM PSFSILGSDV RVPSYTLILP
3310 3320 3330 3340 3350
SLELPVLHVP RNLKLSLPDF KELCTISHIF IPAMGNITYD FSFKSSVITL
3360 3370 3380 3390 3400
NTNAELFNQS DIVAHLLSSS SSVIDALQYK LEGTTRLTRK RGLKLATALS
3410 3420 3430 3440 3450
LSNKFVEGSH NSTVSLTTKN MEVSVATTTK AQIPILRMNF KQELNGNTKS
3460 3470 3480 3490 3500
KPTVSSSMEF KYDFNSSMLY STAKGAVDHK LSLESLTSYF SIESSTKGDV
3510 3520 3530 3540 3550
KGSVLSREYS GTIASEANTY LNSKSTRSSV KLQGTSKIDD IWNLEVKENF
3560 3570 3580 3590 3600
AGEATLQRIY SLWEHSTKNH LQLEGLFFTN GEHTSKATLE LSPWQMSALV
3610 3620 3630 3640 3650
QVHASQPSSF HDFPDLGQEV ALNANTKNQK IRWKNEVRIH SGSFQSQVEL
3660 3670 3680 3690 3700
SNDQEKAHLD IAGSLEGHLR FLKNIILPVY DKSLWDFLKL DVTTSIGRRQ
3710 3720 3730 3740 3750
HLRVSTAFVY TKNPNGYSFS IPVKVLADKF IIPGLKLNDL NSVLVMPTFH
3760 3770 3780 3790 3800
VPFTDLQVPS CKLDFREIQI YKKLRTSSFA LNLPTLPEVK FPEVDVLTKY
3810 3820 3830 3840 3850
SQPEDSLIPF FEITVPESQL TVSQFTLPKS VSDGIAALDL NAVANKIADF
3860 3870 3880 3890 3900
ELPTIIVPEQ TIEIPSIKFS VPAGIVIPSF QALTARFEVD SPVYNATWSA
3910 3920 3930 3940 3950
SLKNKADYVE TVLDSTCSST VQFLEYELNV LGTHKIEDGT LASKTKGTFA
3960 3970 3980 3990 4000
HRDFSAEYEE DGKYEGLQEW EGKAHLNIKS PAFTDLHLRY QKDKKGISTS
4010 4020 4030 4040 4050
AASPAVGTVG MDMDEDDDFS KWNFYYSPQS SPDKKLTIFK TELRVRESDE
4060 4070 4080 4090 4100
ETQIKVNWEE EAASGLLTSL KDNVPKATGV LYDYVNKYHW EHTGLTLREV
4110 4120 4130 4140 4150
SSKLRRNLQN NAEWVYQGAI RQIDDIDVRF QKAASGTTGT YQEWKDKAQN
4160 4170 4180 4190 4200
LYQELLTQEG QASFQGLKDN VFDGLVRVTQ EFHMKVKHLI DSLIDFLNFP
4210 4220 4230 4240 4250
RFQFPGKPGI YTREELCTMF IREVGTVLSQ VYSKVHNGSE ILFSYFQDLV
4260 4270 4280 4290 4300
ITLPFELRKH KLIDVISMYR ELLKDLSKEA QEVFKAIQSL KTTEVLRNLQ
4310 4320 4330 4340 4350
DLLQFIFQLI EDNIKQLKEM KFTYLINYIQ DEINTIFSDY IPYVFKLLKE
4360 4370 4380 4390 4400
NLCLNLHKFN EFIQNELQEA SQELQQIHQY IMALREEYFD PSIVGWTVKY
4410 4420 4430 4440 4450
YELEEKIVSL IKNLLVALKD FHSEYIVSAS NFTSQLSSQV EQFLHRNIQE
4460 4470 4480 4490 4500
YLSILTDPDG KGKEKIAELS ATAQEIIKSQ AIATKKIISD YHQQFRYKLQ
4510 4520 4530 4540 4550
DFSDQLSDYY EKFIAESKRL IDLSIQNYHT FLIYITELLK KLQSTTVMNP
4560 4563
YMKLAPGELT IIL

