PEPD, CPTAC-1170 - CPTAC Assay Portal (original) (raw)
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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.
PEPD
Protein Sequence hover to view complete sequence
CPTAC-1170: View additional VPLALFALNR data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MAAATGPSFW | LGNETLKVPL | ALFALNRQRL | CERLRKNPAV | QAGSIVVLQG |
| 60 | 70 | 80 | 90 | 100 |
| GEETQRYCTD | TGVLFRQESF | FHWAFGVTEP | GCYGVIDVDT | GKSTLFVPRL |
| 110 | 120 | 130 | 140 | 150 |
| PASHATWMGK | IHSKEHFKEK | YAVDDVQYVD | EIASVLTSQK | PSVLLTLRGV |
| 160 | 170 | 180 | 190 | 200 |
| NTDSGSVCRE | ASFDGISKFE | VNNTILHPEI | VECRVFKTDM | ELEVLRYTNK |
| 210 | 220 | 230 | 240 | 250 |
| ISSEAHREVM | KAVKVGMKEY | ELESLFEHYC | YSRGGMRHSS | YTCICGSGEN |
| 260 | 270 | 280 | 290 | 300 |
| SAVLHYGHAG | APNDRTIQNG | DMCLFDMGGE | YYCFASDITC | SFPANGKFTA |
| 310 | 320 | 330 | 340 | 350 |
| DQKAVYEAVL | RSSRAVMGAM | KPGVWWPDMH | RLADRIHLEE | LAHMGILSGS |
| 360 | 370 | 380 | 390 | 400 |
| VDAMVQAHLG | AVFMPHGLGH | FLGIDVHDVG | GYPEGVERID | EPGLRSLRTA |
| 410 | 420 | 430 | 440 | 450 |
| RHLQPGMVLT | VEPGIYFIDH | LLDEALADPA | RASFLNREVL | QRFRGFGGVR |
| 460 | 470 | 480 | 490 | 493 |
| IEEDVVVTDS | GIELLTCVPR | TVEEIEACMA | GCDKAFTPFS | GPK |
Data source: UniProt
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-1192 Collapse assay details
Data source: Panorama
Official Gene Symbol
PEPD
Peptide Modified Sequence
FEVNNTILHPEIVEC[+57.0]R
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
183
Peptide - Site of Modification
15
Peptide Start
169
Peptide End
184
CPTAC ID
CPTAC-1192
Peptide Molecular Mass
1,968.9727
Species
Homo sapiens (Human)
Assay Type
Direct MRM or SRM
Matrix
Ovarian cancer tumor tissue lysate
Submitting Laboratory
Pacific Northwest National Laboratory
Submitting Lab PI
Tao Liu
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TSQ Vantage
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Waters nanoACQUITY (Part Number 176016000)
Column Packing
Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions
100 um x 100 mm
Flow Rate
0.5 uL/min
Assay Multiplexing Expand assay panel
Pacific Northwest National Laboratory-DirectMRM
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV
| n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 38.3 | 33.2 | 27.9 | 44.9 | 22.1 | 30.6 | 59 | 39.9 | 41.4 | 15 | 15 | 15 |
| y7 (1+) | 28.3 | 12.6 | 12.1 | 26.1 | 13.8 | 20.2 | 38.5 | 18.7 | 23.5 | 15 | 15 | 15 |
| y8 (1+) | 51.8 | 19.6 | 23.6 | 77.5 | 24.8 | 23.6 | 93.2 | 31.6 | 33.4 | 15 | 15 | 15 |
| sum | 16.2 | 10.1 | 13 | 14.6 | 12.8 | 18.5 | 21.8 | 16.3 | 22.6 | 15 | 15 | 15 |
Selectivity
Data source: Panorama
| Slope of Curve Fit for cell line | ||||||
|---|---|---|---|---|---|---|
| fragment_ion | 1 | 2 | 3 | 4 | 5 | 6 |
| y7 (1+) | 0.64 | 0.56 | 1.42 | 1.37 | 1.19 | 1.72 |
| y8 (1+) | 0.46 | 0.52 | 2.88 | 0.87 | 1.42 | 1.33 |
| y5 (1+) | 0.41 | 0.75 | 2.19 | 1.12 | 1.42 | 2.54 |
