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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.

EPHB2

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
EPHB2 DRT, EPHT3, EPTH3, ERK, HEK5, TYRO5
Sequence Length (AA) Molecular Weight (Da)
1055 117493
Protein Name
Ephrin type-B receptor 2
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MALRRLGAAL LLLPLLAAVE ETLMDSTTAT AELGWMVHPP SGWEEVSGYD
60 70 80 90 100
ENMNTIRTYQ VCNVFESSQN NWLRTKFIRR RGAHRIHVEM KFSVRDCSSI
110 120 130 140 150
PSVPGSCKET FNLYYYEADF DSATKTFPNW MENPWVKVDT IAADESFSQV
160 170 180 190 200
DLGGRVMKIN TEVRSFGPVS RSGFYLAFQD YGGCMSLIAV RVFYRKCPRI
210 220 230 240 250
IQNGAIFQET LSGAESTSLV AARGSCIANA EEVDVPIKLY CNGDGEWLVP
260 270 280 290 300
IGRCMCKAGF EAVENGTVCR GCPSGTFKAN QGDEACTHCP INSRTTSEGA
310 320 330 340 350
TNCVCRNGYY RADLDPLDMP CTTIPSAPQA VISSVNETSL MLEWTPPRDS
360 370 380 390 400
GGREDLVYNI ICKSCGSGRG ACTRCGDNVQ YAPRQLGLTE PRIYISDLLA
410 420 430 440 450
HTQYTFEIQA VNGVTDQSPF SPQFASVNIT TNQAAPSAVS IMHQVSRTVD
460 470 480 490 500
SITLSWSQPD QPNGVILDYE LQYYEKELSE YNATAIKSPT NTVTVQGLKA
510 520 530 540 550
GAIYVFQVRA RTVAGYGRYS GKMYFQTMTE AEYQTSIQEK LPLIIGSSAA
560 570 580 590 600
GLVFLIAVVV IAIVCNRRGF ERADSEYTDK LQHYTSGHMT PGMKIYIDPF
610 620 630 640 650
TYEDPNEAVR EFAKEIDISC VKIEQVIGAG EFGEVCSGHL KLPGKREIFV
660 670 680 690 700
AIKTLKSGYT EKQRRDFLSE ASIMGQFDHP NVIHLEGVVT KSTPVMIITE
710 720 730 740 750
FMENGSLDSF LRQNDGQFTV IQLVGMLRGI AAGMKYLADM NYVHRDLAAR
760 770 780 790 800
NILVNSNLVC KVSDFGLSRF LEDDTSDPTY TSALGGKIPI RWTAPEAIQY
810 820 830 840 850
RKFTSASDVW SYGIVMWEVM SYGERPYWDM TNQDVINAIE QDYRLPPPMD
860 870 880 890 900
CPSALHQLML DCWQKDRNHR PKFGQIVNTL DKMIRNPNSL KAMAPLSSGI
910 920 930 940 950
NLPLLDRTIP DYTSFNTVDE WLEAIKMGQY KESFANAGFT SFDVVSQMMM
960 970 980 990 1000
EDILRVGVTL AGHQKKILNS IQVMRAQMNQ IQSVEGQPLA RRPRATGRTK
1010 1020 1030 1040 1050
RCQPRDVTKK TCNSNDGKKK GMGKKKTDPG RGREIQGIFF KEDSHKESND
1055
CSCGG

Data source: UniProt

Protein Map Collapse protein map

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

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Assay Details for CPTAC-2786 Collapse assay details

Data source: Panorama

Official Gene Symbol
EPHB2
Peptide Modified Sequence
LQHY[+80.0]TSGHMTPGMK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
581
Peptide End
594
CPTAC ID
CPTAC-2786
Peptide Molecular Mass
1,666.6997
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
Mammalian Cell Lysate
Submitting Laboratory
Johns Hopkins University / Pandey
Submitting Lab PI
Akhilesh Pandey

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Orbitrap Fusion Lumos
Internal Standard
100fmol
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Easy nLC 1200 System
Column Packing
C18 2um 100A
Column Dimensions
75um i.d. x 50cm
Flow Rate
250nl/min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  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
y5 (1+) 38.2 11 6.3 39.2 14.2 7 54.7 18 9.4 15 15 15
y4 (1+) 14 7.1 6.1 17.4 8 5.9 22.3 10.7 8.5 15 15 15
b3 (1+) 33.5 13.3 9.3 35.7 13.2 9.1 49 18.7 13 15 15 15
sum 16.7 8.2 6 19.6 9 6.1 25.7 12.2 8.6 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments

Assay Details for CPTAC-3205 Collapse assay details

Data source: Panorama

Official Gene Symbol
EPHB2
Peptide Sequence
FLEDDTSDPTYTSALGGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
770
Peptide End
787
CPTAC ID
CPTAC-3205
Peptide Molecular Mass
1,915.8687
Species
Homo Sapiens
Assay Type
Direct PRM
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

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  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
y3 (1+) 11.2 2.8 2.5 10.6 4 3.1 15.4 4.9 4 15 15 15
y7 (1+) 7.5 2.8 2.7 10.6 4.1 3.3 13 5 4.3 15 15 15
y10 (1+) 6.7 3.8 2.4 7.6 5.2 3.8 10.1 6.4 4.5 15 15 15
sum 6.3 3.2 2.2 7.6 4.4 3.3 9.9 5.4 4 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments
'); all_in_one_graph.append('
Sequence Domains
'); all_in_one_graph.append('
'); all_in_one_graph.append('
Isoforms
'); all_in_one_graph.append('
'); all_in_one_graph.append('
SNPs
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'); all_in_one_graph.append('
Targeted MS Assays
'); // Chart legend links $('.sequence-domains-chart-legend, .sequence-domains-chart-legend-text').on('click', function (event) { var url_sequence_domains = 'http://www.uniprot.org/uniprot/' + uniprot_id + '#section_features'; window.open(url_sequence_domains, '_blank'); }); $('.isoforms-chart-legend, .isoforms-chart-legend-text').on('click', function (event) { var url_isoforms = 'http://www.uniprot.org/uniprot/' + uniprot_id + '#' + uniprot_id + '-1'; window.open(url_isoforms, '_blank'); }); $('.snps-chart-legend, .snps-chart-legend-text').on('click', function (event) { var url_snps = 'http://www.uniprot.org/uniprot/' + uniprot_id + ''; window.open(url_isoforms, '_blank'); }); /////////////////////////////////////////////////////////// // Set the height of the chart var graph_height = ((last_x_plot * 30) != 0) ? (last_x_plot * 30) : 300; $(all_in_one_graph).css('height', graph_height); // (all_in_one_data.length * 11) // Add the zoom in button $("
zoom in
") .appendTo(all_in_one_graph) .click(function (event) { event.preventDefault(); all_in_one_plot.zoom(); }); // Add the zoom out button $("
zoom out
") .appendTo(all_in_one_graph) .click(function (event) { event.preventDefault(); all_in_one_plot.zoomOut(); }); // Helper for taking the repetitive work out of placing panning arrows function addArrow(dir, right, top, offset) { $("") .appendTo(all_in_one_graph) .click(function (e) { e.preventDefault(); all_in_one_plot.pan(offset); }); } addArrow("left", 55, 40, {left: -100}); addArrow("right", 25, 40, {left: 100}); addArrow("up", 40, 25, {top: -100}); addArrow("down", 40, 55, {top: 100}); // Disable the mouse wheel functionality for panning and zooming $('#all_in_one_graph canvas.flot-overlay').unmousewheel(); $(all_in_one_graph).bind("plotclick", function (event, pos, item) { // Splice Junctions // http://www.uniprot.org/uniprot/P04626#section_features if ((item != null) && (item.series.data[0][3] != null) && (item.series.data[0][3] == 'splice_junction')) { var url = 'http://www.uniprot.org/uniprot/' + uniprot_id + '#section_features'; window.open(url, '_blank'); } // Isoforms if ((item != null) && (item.series.data[0][4] != null) && (item.series.data[0][4] == 'isoform')) { var url = 'http://www.uniprot.org/uniprot/' + item.series.data[item.dataIndex][3]; window.open(url, '_blank'); } // SNPs if ((item != null) && (item.series.data[0][3] != null) && (item.series.data[0][3] == 'snp')) { var url = 'http://www.uniprot.org/blast/?about=' + uniprot_id + '[' + item.datapoint[0] + ']'; window.open(url, '_blank'); } // MRM Assays if ((item != null) && (item.series.data[0][4] != null) && (item.series.data[0][4] == 'mrm_assay')) { var this_peptide_sequence = item.series.data[item.dataIndex][3]; var this_protein_id = item.series.data[item.dataIndex][5]; var div_id = '.' + this_protein_id; // Change our States (URL, title in title bar) History.replaceState({state: 1}, "EPHB2, CPTAC-" + this_protein_id + " - CPTAC Assay Portal", "CPTAC-" + this_protein_id); // Scroll to assays area scrollToAnchor('assay_details_anchor'); $('.assay-details-wrapper').hide(); $('#preloader_loading_assay_details').fadeIn(500); $('#preloader_loading_assay_details').hide(); $(div_id).fadeIn(300); // Load