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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.

ATM

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
ATM N/A
Sequence Length (AA) Molecular Weight (Da)
3056 350687
Protein Name
Serine-protein kinase ATM
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK
60 70 80 90 100
QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQASR QKKMQEISSL
110 120 130 140 150
VKYFIKCANR RAPRLKCQEL LNYIMDTVKD SSNGAIYGAD CSNILLKDIL
160 170 180 190 200
SVRKYWCEIS QQQWLELFSV YFRLYLKPSQ DVHRVLVARI IHAVTKGCCS
210 220 230 240 250
QTDGLNSKFL DFFSKAIQCA RQEKSSSGLN HILAALTIFL KTLAVNFRIR
260 270 280 290 300
VCELGDEILP TLLYIWTQHR LNDSLKEVII ELFQLQIYIH HPKGAKTQEK
310 320 330 340 350
GAYESTKWRS ILYNLYDLLV NEISHIGSRG KYSSGFRNIA VKENLIELMA
360 370 380 390 400
DICHQVFNED TRSLEISQSY TTTQRESSDY SVPCKRKKIE LGWEVIKDHL
410 420 430 440 450
QKSQNDFDLV PWLQIATQLI SKYPASLPNC ELSPLLMILS QLLPQQRHGE
460 470 480 490 500
RTPYVLRCLT EVALCQDKRS NLESSQKSDL LKLWNKIWCI TFRGISSEQI
510 520 530 540 550
QAENFGLLGA IIQGSLVEVD REFWKLFTGS ACRPSCPAVC CLTLALTTSI
560 570 580 590 600
VPGTVKMGIE QNMCEVNRSF SLKESIMKWL LFYQLEGDLE NSTEVPPILH
610 620 630 640 650
SNFPHLVLEK ILVSLTMKNC KAAMNFFQSV PECEHHQKDK EELSFSEVEE
660 670 680 690 700
LFLQTTFDKM DFLTIVRECG IEKHQSSIGF SVHQNLKESL DRCLLGLSEQ
710 720 730 740 750
LLNNYSSEIT NSETLVRCSR LLVGVLGCYC YMGVIAEEEA YKSELFQKAK
760 770 780 790 800
SLMQCAGESI TLFKNKTNEE FRIGSLRNMM QLCTRCLSNC TKKSPNKIAS
810 820 830 840 850
GFFLRLLTSK LMNDIADICK SLASFIKKPF DRGEVESMED DTNGNLMEVE
860 870 880 890 900
DQSSMNLFND YPDSSVSDAN EPGESQSTIG AINPLAEEYL SKQDLLFLDM
910 920 930 940 950
LKFLCLCVTT AQTNTVSFRA ADIRRKLLML IDSSTLEPTK SLHLHMYLML
960 970 980 990 1000
LKELPGEEYP LPMEDVLELL KPLSNVCSLY RRDQDVCKTI LNHVLHVVKN
1010 1020 1030 1040 1050
LGQSNMDSEN TRDAQGQFLT VIGAFWHLTK ERKYIFSVRM ALVNCLKTLL
1060 1070 1080 1090 1100
EADPYSKWAI LNVMGKDFPV NEVFTQFLAD NHHQVRMLAA ESINRLFQDT
1110 1120 1130 1140 1150
KGDSSRLLKA LPLKLQQTAF ENAYLKAQEG MREMSHSAEN PETLDEIYNR
1160 1170 1180 1190 1200
KSVLLTLIAV VLSCSPICEK QALFALCKSV KENGLEPHLV KKVLEKVSET
1210 1220 1230 1240 1250
FGYRRLEDFM ASHLDYLVLE WLNLQDTEYN LSSFPFILLN YTNIEDFYRS
1260 1270 1280 1290 1300
CYKVLIPHLV IRSHFDEVKS IANQIQEDWK SLLTDCFPKI LVNILPYFAY
1310 1320 1330 1340 1350
EGTRDSGMAQ QRETATKVYD MLKSENLLGK QIDHLFISNL PEIVVELLMT
1360 1370 1380 1390 1400
LHEPANSSAS QSTDLCDFSG DLDPAPNPPH FPSHVIKATF AYISNCHKTK
1410 1420 1430 1440 1450
LKSILEILSK SPDSYQKILL AICEQAAETN NVYKKHRILK IYHLFVSLLL
1460 1470 1480 1490 1500
