SERPINA1, CPTAC-651 - 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.

SERPINA1

Protein Sequence hover to view complete sequence

non-CPTAC-1063: View additional LSITGTYDLK data

10 20 30 40 50
MPSSVSWGIL LLAGLCCLVP VSLAEDPQGD AAQKTDTSHH DQDHPTFNKI
60 70 80 90 100
TPNLAEFAFS LYRQLAHQSN STNIFFSPVS IATAFAMLSL GTKADTHDEI
110 120 130 140 150
LEGLNFNLTE IPEAQIHEGF QELLRTLNQP DSQLQLTTGN GLFLSEGLKL
160 170 180 190 200
VDKFLEDVKK LYHSEAFTVN FGDTEEAKKQ INDYVEKGTQ GKIVDLVKEL
210 220 230 240 250
DRDTVFALVN YIFFKGKWER PFEVKDTEEE DFHVDQVTTV KVPMMKRLGM
260 270 280 290 300
FNIQHCKKLS SWVLLMKYLG NATAIFFLPD EGKLQHLENE LTHDIITKFL
310 320 330 340 350
ENEDRRSASL HLPKLSITGT YDLKSVLGQL GITKVFSNGA DLSGVTEEAP
360 370 380 390 400
LKLSKAVHKA VLTIDEKGTE AAGAMFLEAI PMSIPPEVKF NKPFVFLMIE
410 418
QNTKSPLFMG KVVNPTQK

Data source: UniProt

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node

to view detailed assay information below

All other points link out to UniProt

Phosphorylation Acetylation Ubiquitylation Other

loading

Loader

Assay Details for CPTAC-651 Collapse assay details

Data source: Panorama

Official Gene Symbol

SERPINA1

Peptide Modified Sequence

YLGN[+1.0]ATAIFFLPDEGK

Modification Type

Deamidated (NQ)

Protein - Site of Modification

271

Peptide - Site of Modification

4

Peptide Start

268

Peptide End

283

CPTAC ID

CPTAC-651

Peptide Molecular Mass

1,755.8719

Species

Homo sapiens (Human)

Assay Type

Enrichment PRM

Enrichment Method

N-linked glycopeptide solid phase extraction

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 K

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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 | | y8 (1+) | 3.6 | 2.2 | 2.5 | 4.4 | 2.5 | 3.3 | 5.7 | 3.3 | 4.1 | 15 | 15 | 15 | | y5 (1+) | 2.6 | 2.4 | 2.1 | 4.2 | 2.8 | 2.9 | 4.9 | 3.7 | 3.6 | 15 | 15 | 15 | | b9 (1+) | 20.6 | 14.6 | 9.9 | 26.6 | 15.1 | 9.6 | 33.6 | 21 | 13.8 | 15 | 15 | 15 | | sum | 2.5 | 2.3 | 2 | 3.8 | 2.7 | 2.9 | 4.5 | 3.5 | 3.5 | 15 | 15 | 15 |

Additional Resources and Comments

Comments

Assay Details for non-CPTAC-1063 Collapse assay details

Data source: Panorama

Official Gene Symbol

SERPINA1

Peptide Sequence

LSITGTYDLK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

315

Peptide End

324

CPTAC ID

non-CPTAC-1063

Peptide Molecular Mass

1,109.5968

Species

Homo sapiens (Human)

Assay Type

Direct PRM

Matrix

plasma

Submitting Laboratory

UVic-Genome BC Proteomics Centre

Submitting Lab PI

Christoph Borchers

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

6490 Triple Quad (Agilent)

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

Assay Multiplexing Expand assay panel

Johns Hopkins University-A

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 | | y8 (2+) | 5.7 | 3.6 | 3.5 | 8.5 | 13.3 | 4.6 | 10.2 | 13.8 | 5.8 | 15 | 15 | 15 | | y3 (1+) | 9.1 | 5 | 5.5 | 11.6 | 12.6 | 6.9 | 14.7 | 13.6 | 8.8 | 15 | 15 | 15 | | y6 (1+) | 10.5 | 6.3 | 6.3 | 9.6 | 11.1 | 6.7 | 14.2 | 12.8 | 9.2 | 15 | 15 | 15 | | y7 (1+) | 6.2 | 6.5 | 5.7 | 9.5 | 14.2 | 6.3 | 11.3 | 15.6 | 8.5 | 15 | 15 | 15 | | y8 (1+) | 7.1 | 5.6 | 2.9 | 9.7 | 9.9 | 4.5 | 12 | 11.4 | 5.4 | 15 | 15 | 15 | | sum | 5.2 | 3.9 | 3.6 | 8.2 | 11.8 | 3.7 | 9.7 | 12.4 | 5.2 | 15 | 15 | 15 |

Additional Resources and Comments

Comments