LAMP2, CPTAC-689 - 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.

LAMP2

Protein Sequence hover to view complete sequence

10 20 30 40 50
MVCFRLFPVP GSGLVLVCLV LGAVRSYALE LNLTDSENAT CLYAKWQMNF
60 70 80 90 100
TVRYETTNKT YKTVTISDHG TVTYNGSICG DDQNGPKIAV QFGPGFSWIA
110 120 130 140 150
NFTKAASTYS IDSVSFSYNT GDNTTFPDAE DKGILTVDEL LAIRIPLNDL
160 170 180 190 200
FRCNSLSTLE KNDVVQHYWD VLVQAFVQNG TVSTNEFLCD KDKTSTVAPT
210 220 230 240 250
IHTTVPSPTT TPTPKEKPEA GTYSVNNGND TCLLATMGLQ LNITQDKVAS
260 270 280 290 300
VININPNTTH STGSCRSHTA LLRLNSSTIK YLDFVFAVKN ENRFYLKEVN
310 320 330 340 350
ISMYLVNGSV FSIANNNLSY WDAPLGSSYM CNKEQTVSVS GAFQINTFDL
360 370 380 390 400
RVQPFNVTQG KYSTAQDCSA DDDNFLVPIA VGAALAGVLI LVLLAYFIGL
410
KHHHAGYEQF

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-1494 Collapse assay details

Data source: Panorama

Official Gene Symbol

LAMP2

Peptide Modified Sequence

VASVININPN[+1.0]TTHSTGSC[+57.0]R

Modification Type

Deamidated (N), Carbamidomethyl (C)

Protein - Site of Modification

257, 265

Peptide - Site of Modification

10, 18

Peptide Start

248

Peptide End

266

CPTAC ID

CPTAC-1494

Peptide Molecular Mass

2,027.9695

Species

Homo sapiens (Human)

Assay Type

Direct PRM

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

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 | | y11 (2+) | 8.1 | 9.5 | 5.5 | 7.8 | 6.8 | 7.1 | 11.2 | 11.7 | 9 | 15 | 15 | 15 | | y6 (1+) | 7.3 | 6.9 | 5.2 | 8.2 | 7.1 | 7 | 11 | 9.9 | 8.7 | 15 | 15 | 15 | | y11 (1+) | 8.3 | 9.1 | 7.9 | 11.3 | 8.9 | 8.1 | 14 | 12.7 | 11.3 | 15 | 15 | 15 | | sum | 3.2 | 4.5 | 3.3 | 4.3 | 5.1 | 4.1 | 5.4 | 6.8 | 5.3 | 15 | 15 | 15 |

Additional Resources and Comments

Comments

Assay Details for CPTAC-689 Collapse assay details

Data source: Panorama

Official Gene Symbol

LAMP2

Peptide Modified Sequence

VQPFN[+1.0]VTQGK

Modification Type

Deamidated (NQ)

Protein - Site of Modification

356

Peptide - Site of Modification

5

Peptide Start

352

Peptide End

361

CPTAC ID

CPTAC-689

Peptide Molecular Mass

1,117.5768

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+) | 12.7 | 7.4 | 7.3 | 12.6 | 7.9 | 7.8 | 17.9 | 10.8 | 10.7 | 15 | 15 | 15 | | y7 (1+) | 10.4 | 12.5 | 14.9 | 11.2 | 11.3 | 14.7 | 15.3 | 16.9 | 20.9 | 15 | 15 | 15 | | y6 (1+) | 13.5 | 12.4 | 8.2 | 16.6 | 13 | 9.4 | 21.4 | 18 | 12.5 | 15 | 15 | 15 | | sum | 9.2 | 8.3 | 8.1 | 9.9 | 8.5 | 8.3 | 13.5 | 11.9 | 11.6 | 15 | 15 | 15 |

Additional Resources and Comments

Comments