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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.

PLOD3

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PLOD3 N/A
Sequence Length (AA) Molecular Weight (Da)
738 84785
Protein Name
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE
60 70 80 90 100
GYLRFLRSAE FFNYTVRTLG LGEEWRGGDV ARTVGGGQKV RWLKKEMEKY
110 120 130 140 150
ADREDMIIMF VDSYDVILAG SPTELLKKFV QSGSRLLFSA ESFCWPEWGL
160 170 180 190 200
AEQYPEVGTG KRFLNSGGFI GFATTIHQIV RQWKYKDDDD DQLFYTRLYL
210 220 230 240 250
DPGLREKLSL NLDHKSRIFQ NLNGALDEVV LKFDRNRVRI RNVAYDTLPI
260 270 280 290 300
VVHGNGPTKL QLNYLGNYVP NGWTPEGGCG FCNQDRRTLP GGQPPPRVFL
310 320 330 340 350
AVFVEQPTPF LPRFLQRLLL LDYPPDRVTL FLHNNEVFHE PHIADSWPQL
360 370 380 390 400
QDHFSAVKLV GPEEALSPGE ARDMAMDLCR QDPECEFYFS LDADAVLTNL
410 420 430 440 450
QTLRILIEEN RKVIAPMLSR HGKLWSNFWG ALSPDEYYAR SEDYVELVQR
460 470 480 490 500
KRVGVWNVPY ISQAYVIRGD TLRMELPQRD VFSGSDTDPD MAFCKSFRDK
510 520 530 540 550
GIFLHLSNQH EFGRLLATSR YDTEHLHPDL WQIFDNPVDW KEQYIHENYS
560 570 580 590 600
RALEGEGIVE QPCPDVYWFP LLSEQMCDEL VAEMEHYGQW SGGRHEDSRL
610 620 630 640 650
AGGYENVPTV DIHMKQVGYE DQWLQLLRTY VGPMTESLFP GYHTKARAVM
660 670 680 690 700
NFVVRYRPDE QPSLRPHHDS STFTLNVALN HKGLDYEGGG CRFLRYDCVI
710 720 730 738
SSPRKGWALL HPGRLTHYHE GLPTTWGTRY IMVSFVDP

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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All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-113 Collapse assay details

Data source: Panorama

Official Gene Symbol
PLOD3
Peptide Sequence
LVGPEEALSPGEAR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
359
Peptide End
372
CPTAC ID
CPTAC-113
Peptide Molecular Mass
1,423.7307
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 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
y12 (1+) 8.2 9.5 9.2 7.1 11.7 7 10.8 15.1 11.6 15 25 15
y8 (1+) 11.2 14.3 10 10.3 14.5 22.6 15.2 20.4 24.7 15 25 15
y7 (1+) 9.3 11 13.9 8.7 10.7 19.5 12.7 15.3 23.9 15 25 15
sum 6.5 9.1 6.7 6.5 10.2 14.5 9.2 13.7 16 15 25 15

Selectivity

Data source: Panorama

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Slope of Curve Fit for cell line
fragment_ion HCC1187 HCC1419 HCC1954 HCC70 MCF12A MDAMB175VII ZR751 ZR7530
y7 (1+) -4.02 -5.65 -1.9 -1.44 -1.61 -5.49 -4.83 -4.93
y12 (1+) -3.94 -7.83 -2.85 -1.9 -1.84 -4.67 -5.24 -5.19
y8 (1+) -4.68 -4.47 -2.22 -1.66 -1.46 -5.29 -5.97 -6.91
sum -4.2 -5.58 -2.22 -1.62 -1.61 -5.16 -5.22 -5.55

Stability

Data source: Panorama

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Fragment ion / Transition control_intra_CV actual_temp_intra_CV frozen_intra_CV FTx1_intra_CV FTx2_intra_CV
y7 (1+) 9.2 8.3 5.8 NA 5.5
y8 (1+) 16.8 19.9 2.1 NA 16
y12 (1+) 5.7 3.2 3.8 NA 6.4
sum 4.1 6.9 2.2 NA 3.8
Fragment ion / Transition all_intra_CV all_inter_CV
y7 (1+) 7.4 6.2
y8 (1+) 14.9 14.4
y12 (1+) 4.4 4
sum 4.8 5.3

Endogenous

Data source: Panorama

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Fragment ion / Transition intra_CV inter_CV total_CV
y7 (1+) 10.6 11.1 15.3
y12 (1+) 9.8 12.2 15.6
y8 (1+) 14.4 14.1 20.2
sum 8.9 10.2 13.5

Additional Resources and Comments

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

Assay Details for CPTAC-114 Collapse assay details

Data source: Panorama

Official Gene Symbol
PLOD3
Peptide Sequence
LWSNFWGALSPDEYYAR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
424
Peptide End
440
CPTAC ID
CPTAC-114
Peptide Molecular Mass
2,073.9585
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / 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
y8 (1+) 53.4 34.3 30.6 69.3 41.6 30.2 87.5 53.9 43 15 15 15
y7 (1+) 39.7 25.2 22.4 43 35.5 27.1 58.5 43.5 35.2 15 15 15
y6 (1+) 75.1 45.1 63.6 89.7 38 71.7 117 59 95.8 15 15 15
sum 26 20.7 21.6 34.6 24.3 22.3 43.3 31.9 31 15 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-1501 Collapse assay details

Data source: Panorama

Official Gene Symbol
PLOD3
Peptide Modified Sequence
EQYIHEN[+1.0]YSR
Modification Type
Deamidated (N)
Protein - Site of Modification
548
Peptide - Site of Modification
7
Peptide Start
542
Peptide End
551
CPTAC ID
CPTAC-1501
Peptide Molecular Mass
1,338.5840
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

view larger image
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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
y6 (2+) 3.7 3.7 3.6 5.3 2.9 4.9 6.5 4.7 6.1 15 15 15
y3 (1+) 6.1 5.5 5.5 4.8 6.5 6.9 7.8 8.5 8.8 15 15 15
y5 (1+) 4 5.1 6 3 5 5.5 5 7.1 8.1 15 15 15
sum 2.1 2.8 2.6 3.1 2.8 2.9 3.7 4 3.9 15 15 15

Additional Resources and Comments

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