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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)
4505 509432
Protein Name
Apolipoprotein B-100
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MGPRKPALRT PLLLLFLLLF LDTSVWAQDE VLENLSFSCP KDATRFKHLR
60 70 80 90 100
KYVYNYEAES SSGVQGTADS RSATKINCKV ELEVPQICGF IMRTNQCTLK
110 120 130 140 150
EVYGFNPEGK ALMKKTKNSE EFAAAMSRYE LKLAIPEGKQ IVLYPDKDEP
160 170 180 190 200
KYILNIKRGI ISALLVPPET EEDQQELFLD TVYGNCSTQV TVNSRKGTVP
210 220 230 240 250
TEMSTERNLQ QCDGFQPIST SVSPLALIKG LVHPLSTLIS SSQTCQYTLD
260 270 280 290 300
PKRKHVSEAV CDEQHLFLPF SYKNKYGIMT RVTQKLSLED TPKINSRFFS
310 320 330 340 350
EGTNRMGLAF ESTKSTSSPK QADAVLKTLQ ELKKLSISEQ NAQRANLFNK
360 370 380 390 400
LVTELRGLTG EAITSLLPQL IEVSSPITLQ ALVQCGQPQC YTHILQWLKT
410 420 430 440 450
EKAHPLLVDI VTYLMALIPN PSTQRLQEIF NTAKEQQSRA TLYALSHAVN
460 470 480 490 500
SYFDVDHSRS PVLQDIAGYL LKQIDNECTG NEDHTFLILR VIGNMGRTME
510 520 530 540 550
QVMPALKSSV LSCVRSTKPS LLIQKAALQA LRKMELEDEV RTILFDTFVN
560 570 580 590 600
GVAPVEKRLA AYLLLMKNPS SSDINKIAQL LQWEQSEQVK NFVASHIANI
610 620 630 640 650
LNSEELYVQD LKVLIKNALE NSQFPTIMDF RKFSRNYQIS KSASLPMFDP
660 670 680 690 700
VSVKIEGNLI FDPSSYLPRE SLLKTTLTVF GLASLDLFEI GLEGKGFEPT
710 720 730 740 750
LEALFGKQGF FPDSVNKALY WVNGRVPDGV SKVLVDHFGY TTDGKHEQDM
760 770 780 790 800
VNGIMPIVDK LIKDLKSKEI PEARAYLRIL GKELSFVRLQ DLQVLGKLLL
810 820 830 840 850
SGAQTLQGIP QMVVQAIREG SKNDLFLHYI FMDNAFELPT GAGLQLQVSS
860 870 880 890 900
SGVFTPGIKA GVRLELANIQ AELVAKPSVS LEFVTNMGII IPDFAKSSVQ
910 920 930 940 950
MNTNFFHESG LEARVALKAG QLKVIIPSPK RPVKLFSGSN TLHLVSTTKT
960 970 980 990 1000
EVIPPLVENR QSWSTCKPLF TGMNYCTTGA YSNASSTESA SYYPLTGDTR
1010 1020 1030 1040 1050
YELELRPTGE VEQYSATATY ELLKEDKSLV DTLKFLVQAE GVQQSEATVL
1060 1070 1080 1090 1100
FKYNRRSRTL SSEVLIPGFD VNFGTILRVN DESAKDKNTY KLILDIQNKK
1110 1120 1130 1140 1150
ITEVSLVGHL SYDKKGDGKI KGVVSIPRLQ AEARSEVHTH WSSTKLLFQM
1160 1170 1180 1190 1200
DSSATAYGST ISKRVTWRYD NEIIEFDWNT GTNVDTKKVA SNFPVDLSHY
1210 1220 1230 1240 1250
PRMLHEYANG LLDHRVPQTD VTFRDMGSKL IVATNTWLQM ATRGLPYPQT
1260 1270 1280 1290 1300
LQDHLNSLSE LNLLKMGLSD FHIPDNLFLK TDGRVKYTMN RNKINIDIPL
1310 1320 1330 1340 1350
PLGGKSSKDL KMPESVRTPA LNFKSVGFHL PSREVQVPTF TIPKTHQLQV
1360 1370 1380 1390 1400
PLLGVLDLST NVYSNLYNWS ASYTGGNTSR DHFSLQAQYR MKTDSVVDLF
1410 1420 1430 1440 1450
SYSVQGSGET TYDSKNTFTL SCDGSLHHKF LDSKFKVSHV EKFGNSPVSK
1460 1470 1480 1490 1500
GLLTFETSSA LGPQMSATVH LDSKKKQHLY VKDIKVDGQF RASSFYAQGK
1510 1520 1530 1540 1550
YGLSCERDVT TGQLSGESNM RFNSTYFQGT NQIVGMYQDG ALSITSTSDL
1560 1570 1580 1590 1600
QDGIFKNTAS LKYENYELTL KSDSSGQYEN FAASNKLDVT FSTQSALLRS
1610 1620 1630 1640 1650
EHQANYKSLR LVTLLSGSLT SQGVELNADI LGTDKINTGA HKATLKIARD
1660 1670 1680 1690 1700
GLSTSATTNL KYSPLLLENE LNAELGLSGA SMKLSTNGRF KEHHAKFSLD
1710 1720 1730 1740 1750
GRAALTEVSL GSIYQAMILG ADSKNIFNFK LSREGLRLSN DLMGSYAEMK
1760 1770 1780 1790 1800