KDIKSGLGGA WAFVLRDVIY TLIHYINQRP SCIMDVSLRS FSLCCDLLSQ
1510 1520 1530 1540 1550
VCQTAVTYCK DALENHLHVI VGTLIPLVYE QVEVQKQVLD LLKYLVIDNK
1560 1570 1580 1590 1600
DNENLYITIK LLDPFPDHVV FKDLRITQQK IKYSRGPFSL LEEINHFLSV
1610 1620 1630 1640 1650
SVYDALPLTR LEGLKDLRRQ LELHKDQMVD IMRASQDNPQ DGIMVKLVVN
1660 1670 1680 1690 1700
LLQLSKMAIN HTGEKEVLEA VGSCLGEVGP IDFSTIAIQH SKDASYTKAL
1710 1720 1730 1740 1750
KLFEDKELQW TFIMLTYLNN TLVEDCVKVR SAAVTCLKNI LATKTGHSFW
1760 1770 1780 1790 1800
EIYKMTTDPM LAYLQPFRTS RKKFLEVPRF DKENPFEGLD DINLWIPLSE
1810 1820 1830 1840 1850
NHDIWIKTLT CAFLDSGGTK CEILQLLKPM CEVKTDFCQT VLPYLIHDIL
1860 1870 1880 1890 1900
LQDTNESWRN LLSTHVQGFF TSCLRHFSQT SRSTTPANLD SESEHFFRCC
1910 1920 1930 1940 1950
LDKKSQRTML AVVDYMRRQK RPSSGTIFND AFWLDLNYLE VAKVAQSCAA
1960 1970 1980 1990 2000
HFTALLYAEI YADKKSMDDQ EKRSLAFEEG SQSTTISSLS EKSKEETGIS
2010 2020 2030 2040 2050
LQDLLLEIYR SIGEPDSLYG CGGGKMLQPI TRLRTYEHEA MWGKALVTYD
2060 2070 2080 2090 2100
LETAIPSSTR QAGIIQALQN LGLCHILSVY LKGLDYENKD WCPELEELHY
2110 2120 2130 2140 2150
QAAWRNMQWD HCTSVSKEVE GTSYHESLYN ALQSLRDREF STFYESLKYA
2160 2170 2180 2190 2200
RVKEVEEMCK RSLESVYSLY PTLSRLQAIG ELESIGELFS RSVTHRQLSE
2210 2220 2230 2240 2250
VYIKWQKHSQ LLKDSDFSFQ EPIMALRTVI LEILMEKEMD NSQRECIKDI
2260 2270 2280 2290 2300
LTKHLVELSI LARTFKNTQL PERAIFQIKQ YNSVSCGVSE WQLEEAQVFW
2310 2320 2330 2340 2350
AKKEQSLALS ILKQMIKKLD ASCAANNPSL KLTYTECLRV CGNWLAETCL
2360 2370 2380 2390 2400
ENPAVIMQTY LEKAVEVAGN YDGESSDELR NGKMKAFLSL ARFSDTQYQR
2410 2420 2430 2440 2450
IENYMKSSEF ENKQALLKRA KEEVGLLREH KIQTNRYTVK VQRELELDEL
2460 2470 2480 2490 2500
ALRALKEDRK RFLCKAVENY INCLLSGEEH DMWVFRLCSL WLENSGVSEV
2510 2520 2530 2540 2550
NGMMKRDGMK IPTYKFLPLM YQLAARMGTK MMGGLGFHEV LNNLISRISM
2560 2570 2580 2590 2600
DHPHHTLFII LALANANRDE FLTKPEVARR SRITKNVPKQ SSQLDEDRTE
2610 2620 2630 2640 2650
AANRIICTIR SRRPQMVRSV EALCDAYIIL ANLDATQWKT QRKGINIPAD
2660 2670 2680 2690 2700
QPITKLKNLE DVVVPTMEIK VDHTGEYGNL VTIQSFKAEF RLAGGVNLPK
2710 2720 2730 2740 2750
IIDCVGSDGK ERRQLVKGRD DLRQDAVMQQ VFQMCNTLLQ RNTETRKRKL
2760 2770 2780 2790 2800
TICTYKVVPL SQRSGVLEWC TGTVPIGEFL VNNEDGAHKR YRPNDFSAFQ
2810 2820 2830 2840 2850
CQKKMMEVQK KSFEEKYEVF MDVCQNFQPV FRYFCMEKFL DPAIWFEKRL
2860 2870 2880 2890 2900
AYTRSVATSS IVGYILGLGD RHVQNILINE QSAELVHIDL GVAFEQGKIL
2910 2920 2930 2940 2950
PTPETVPFRL TRDIVDGMGI TGVEGVFRRC CEKTMEVMRN SQETLLTIVE
2960 2970 2980 2990 3000
VLLYDPLFDW TMNPLKALYL QQRPEDETEL HPTLNADDQE CKRNLSDIDQ
3010 3020 3030 3040 3050
SFNKVAERVL MRLQEKLKGV EEGTVLSVGG QVNLLIQQAI DPKNLSRLFP
3056
GWKAWV

