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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.

Overview Data source: UniProt

Official Gene Symbol Other Aliases
Ctsd N/A
Sequence Length (AA) Molecular Weight (Da)
410 44954
Protein Name
Cathepsin D
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MKTPGVLLLI LGLLASSSFA IIRIPLRKFT SIRRTMTEVG GSVEDLILKG
60 70 80 90 100
PITKYSMQSS PKTTEPVSEL LKNYLDAQYY GDIGIGTPPQ CFTVVFDTGS
110 120 130 140 150
SNLWVPSIHC KILDIACWVH HKYNSDKSST YVKNGTSFDI HYGSGSLSGY
160 170 180 190 200
LSQDTVSVPC KSDQSKARGI KVEKQIFGEA TKQPGIVFVA AKFDGILGMG
210 220 230 240 250
YPHISVNNVL PVFDNLMQQK LVDKNIFSFY LNRDPEGQPG GELMLGGTDS
260 270 280 290 300
KYYHGELSYL NVTRKAYWQV HMDQLEVGNE LTLCKGGCEA IVDTGTSLLV
310 320 330 340 350
GPVEEVKELQ KAIGAVPLIQ GEYMIPCEKV SSLPTVYLKL GGKNYELHPD
360 370 380 390 400
KYILKVSQGG KTICLSGFMG MDIPPPSGPL WILGDVFIGS YYTVFDRDNN
410
RVGFANAVVL

Data source: UniProt


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-658 Collapse assay details

Data source: Panorama

Official Gene Symbol
CTSD
Peptide Modified Sequence
GSLSYLN[+1.0]VTR
Modification Type
Deamidated (NQ)
Protein - Site of Modification
263
Peptide - Site of Modification
7
Peptide Start
257
Peptide End
266
CPTAC ID
CPTAC-658
Peptide Molecular Mass
1,109.5717
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


Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

  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+) 5.7 7.1 5.9 6.9 6.7 7.8 8.9 9.8 9.8 15 15 15
y6 (1+) 8.3 8 5.7 9.7 7 7.6 12.8 10.6 9.5 15 15 15
y5 (1+) 6.6 7.1 10.1 9.1 7.8 11.4 11.2 10.5 15.2 15 15 15
sum 3.2 6.1 1.7 6.3 4.7 5.8 7.1 7.7 6 15 15 15


Additional Resources and Comments


Assay Details for CPTAC-487 Collapse assay details

Data source: Panorama

Official Gene Symbol
CTSD
Peptide Sequence
LSPEDYTLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
349
Peptide End
357
CPTAC ID
CPTAC-487
Peptide Molecular Mass
1,064.5390
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim

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


Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.


Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.


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


Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

  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+) 3.9 5.3 3 7.1 6.6 5.4 8.1 8.5 6.2 15 25 15
y6 (1+) 6.5 6.5 3.1 6.4 6.8 4.6 9.1 9.4 5.5 15 25 15
y5 (1+) 25.5 13.7 4.1 51.6 18.7 4.4 57.6 23.2 6 15 25 15
sum 3.8 5.8 2.9 9.1 6.2 4.9 9.9 8.5 5.7 15 25 15


Additional Resources and Comments


Assay Details for CPTAC-486 Collapse assay details

Data source: Panorama

Official Gene Symbol
CTSD
Peptide Sequence
LVDQNIFSFYLSR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
223
Peptide End
235
CPTAC ID
CPTAC-486
Peptide Molecular Mass
1,600.8249
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim

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


Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.


Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.


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


Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

  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+) 10.5 6.3 8.2 29.7 25.4 28.7 31.5 26.2 29.8 25 15 15
y8 (1+) 12.1 7 9.5 30.7 26.3 29.7 33 27.2 31.2 25 15 15
y7 (1+) 11.5 7.5 7.9 31.3 28.5 29 33.3 29.5 30.1 25 15 15
sum 10.2 7.1 8.1 30.7 27.5 29 32.4 28.4 30.1 25 15 15


Additional Resources and Comments


Assay Details for non-CPTAC-3403 Collapse assay details

Data source: Panorama

Official Gene Symbol
Ctsd
Peptide Sequence
NIFSFYLNR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
225
Peptide End
233
CPTAC ID
non-CPTAC-3403
Peptide Molecular Mass
1,172.5978
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
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
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


Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

  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+) 16.4 6.6 5.3 21 8.2 5.2 26.6 10.5 7.4 15 14 15
b2 (1+) 10.6 5.8 7 13.7 5.5 7.4 17.3 8 10.2 15 14 15
y5 (1+) 21.4 5.7 11.4 27.1 5.9 12 34.5 8.2 16.6 15 14 15
y6 (1+) 8 5.2 7.5 11.1 6.4 8.7 13.7 8.2 11.5 15 14 15
y7 (1+) 6.8 4 8.8 9.8 5.4 13.1 11.9 6.7 15.8 15 14 15
sum 7.7 2.2 6 11.1 3 9.4 13.5 3.7 11.2 15 14 15


Additional Resources and Comments


Assay Details for non-CPTAC-3695 Collapse assay details

Data source: Panorama

Official Gene Symbol
Ctsd
Peptide Sequence
VSSLPTVYLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
330
Peptide End
339
CPTAC ID
non-CPTAC-3695
Peptide Molecular Mass
1,105.6383
Species
Mus musculus (Mouse)
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
Agilent 6490/6495 QQQ
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


Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

  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+) 7.2 5.7 5.4 9.6 4.1 5.6 12 7 7.8 15 15 15
y9 (1+) 19.4 8.2 4.3 18.8 6.5 5.3 27 10.5 6.8 15 15 15
b4 (1+) 20.3 5.3 4.1 24.4 3.7 6.7 31.7 6.5 7.9 15 15 15
y6 (2+) 30.3 9.8 7.1 32.7 9.7 6 44.6 13.8 9.3 15 15 15
y6 (1+) 14.3 5.5 3.6 14.3 6.4 3.1 20.2 8.4 4.8 15 15 15
sum 9.2 2.2 1.6 10.3 2.6 2.8 13.8 3.4 3.2 15 15 15


Additional Resources and Comments