LDHTHSLNIA GLSLDFFSKM DNIYSGDKFY KQNFNLQLQP YSFITTLSND
1810 1820 1830 1840 1850
LRYGALDLTN NGRFRLEPLK LNVGGNFKGT YQNNELKHIY TISYTDLVVA
1860 1870 1880 1890 1900
SYRADTVAKV QGVEFSHRLN ADIEGLTSSV DVTTSYNSDP LHFNNVFHFS
1910 1920 1930 1940 1950
LAPFTLGIDT HTSGDGKLSF WGEHTGQLYS KFLLKAEPLA LIVSHDYKGS
1960 1970 1980 1990 2000
TSHSLPYESS ISTALEHTVS ALLTPAEQTS TWKFKTKLND KVYSQDFEAY
2010 2020 2030 2040 2050
NTKDKIGVEL SGRADLSGLY SPIKLPFFYS EPVNVLNGLE VNDAVDKPQE
2060 2070 2080 2090 2100
FTIIAVVKYD KNQDVHTINL PFFKSLPDYL ERNRRGMISL LEAMRGELQR
2110 2120 2130 2140 2150
LSVDQFVRKY RAALSRLPQQ IHHYLNASDW ERQVAGAKEK ITSFMENYRI
2160 2170 2180 2190 2200
TDNDVLIAID SAKINFNEKL SQLETYAIQF DQYIKDNYDP HDLKRTIAEI
2210 2220 2230 2240 2250
IDRIIEKLKI LDEQYHIRVN LAKSIHNLYL FVENVDLNQV SSSNTSWIQN
2260 2270 2280 2290 2300
VDSNYQVRIQ IQEKLQQLRT QIQNIDIQQL AAEVKRQMDA IDVTMHLDQL
2310 2320 2330 2340 2350
RTAILFQRIS DIIDRVKYFV MNLIEDFKVT EKINTFRVIV RELIEKYEVD
2360 2370 2380 2390 2400
QHIQVLMDKS VELAHRYSLS EPLQKLSNVL QRIEIKDYYE KLVGFIDDTV
2410 2420 2430 2440 2450
EWLKALSFKN TIEELNRLTD MLVKKLKAFD YHQFVDKTNS KIREMTQRIN
2460 2470 2480 2490 2500
AEIQALKLPQ KMEALKLLVE DFKTTVSNSL ERLKDTKVTV VIDWLQDILT
2510 2520 2530 2540 2550
QMKDHFQDTL EDVRDRIYQM DIQRELEHFL SLVNQVYSTL VTYMSDWWTL
2560 2570 2580 2590 2600
TAKNITDFAE QYSIQNWAES IKVLVEQGFI VPEMQTFLWT MPAFEVSLRA
2610 2620 2630 2640 2650
LQEGNFQTPV FIVPLTDLRI PSIRINFKML KNIKIPLRFS TPEFTLLNTF
2660 2670 2680 2690 2700
HVHSFTIDLL EIKAKIIRTI DQILSSELQW PLPEMYLRDL DVVNIPLARL
2710 2720 2730 2740 2750
TLPDFHVPEI TIPEFTIPNV NLKDLHVPDL HIPEFQLPHL SHTIEIPAFG
2760 2770 2780 2790 2800
KLHSILKIQS PLFILDANAN IQNVTTSGNK AEIVASVTAK GESQFEALNF
2810 2820 2830 2840 2850
DFQAQAQFLE LNPHPPVLKE SMNFSSKHVR MEHEGEIVFD GKAIEGKSDT
2860 2870 2880 2890 2900
VASLHTEKNE VEFNNGMTVK VNNQLTLDSH TKYFHKLSVP RLDFSSKASL
2910 2920 2930 2940 2950
NNEIKTLLEA GHVALTSSGT GSWNWACPNF SDEGIHSSQI SFTVDGPIAF
2960 2970 2980 2990 3000
VGLSNNINGK HLRVIQKLTY ESGFLNYSKF EVESKVESQH VGSSILTANG
3010 3020 3030 3040 3050
RALLKDAKAE MTGEHNANLN GKVIGTLKNS LFFSAQPFEI TASTNNEGNL
3060 3070 3080 3090 3100
KVGFPLKLTG KIDFLNNYAL FLSPRAQQAS WQASTRFNQY KYNQNFSAIN
3110 3120 3130 3140 3150
NEHNIEASIG MNGDANLDFL NIPLTIPEIN LPYTEFKTPL LKDFSIWEET
3160 3170 3180 3190 3200
GLKEFLKTTK QSFDLSVKAQ YKKNSDKHSI VVPLGMFYEF ILNNVNSWDR
3210 3220 3230 3240 3250
KFEKVRNNAL HFLTTSYNEA KIKVDKYKTE NSLNQPSGTF QNHGYTIPVV
3260 3270 3280 3290 3300
NIEVSPFAVE TLASSHVIPT AISTPSVTIP GPNIMVPSYK LVLPPLELPV
3310 3320 3330 3340 3350
FHGPGNLFKF FLPDFKGFNT IDNIYIPAMG NFTYDFSFKS SVITLNTNAG
3360 3370 3380 3390 3400
LYNQSDIVAH FLSSSSFVTD ALQYKLEGTS RLMRKRGLKL ATAVSLTNKF
3410 3420 3430 3440 3450
VKGSHDSTIS LTKKNMEASV RTTANLHAPI FSMNFKQELN GNTKSKPTVS
3460 3470 3480 3490 3500
SSIELNYDFN SSKLHSTATG GIDHKFSLES LTSYFSIESF TKGNIKSSFL
3510 3520 3530 3540 3550
SQEYSGSVAN EANVYLNSKG TRSSVRLQGA SKVDGIWNVE VGENFAGEAT
3560 3570 3580 3590 3600
LQRIYTTWEH NMKNHLQVYS YFFTKGKQTC RATLELSPWT MSTLLQVHVS
3610 3620 3630 3640 3650