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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to view detailed assay information below
All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-913 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
NLS[+80.0]DIDQSFNK
Modification Type
Phospho (ST)
Protein - Site of Modification
2996
Peptide - Site of Modification
3
Peptide Start
2994
Peptide End
3004
CPTAC ID
CPTAC-913
Peptide Molecular Mass
1,359.5708
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTrap 5500 (Sciex)
Internal Standard
Peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
nanoLC-2D (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
75 µm x 15cm
Flow Rate
300 nL/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
y5 (1+) 30.8 15.8 14 53.4 15.1 24 61.6 21.9 27.8 15 24 15
y6 (1+) 31.6 9.8 5.3 23.7 9.8 7.2 39.5 13.9 8.9 15 24 15
y9 (1+) 33.1 9.8 7.5 23.8 10.9 11.8 40.8 14.7 14 15 24 15
sum 21.9 10.2 7.2 21.7 10.4 11.5 30.8 14.6 13.6 15 24 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-3212 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Sequence
NLSDIDQSFNK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
2994
Peptide End
3004
CPTAC ID
CPTAC-3212
Peptide Molecular Mass
1,279.6044
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 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
y4 (1+) 19.8 9.7 13.2 86.1 15 12.9 88.3 17.9 18.5 15 15 15
y5 (1+) 26.4 13.9 14.8 75.1 17.6 16.7 79.6 22.4 22.3 15 15 15
y6 (1+) 8.9 8.9 12.8 11 11.1 13.8 14.1 14.2 18.8 15 15 15
y9 (1+) 11.8 7.1 11.1 14 12 12 18.3 13.9 16.3 15 15 15
y7 (1+) 16.9 15.9 11.4 24 15.6 11.7 29.4 22.3 16.3 15 15 15
y8 (1+) 12.6 10.5 9.8 16 16.5 10 20.4 19.6 14 15 15 15
sum 7.5 5.3 9.2 21 10.3 8.8 22.3 11.6 12.7 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-3213 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
NLS[+80.0]DIDQSFNK
Modification Type
Phospho (ST)
Protein - Site of Modification
2996
Peptide - Site of Modification
3
Peptide Start
2994
Peptide End
3004
CPTAC ID
CPTAC-3213
Peptide Molecular Mass
1,359.5708
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

