SYK, CPTAC-1173 - CPTAC Assay Portal (original) (raw)

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.

Protein Sequence hover to view complete sequence

CPTAC-1174: View additional LIATTAHEK data

CPTAC-3143: View additional NVLLVTQHYAK data

10 20 30 40 50
MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
60 70 80 90 100
FALSVAHGRK AHHYTIEREL NGTYAIAGGR THASPADLCH YHSQESDGLV
110 120 130 140 150
CLLKKPFNRP QGVQPKTGPF EDLKENLIRE YVKQTWNLQG QALEQAIISQ
160 170 180 190 200
KPQLEKLIAT TAHEKMPWFH GKISREESEQ IVLIGSKTNG KFLIRARDNN
210 220 230 240 250
GSYALCLLHE GKVLHYRIDK DKTGKLSIPE GKKFDTLWQL VEHYSYKADG
260 270 280 290 300
LLRVLTVPCQ KIGTQGNVNF GGRPQLPGSH PATWSAGGII SRIKSYSFPK
310 320 330 340 350
PGHRKSSPAQ GNRQESTVSF NPYEPELAPW AADKGPQREA LPMDTEVYES
360 370 380 390 400
PYADPEEIRP KEVYLDRKLL TLEDKELGSG NFGTVKKGYY QMKKVVKTVA
410 420 430 440 450
VKILKNEAND PALKDELLAE ANVMQQLDNP YIVRMIGICE AESWMLVMEM
460 470 480 490 500
AELGPLNKYL QQNRHVKDKN IIELVHQVSM GMKYLEESNF VHRDLAARNV
510 520 530 540 550
LLVTQHYAKI SDFGLSKALR ADENYYKAQT HGKWPVKWYA PECINYYKFS
560 570 580 590 600
SKSDVWSFGV LMWEAFSYGQ KPYRGMKGSE VTAMLEKGER MGCPAGCPRE
610 620 630 635
MYDLMNLCWT YDVENRPGFA AVELRLRNYY YDVVN

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-1174 Collapse assay details

Data source: Panorama

Official Gene Symbol

SYK

Peptide Sequence

LIATTAHEK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

157

Peptide End

165

CPTAC ID

CPTAC-1174

Peptide Molecular Mass

982.5447

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 K

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

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y3 (1+) | 26.1 | 28.5 | 15.1 | 28.4 | 32.1 | 16 | 38.6 | 42.9 | 22 | 15 | 15 | 15 | | y5 (1+) | 17 | 9 | 10.3 | 15.2 | 12.2 | 12.9 | 22.8 | 15.2 | 16.5 | 15 | 15 | 15 | | y6 (1+) | 13.8 | 12.3 | 14.3 | 18.1 | 13.4 | 13 | 22.8 | 18.2 | 19.3 | 15 | 15 | 15 | | sum | 11.4 | 7.1 | 5.6 | 13.2 | 8.8 | 7.2 | 17.4 | 11.3 | 9.1 | 15 | 15 | 15 |

Selectivity

Data source: Panorama

Slope of Curve Fit for cell line
fragment_ion 1 2 3 4 5 6
y6 (1+) 10.67 14.24 14.09 11.75 8.62 12.17
y5 (1+) 9.3 11.37 13.49 9.74 9.79 10.42
y3 (1+) 8.35 7.84 11.16 7.81 9.31 9.63
sum 9.4 11.12 13.19 9.75 9.24 10.64

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
y6 (1+) 39.4 34.9 52.6
y5 (1+) 49 41.9 64.5
y3 (1+) 60.9 65.6 89.5
sum 40.3 38 55.4

Additional Resources and Comments

Assay Details for CPTAC-1173 Collapse assay details

Data source: Panorama

Official Gene Symbol

SYK

Peptide Sequence

NYLGGFALSVAHGR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

46

Peptide End

59

CPTAC ID

CPTAC-1173

Peptide Molecular Mass

1,460.7524

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

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y4 (1+) | 20.5 | 5.7 | 10 | 20.9 | 10 | 10.7 | 29.3 | 11.5 | 14.6 | 15 | 15 | 15 | | y6 (1+) | 11.3 | 3.5 | 7 | 10.3 | 7.4 | 7.2 | 15.3 | 8.2 | 10 | 15 | 15 | 15 | | y7 (1+) | 18.4 | 7.8 | 4.7 | 18.2 | 13.2 | 4.6 | 25.9 | 15.3 | 6.6 | 15 | 15 | 15 | | sum | 12.2 | 3.2 | 4.9 | 8.7 | 8.2 | 5.4 | 15 | 8.8 | 7.3 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-3143 Collapse assay details

Data source: Panorama

Official Gene Symbol

SYK

Peptide Sequence

NVLLVTQHYAK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

499

Peptide End

509

CPTAC ID

CPTAC-3143

Peptide Molecular Mass

1,284.7190

Species

Homo Sapiens

Assay Type

Direct MRM or SRM

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

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectMRM

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 CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y7 (1+) | 6.7 | 7.7 | 3.8 | 8.3 | 8.5 | 3.7 | 10.7 | 11.5 | 5.3 | 15 | 15 | 15 | | y6 (1+) | 4.5 | 5.7 | 3.7 | 6.1 | 6.6 | 3.7 | 7.6 | 8.7 | 5.2 | 15 | 15 | 15 | | y4 (1+) | 7.1 | 7.1 | 3.8 | 13 | 7.4 | 4 | 14.8 | 10.3 | 5.5 | 15 | 15 | 15 | | sum | 4.5 | 6.4 | 3.4 | 7 | 7.2 | 3.3 | 8.3 | 9.6 | 4.7 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-3142 Collapse assay details

Data source: Panorama

Official Gene Symbol

SYK

Peptide Modified Sequence

WYAPEC[+57.0]INYYK

Modification Type

Carbamidomethyl (C)

Protein - Site of Modification

544

Peptide - Site of Modification

6

Peptide Start

538

Peptide End

548

CPTAC ID

CPTAC-3142

Peptide Molecular Mass

1,505.6649

Species

Homo Sapiens

Assay Type

Direct MRM or SRM

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

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectMRM

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 CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y9 (1+) | 5 | 5.3 | 3.9 | 5.7 | 6.7 | 4.2 | 7.6 | 8.5 | 5.7 | 15 | 15 | 15 | | y8 (1+) | 4.9 | 5.1 | 3.9 | 5.3 | 6.3 | 4.2 | 7.2 | 8.1 | 5.7 | 15 | 15 | 15 | | y4 (1+) | 6.4 | 4.5 | 2.8 | 6.8 | 5.1 | 3.2 | 9.3 | 6.8 | 4.3 | 15 | 15 | 15 | | sum | 4.8 | 4.9 | 3.7 | 5.2 | 6.1 | 4 | 7.1 | 7.8 | 5.4 | 15 | 15 | 15 |

Additional Resources and Comments