QLSSLLDLHH FDQEVILKAN TKNQKISWKG GVQVESRVLQ HNAQFSNDQE
3660 3670 3680 3690 3700
EIRLDLAGSL DGQLWDLEAI FLPVYGKSLQ ELLQMDGKRQ YLQASTSLLY
3710 3720 3730 3740 3750
TKNPNGYLLS LPVQELADRF IIPGIKLNDF SGVKIYKKLS TSPFALNLTM
3760 3770 3780 3790 3800
LPKVKFPGID LLTQYSTPEG SSVPIFEATI PEIHLTVSQF TLPKSLPVGN
3810 3820 3830 3840 3850
TVFDLNKLAN MIADVDLPSV TLPEQTIVIP PLEFSVPAGI FIPFFGELTA
3860 3870 3880 3890 3900
RAGMASPLYN VTWSAGWKTK ADHVETFLDS MCTSTLQFLE YALKVVETHK
3910 3920 3930 3940 3950
IEEDLLTYNI KGTLQHCDFN VEYNEDGLFK GLWDWQGEAH LDITSPALTD
3960 3970 3980 3990 4000
FHLYYKEDKT SLSASAASST IGTVGLDSST DDQSVELNVY FHPQSPPEKK
4010 4020 4030 4040 4050
LSIFKTEWRY KESDGERYIK INWEEEAASR LLGSLKSNVP KASKAIYDYA
4060 4070 4080 4090 4100
NKYHLEYVSS ELRKSLQVNA EHARRMVDEM NMSFQRVARD TYQNLYEEML
4110 4120 4130 4140 4150
AQKSLSIPEN LKKRVLDSIV HVTQKYHMAV MWLMDSFIHF LKFNRVQFPG
4160 4170 4180 4190 4200
YAGTYTVDEL YTIVMKETKK SLSQLFNGLG NLLSYVQNQV EKSRLINDIT
4210 4220 4230 4240 4250
FKCPFFSKPC KLKDLILIFR EELNILSNIG QQDIKFTTIL SSLQGFLERV
4260 4270 4280 4290 4300
LDIIEEQIKC LKDNESTCVA DHINMVFKIQ VPYAFKSLRE DIYFVLGEFN
4310 4320 4330 4340 4350
DFLQSILQEG SYKLQQVHQY MKALREEYFD PSMVGWTVKY YEIEENMVEL
4360 4370 4380 4390 4400
IKTLLVSFRD VYSEYSVTAA DFASKMSTQV EQFVSRDIRE YLSMLTDING
4410 4420 4430 4440 4450
KWMEKIAELS IVAKETMKSW VTAVAKIMSD YPQQFHSNLQ DFSDQLSSYY
4460 4470 4480 4490 4500
EKFVGESTRL IDLSIQNYHV FLRYITELLR KLQVATANNV SPYIKLAQGE
4505
LMITF

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

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

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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

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

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
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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

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

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

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

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
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

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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

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

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

Resources
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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

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

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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

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

Resources
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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

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

Resources
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Comments