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view larger image

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
y9-98 (1+) 31.9 9.2 10.5 40.5 18 11.3 51.6 20.2 15.4 15 15 15
y9 (1+) 39.6 14 17.5 51.8 16.2 21.8 65.2 21.4 28 15 15 15
y6 (1+) 19.2 12.6 11.8 50.8 17 17.1 54.3 21.2 20.8 15 15 15
y8 (1+) 27.9 12.3 13.1 59.3 25.9 16.3 65.5 28.7 20.9 15 15 15
y7 (1+) 41.5 23.5 24 96 29.8 32.6 104.6 38 40.5 15 15 15
sum 20.5 6.6 7.4 40.9 10.1 12.1 45.7 12.1 14.2 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
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View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-5978 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Sequence
NLSDIDQSFNK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
2994
Peptide End
3004
CPTAC ID
CPTAC-5978
Peptide Molecular Mass
1,279.6044
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 µL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
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view larger image

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
y9 (1+) 41.4 5.7 9.9 75.8 94.1 80.5 86.4 94.3 81.1 13 25 14
y8 (1+) 48.4 9.8 10.3 74.8 92 77.3 89.1 92.5 78 13 25 14
y6 (1+) 38.7 6 9.7 68.7 89.2 77.7 78.9 89.4 78.3 13 25 14
y5 (1+) 48.4 9.9 9.7 63.9 89.2 77 80.2 89.7 77.6 13 25 14
y4 (1+) 30.4 11.2 9.7 59 89.4 77.9 66.4 90.1 78.5 13 25 14
sum 38.5 5.5 9.7 71 92 78.6 80.8 92.2 79.2 13 25 14

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-5979 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
NLS[+79.966331]DIDQSFNK
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
2994
Peptide End
3004
CPTAC ID
CPTAC-5979
Peptide Molecular Mass
1,359.5708
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 µL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

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
y9-98 (1+) 48.8 11.6 11.8 68.7 96.3 81.8 84.3 97 82.6 13 25 14
y8 (1+) 58.6 12.3 14.7 77.1 93.9 82.8 96.8 94.7 84.1 13 25 14
y7 (1+) 46.8 12.9 15.5 74.2 93.2 83.1 87.7 94.1 84.5 13 25 14
y9 (1+) 51.8 12.5 16.1 82.4 97.3 83.1 97.3 98.1 84.6 13 25 14
sum 45.9 8.7 13.2 75.4 95.4 82.5 88.3 95.8 83.5 13 25 14

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-912 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
SLEIS[+80.0]QSYTTTQR
Modification Type
Phospho (ST)
Protein - Site of Modification
367
Peptide - Site of Modification
5
Peptide Start
363
Peptide End
375
CPTAC ID
CPTAC-912
Peptide Molecular Mass
1,592.7083
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTrap 5500 (Sciex)
Internal Standard
Peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
nanoLC-2D (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
75 µm x 15cm
Flow Rate
300 nL/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

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
y6 (1+) 46.1 33.2 35.8 48.7 25.8 59.5 67.1 42 69.4 13 23 15
y7 (1+) 36.2 11.6 13.6 35.9 14.4 12 51 18.5 18.1 13 23 15
y9 (1+) 28.8 24.6 18.2 39.7 23.5 21.8 49 34 28.4 13 23 15
sum 26.5 11.2 9.1 26.2 11.9 16.1 37.3 16.3 18.5 13 23 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments

Assay Details for CPTAC-3210 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Sequence
SLEISQSYTTTQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
363
Peptide End
375
CPTAC ID
CPTAC-3210
Peptide Molecular Mass
1,512.7420
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 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