| sum | 0.58 | 0.56 | 1.46 | 1.19 | 1.23 | 1.64 |
Stability
Data source: Panorama
| Fragment ion / Transition | control_intra_CV | actual_temp_intra_CV | frozen_intra_CV | FTx1_intra_CV | FTx2_intra_CV |
|---|
| Fragment ion / Transition | all_intra_CV | all_inter_CV |
|---|
Endogenous
Data source: Panorama
| Fragment ion / Transition | intra_CV | inter_CV | total_CV |
|---|---|---|---|
| y5 (1+) | 35.6 | 83.1 | 90.4 |
| y7 (1+) | 44.9 | 93.2 | 103.5 |
| y8 (1+) | 40.7 | 90.6 | 99.3 |
| sum | 37.6 | 87.8 | 95.5 |
Additional Resources and Comments
Comments
Assay Details for CPTAC-1170 Collapse assay details
Data source: Panorama
Official Gene Symbol
PEPD
Peptide Sequence
VPLALFALNR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
18
Peptide End
27
CPTAC ID
CPTAC-1170
Peptide Molecular Mass
1,112.6706
Species
Homo sapiens (Human)
Assay Type
Direct MRM or SRM
Matrix
Ovarian cancer tumor tissue lysate
Submitting Laboratory
Pacific Northwest National Laboratory
Submitting Lab PI
Tao Liu
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
TSQ Vantage
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Waters nanoACQUITY (Part Number 176016000)
Column Packing
Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions
100 um x 100 mm
Flow Rate
0.5 uL/min
Assay Multiplexing Expand assay panel
Pacific Northwest National Laboratory-DirectMRM
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CV | n= | | | | | | | | | |
| ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- |
| Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High |
| y5 (1+) | 7.7 | 7.1 | 5.7 | 10.3 | 10.8 | 6.6 | 12.9 | 12.9 | 8.7 | 15 | 15 | 15 |
| y6 (1+) | 13.7 | 6.4 | 6.8 | 14.3 | 8.5 | 8.1 | 19.8 | 10.6 | 10.6 | 15 | 15 | 15 |
| y7 (1+) | 10.1 | 4.2 | 4.1 | 10.1 | 7.9 | 5.7 | 14.3 | 8.9 | 7 | 15 | 15 | 15 |
| sum | 6.5 | 4.7 | 3.2 | 7.5 | 8.2 | 5.1 | 9.9 | 9.5 | 6 | 15 | 15 | 15 |
Selectivity
Data source: Panorama
| Slope of Curve Fit for cell line | ||||||
|---|---|---|---|---|---|---|
| fragment_ion | 1 | 2 | 3 | 4 | 5 | 6 |
| y6 (1+) | 3.55 | 3.72 | 7.02 | 5.81 | 5.24 | 6.61 |
| y7 (1+) | 3.33 | 3.52 | 7.17 | 5.71 | 5.54 | 6.94 |
| y5 (1+) | 3.23 | 3.56 | 7.49 | 5.36 | 5.2 | 6.49 |
| sum | 3.35 | 3.58 | 7.22 | 5.62 | 5.35 | 6.69 |
Stability
Data source: Panorama
| Fragment ion / Transition | control_intra_CV | actual_temp_intra_CV | frozen_intra_CV | FTx1_intra_CV | FTx2_intra_CV |
|---|---|---|---|---|---|
| y5 (1+) | 5.1 | 4.1 | 5 | 3.1 | 5.8 |
| y6 (1+) | 6.4 | 3.5 | 1.2 | 5.1 | 4.9 |
| y7 (1+) | 5.1 | 3.9 | 0.6 | 1.4 | 4.1 |
| sum | 2.7 | 2.4 | 1.4 | 0.9 | 1.5 |
| Fragment ion / Transition | all_intra_CV | all_inter_CV |
|---|---|---|
| y5 (1+) | 4.5 | 4 |
| y6 (1+) | 4.1 | 4.1 |
| y7 (1+) | 3.2 | 5 |
| sum | 1.9 | 2.3 |
Endogenous
Data source: Panorama
| Fragment ion / Transition | intra_CV | inter_CV | total_CV |
|---|---|---|---|
| y7 (1+) | 38.7 | 44.5 | 59 |
| y6 (1+) | 40.3 | 45.9 | 61.1 |
| y5 (1+) | 38.6 | 43.7 | 58.3 |
| sum | 39 | 44.6 | 59.2 |