Data source: UniProt

Protein Map Collapse protein map

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

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Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-2205 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Modified Sequence
FEVDSPVYN[+1.0]ATWSASLK
Modification Type
Deamidated (N)
Protein - Site of Modification
3895
Peptide - Site of Modification
9
Peptide Start
3887
Peptide End
3903
CPTAC ID
CPTAC-2205
Peptide Molecular Mass
1,913.9047
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
LCMS-8040
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Nexera X2 UHPLC
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y7 (1+) 32 7.6 9.1 33.9 12.2 12.5 46.6 14.4 15.5 15 15 15
y6 (1+) 16.6 6.4 8.5 29.8 8.6 9.4 34.1 10.7 12.7 15 15 15
y5 (1+) 33.2 8 10.2 24.9 12.3 10.1 41.5 14.7 14.4 15 15 15
sum 22.4 3.8 4.9 24.9 3.8 5 33.5 5.4 7 15 15 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-652 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Modified Sequence
FN[+1.0]SSYLQGTNQITGR
Modification Type
Deamidated (NQ)
Protein - Site of Modification
1523
Peptide - Site of Modification
2
Peptide Start
1522
Peptide End
1536
CPTAC ID
CPTAC-652
Peptide Molecular Mass
1,685.8009
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
serum
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Q-Exactive (ThermoFisher)
Internal Standard
synthetic peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Dionex UltiMate 3000 RSLCnano LC (ThermoFisher)
Column Packing
Acclaim PepMap100 C18, 5um (Trap); Acclaim PepMap RSLC C18, 2um (Analytical)
Column Dimensions
300um x 5mm (Trap); 75um x 25cm (Analytical)
Flow Rate
0.5 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y10 (1+) 3.1 4.6 7.3 4.7 4.5 7.3 5.6 6.4 10.3 15 15 15
y9 (1+) 4.5 3.7 5.7 5 3.5 5.9 6.7 5.1 8.2 15 15 15
y8 (1+) 3.6 3.9 6.1 5.2 3.8 6.1 6.3 5.4 8.6 15 15 15
sum 3.4 3.8 5.9 4.4 3.4 6.2 5.6 5.1 8.6 15 15 15

Additional Resources and Comments

Resources
Download SOPs
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Assay Details for CPTAC-1299 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Modified Sequence
FN[+1.0]SSYLQGTNQITGR
Modification Type
Deamidated (N)
Protein - Site of Modification
1523
Peptide - Site of Modification
2
Peptide Start
1522
Peptide End
1536
CPTAC ID
CPTAC-1299
Peptide Molecular Mass
1,685.8009
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tumor tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TSQ Vantage
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Accela 1250 Quaternary Low Pump
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y8 (1+) 16.3 9.2 6.3 19.2 9.8 8.1 25.2 13.4 10.3 15 15 15
y9 (1+) 15.9 7 7.5 25.1 7.4 7.9 29.7 10.2 10.9 15 15 15
y10 (1+) 16.9 16.2 5.5 19.3 16.1 10 25.7 22.8 11.4 15 15 15
sum 9.2 6.3 4.2 15.6 6 5.3 18.1 8.7 6.8 15 15 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-1300 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Modified Sequence
FVEGSHN[+1.0]STVSLTTK
Modification Type
Deamidated (N)
Protein - Site of Modification
3411
Peptide - Site of Modification
7
Peptide Start
3405
Peptide End
3419
CPTAC ID
CPTAC-1300
Peptide Molecular Mass
1,606.7839
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tumor tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TSQ Vantage
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Accela 1250 Quaternary Low Pump
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y13 (2+) 30.7 21.5 20.6 37 21.5 21 48.1 30.4 29.4 15 15 15
y5 (1+) 56 18 31.2 49.1 29.2 30.6 74.5 34.3 43.7 15 15 15
y12 (2+) 40.8 42.8 32.6 45.5 48 30.9 61.1 64.3 44.9 15 15 15
sum 26.3 12.2 16.6 29.1 16.8 17.5 39.2 20.8 24.1 15 15 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-653 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Modified Sequence
YDFN[+1.0]SSM[+16.0]LYSTAK
Modification Type
Deamidated (NQ), Oxidation (M)
Protein - Site of Modification
3465, 3468
Peptide - Site of Modification
4, 7
Peptide Start
3462
Peptide End
3474
CPTAC ID
CPTAC-653
Peptide Molecular Mass
1,542.6548
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
serum
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Q-Exactive (ThermoFisher)
Internal Standard
synthetic peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Dionex UltiMate 3000 RSLCnano LC (ThermoFisher)
Column Packing
Acclaim PepMap100 C18, 5um (Trap); Acclaim PepMap RSLC C18, 2um (Analytical)
Column Dimensions
300um x 5mm (Trap); 75um x 25cm (Analytical)
Flow Rate
0.5 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y10 (1+) 4.8 4.8 5.7 4.9 5.3 6.2 6.9 7.2 8.4 15 15 15
y9 (1+) 3.2 4.2 4.9 4.7 4.6 4.7 5.7 6.2 6.8 15 15 15
y8 (1+) 4.6 5.4 6.4 3.9 4.9 5.5 6 7.3 8.4 15 15 15
sum 3.6 4.4 4.9 4.2 4.6 5.3 5.5 6.4 7.2 15 15 15