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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
y4 (1+) 35.7 12.6 16.5 36.2 12 12.9 50.8 17.4 20.9 15 15 15
y5 (1+) 28.1 10.6 12.3 28.2 11.6 16.8 39.8 15.7 20.8 15 15 15
y6 (1+) 32.4 10.7 15.8 28.4 14 14.8 43.1 17.6 21.6 15 15 15
y7 (1+) 25.8 13.4 8.9 37.2 10.2 9.8 45.3 16.8 13.2 15 15 15
y8 (1+) 24.1 10.4 7.8 29 13.2 14.1 37.7 16.8 16.1 15 15 15
y9 (1+) 16.4 10.9 10.3 15.6 13.6 5.6 22.6 17.4 11.7 15 15 15
y10 (1+) 36.8 13.1 14.4 29.8 12.7 17.7 47.4 18.2 22.8 15 15 15
sum 13.7 5.1 5.9 17.7 6.3 7.2 22.4 8.1 9.3 15 15 15

Additional Resources and Comments

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Assay Details for CPTAC-3211 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
SLEIS[+80.0]QSYTTTQR
Modification Type
Phospho (ST)
Protein - Site of Modification
367
Peptide - Site of Modification
5
Peptide Start
363
Peptide End
375
CPTAC ID
CPTAC-3211
Peptide Molecular Mass
1,592.7083
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 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

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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
y9 (1+) 59.3 15.2 12.7 66.3 17 15.8 89 22.8 20.3 15 15 15
y10-98 (2+) 19.6 18.6 11.4 25.4 20 22.7 32.1 27.3 25.4 15 15 15
y7 (1+) 26.1 13.8 13.7 21.4 11.4 16.5 33.8 17.9 21.4 15 15 15
y6 (1+) 47.3 10.9 19.5 56 12.1 20.2 73.3 16.3 28.1 15 15 15
y11-98 (2+) 31 25.6 27.6 41.3 27.6 28.9 51.6 37.6 40 15 15 15
y5 (1+) 42 19 19.5 50.9 20 16.3 66 27.6 25.4 15 15 15
y4 (1+) 56.2 12.1 17.7 70.8 18 16.8 90.4 21.7 24.4 15 15 15
sum 14.2 5.7 10.8 20.2 7.7 10.7 24.7 9.6 15.2 15 15 15

Additional Resources and Comments

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Assay Details for CPTAC-5976 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Sequence
SLEISQSYTTTQR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
363
Peptide End
375
CPTAC ID
CPTAC-5976
Peptide Molecular Mass
1,512.7420
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 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
y8 (1+) 12.8 8.6 3.3 17.5 11.7 9.7 21.7 14.5 10.2 13 25 14
y9 (1+) 10.6 4.7 3.3 14.3 13.7 12.8 17.8 14.5 13.2 13 25 14
y10 (1+) 12.3 8.6 6 9.3 15.2 13.6 15.4 17.5 14.9 13 25 14
y4 (1+) 14.5 7.7 4.7 16.6 14.8 16.8 22 16.7 17.4 13 25 14
y5 (1+) 8.7 7.1 4.5 14.7 13.6 12.8 17.1 15.3 13.6 13 25 14
y7 (1+) 9.4 7 3.5 11.5 15.1 10.9 14.9 16.6 11.4 13 25 14
y6 (1+) 13.2 7.8 4.6 12.8 13.5 13.4 18.4 15.6 14.2 13 25 14
sum 9.2 5.2 2.8 11.8 13.4 12.2 15 14.4 12.5 13 25 14

Additional Resources and Comments

Resources
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Assay Details for CPTAC-5977 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
SLEIS[+79.966331]QSYTTTQR
Modification Type
Phospho (ST)
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
363
Peptide End
375
CPTAC ID
CPTAC-5977
Peptide Molecular Mass
1,592.7083
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 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
y5 (1+) 16.4 10.3 5.5 16.7 19.6 16.4 23.4 22.1 17.3 13 25 14
y6 (1+) 6.9 8.7 6.8 15.3 20.1 14.8 16.8 21.9 16.3 13 25 14
y7 (1+) 12.4 9.6 4.9 21.6 21.7 16.1 24.9 23.7 16.8 13 25 14
y9 (1+) 18.9 12.5 6.7 17.8 22.4 13.5 26 25.7 15.1 13 25 14
y11-98 (2+) 14.5 13.6 11.8 24.5 19.8 15.5 28.5 24 19.5 13 25 14
y10-98 (2+) 7.2 9.5 5.5 17.2 18 17.5 18.6 20.4 18.3 13 25 14
sum 9.1 6.2 2.7 14.3 18.8 14.1 16.9 19.8 14.4 13 25 14