Additional Resources and Comments

Resources
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Assay Details for non-CPTAC-1082 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Sequence
ATLYALSHAVNNYHK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
440
Peptide End
454
CPTAC ID
non-CPTAC-1082
Peptide Molecular Mass
1,700.8635
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y12 (3+) 5.5 4 4.5 6.9 6 6.5 8.8 7.2 7.9 15 15 15
y13 (3+) 6.7 7.2 4.4 5.4 6.3 4.2 8.6 9.6 6.1 15 15 15
y10 (2+) 8.4 6.2 5.7 9.5 6.4 5.4 12.7 8.9 7.9 15 15 15
y11 (2+) 5.8 6 5.6 8.1 5.9 4.8 10 8.4 7.4 15 15 15
y12 (2+) 6 6.2 3.6 7.8 8.8 5.1 9.8 10.8 6.2 15 15 15
sum 4.2 3.7 3.4 4.9 4.1 2.9 6.5 5.5 4.5 15 15 15

Additional Resources and Comments

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Assay Details for non-CPTAC-1080 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Sequence
FPEVDVLTK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
3791
Peptide End
3799
CPTAC ID
non-CPTAC-1080
Peptide Molecular Mass
1,046.5648
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
b2 (1+) 15.9 4.8 3 8.9 6.3 3.2 18.2 7.9 4.4 9 15 15
y8 (2+) 5.1 4.2 3.2 8.2 4.4 4 9.7 6.1 5.1 15 15 15
y2 (1+) 13.9 3.8 3.6 13.9 6.2 3.3 19.7 7.3 4.9 15 15 15
y7 (1+) 4.5 3.6 3.4 9.5 6.5 3.7 10.5 7.4 5 15 15 15
y8 (1+) 10.2 4.4 3.8 12.6 5.3 5 16.2 6.9 6.3 15 15 15
sum 6.8 3.2 2.5 9.4 4.1 3.3 11.6 5.2 4.1 15 15 15

Additional Resources and Comments

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Assay Details for non-CPTAC-5577 Collapse assay details

Data source: Panorama

Official Gene Symbol
Apob
Peptide Sequence
LSLEDTPK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
286
Peptide End
293
CPTAC ID
non-CPTAC-5577
Peptide Molecular Mass
901.4757
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers

Publication

View Details (opens in a new window)

Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Michaud SA, Sinclair NJ, Petrošová H, Palmer AL, Pistawka AJ, Zhang S, Hardie DB, Mohammed Y Eshghi A1, Richard VR, Sickmann A, Borchers CH. Commun Biol. 2018 Jun 27;1:78. doi: 10.1038/s42003-018-0087-6. eCollection 2018.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>80%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
b2 (1+) 8.4 4.5 4.7 9.6 7.9 4.1 12.8 9.1 6.2 15 15 15
y2 (1+) 6.2 3 6.2 7.6 4.7 5.9 9.8 5.6 8.6 15 15 15
y5 (1+) 8.2 3.4 4.5 8.8 7.2 5.6 12 8 7.2 15 15 15
y6 (1+) 4.1 5.4 4.7 7 6.8 5 8.1 8.7 6.9 15 15 15
y7 (1+) 6.9 5 5.4 7.1 6.5 4.5 9.9 8.2 7 15 15 15
sum 2.6 1.9 1.9 5.1 5.6 3.1 5.7 5.9 3.6 15 15 15

Additional Resources and Comments

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Assay Details for non-CPTAC-1081 Collapse assay details

Data source: Panorama

Official Gene Symbol
APOB
Peptide Sequence
TGISPLALIK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
220
Peptide End
229
CPTAC ID
non-CPTAC-1081
Peptide Molecular Mass
1,011.6328
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6490 Triple Quad (Agilent)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-D

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
b3 (1+) 8.7 2.4 4.8 8.5 3.2 5.1 12.2 4 7 15 15 15
y6 (1+) 5.8 7.7 5.2 11.8 6.9 5.6 13.1 10.3 7.6 15 15 15
y7 (1+) 6.2 5.1 4 9.4 5.8 6.5 11.3 7.7 7.6 15 15 15
sum 4.2 3.2 2.8 8.2 4.4 4.2 9.2 5.4 5 15 15 15

Additional Resources and Comments

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Comments