Additional Resources and Comments

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Assay Details for CPTAC-2876 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Modified Sequence
LDASC[+57.0]AANNPSLK
Modification Type
Carbamidomethyl (C)
Protein - Site of Modification
2324
Peptide - Site of Modification
5
Peptide Start
2319
Peptide End
2331
CPTAC ID
CPTAC-2876
Peptide Molecular Mass
1,359.6453
Species
Homo Sapiens
Assay Type
Direct ImmunoMRM
Matrix
Tumor Digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
ThermoFisher, Q-Exactive
Internal Standard
25 fmol on column
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Easy-nLC 1000 Thermo Scientific
Column Packing
C18
Column Dimensions
75 µm x 50 cm
Flow Rate
300 nL/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
y8 (1+) 6.2 4.5 2.4 6.8 4.8 3.2 9.2 6.6 4 15 15 15
y7 (1+) 4.7 4.6 3.7 5 4.9 4.1 6.9 6.7 5.5 15 15 15
y4 (1+) 5.8 2.9 2.1 6.5 3.3 2.9 8.7 4.4 3.6 15 15 15
sum 5.2 3.8 2.3 5.4 4 2.9 7.5 5.5 3.7 15 15 15

Additional Resources and Comments

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Assay Details for CPTAC-2875 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Sequence
LQQTAFENAYLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1115
Peptide End
1126
CPTAC ID
CPTAC-2875
Peptide Molecular Mass
1,424.7300
Species
Homo Sapiens
Assay Type
Direct ImmunoMRM
Matrix
Tumor Digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
ThermoFisher, Q-Exactive
Internal Standard
25 fmol on column
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Easy-nLC 1000 Thermo Scientific
Column Packing
C18
Column Dimensions
75 µm x 50 cm
Flow Rate
300 nL/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
y9 (1+) 4.7 5.5 5.4 6 5.5 5.6 7.6 7.8 7.8 15 15 15
y7 (1+) 6 3.2 3.9 8.1 5.2 3.9 10.1 6.1 5.5 15 15 15
y10 (1+) 5.9 4.4 5.5 9.3 5.1 7.8 11 6.7 9.5 15 15 15
sum 5 4.1 4.6 7 4.9 5.5 8.6 6.4 7.2 15 15 15

Additional Resources and Comments

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Assay Details for CPTAC-2874 Collapse assay details

Data source: Panorama

Official Gene Symbol
ATM
Peptide Sequence
QDLLFLDMLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
893
Peptide End
902
CPTAC ID
CPTAC-2874
Peptide Molecular Mass
1,234.6631
Species
Homo Sapiens
Assay Type
Direct ImmunoMRM
Matrix
Tumor Digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
ThermoFisher, Q-Exactive
Internal Standard
25 fmol on column
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Easy-nLC 1000 Thermo Scientific
Column Packing
C18
Column Dimensions
75 µm x 50 cm
Flow Rate
300 nL/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
y3 (1+) 5.7 7 5 10.1 11.4 12.7 11.6 13.4 13.6 15 15 15
y6 (1+) 6.5 8.3 6 10.6 14 15.5 12.4 16.3 16.6 15 15 15
y4 (1+) 6.7 7.5 5.8 11.5 12.5 13.8 13.3 14.6 15 15 15 15
sum 5.8 7.8 5.7 10.4 13.1 14.5 11.9 15.2 15.6 15 15 15

Additional Resources and Comments

Resources
Download SOPs
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