Disqus commenting //loadDisqus($('#comments_container_' + this_protein_id), this_peptide_sequence, 'http://assays.cancer.gov/CPTAC-2786/#!' + this_peptide_sequence); } }); /////////////////////////////////////////////////////////// // [BEGIN] Highlighted Peptide Sequence Links /////////////// // Use sequence values from the 'genes_distinct' array var mouseY; var mouseX; $(document).mousemove(function (e) { mouseX = e.pageX; mouseY = e.pageY; }); var starts = JSON.parse('[{"peptide_sequence":"LQHYTSGHMTPGMK","manage":2786},{"peptide_sequence":"FLEDDTSDPTYTSALGGK","manage":3205}]'); var last_clicked = false; $.each(starts, function (index, starts_data) { // On click event for peptide sequence links in the gene sequence var this_peptide_sequence = starts_data.peptide_sequence; var this_protein_id = starts_data.manage; var div_id = '.' + this_protein_id; var clickable_class = 'seq-' + this_peptide_sequence; $('.' + clickable_class).on('click', function () { $("rect, line, .close").tooltip(); if (last_clicked != this_peptide_sequence) { $('.detail-modal').attr('style', 'display: none'); last_clicked = false; } var div_height = $('.all-details-' + this_peptide_sequence).height(); var offset = (div_height > 25) ? 450 : 390; $('.all-details-' + this_peptide_sequence).css({'top': mouseY - offset}).fadeIn('fast'); $('.detail-modal .close').on('click', function () { $('.detail-modal').fadeOut('fast'); }); }); var detail_link_class = this_peptide_sequence + '-' + this_protein_id; $('.protein-sequence').on('click', '.' + detail_link_class, function () { // close the pop up $('.detail-modal').fadeOut('fast'); // Change our States (URL, title in title bar) History.replaceState({state: 1}, "EPHB2, CPTAC-" + this_protein_id + " - CPTAC Assay Portal", "CPTAC-" + this_protein_id); // Scroll to assays area scrollToAnchor('assay_details_anchor'); $('.assay-details-wrapper').hide(); $('#preloader_loading_assay_details').fadeIn(500); $('#preloader_loading_assay_details').hide(); $(div_id).fadeIn(300); // Load Disqus commenting //loadDisqus($('#comments_container_' + this_protein_id), this_peptide_sequence, 'http://assays.cancer.gov/CPTAC-2786/#!' + this_peptide_sequence); }); }); // $("rect, line, .peptide_highlight").tooltip({ // 'container': 'body', // 'placement': 'top' // }); // [END] Highlighted Peptide Sequence Links /////////////// // Tooltips on hover of data points var previousPoint = null; $(all_in_one_graph).bind("plothover", function (event, pos, item) { if (item) { document.body.style.cursor = 'pointer'; if (previousPoint != item.dataIndex) { previousPoint = item.dataIndex; $("#tooltip").remove(); showTooltip(item.pageX, item.pageY, item.series.data[item.dataIndex][2]); } } else { document.body.style.cursor = 'default'; $("#tooltip").remove(); previousPoint = null; } }); // Pop-out entire sequence $('div.sequence').on('mouseenter', '.protein-sequence', function (event) { $(this).attr('style', 'overflow: visible;'); $('table.sequence').addClass('sequence_table_shadow'); }); $('div.sequence').on('mouseleave', '.protein-sequence', function (event) { $(this).attr('style', 'overflow: hidden;'); $('table.sequence').removeClass('sequence_table_shadow'); $('.detail-modal').attr('style', 'display: none'); }); // Tooltips $('.span4 img, .chart-legend, .chart-legend-text').tooltip(); // Show the Assay details for the page id we're on var details_div_id = $('#outer-wrapper .2786'); $(details_div_id).show(); //loadDisqus($('#comments_container_2786'), 'LQHYTSGHMTPGMK', 'http://assays.cancer.gov/CPTAC-2786/#!LQHYTSGHMTPGMK'); // History.js (function (window, undefined) { // Bind to StateChange Event History.Adapter.bind(window, 'statechange', function () { // Note: We are using statechange instead of popstate var State = History.getState(); // Note: We are using History.getState() instead of event.state }); })(window); $.ajax({ type: "GET" , dataType: "html" , url: "/assays/get_protein_map_svg" , data: ({uniprot_ac_id: uniprot_id}) , success: function (svg_return) { d3.select("#proteincartoon").html(svg_return); } }); $('#proteincartoon').click(function () { var win = window.open('http://www.phosphosite.org/uniprotAccAction.do?id=' + uniprot_id, '_blank'); win.focus(); }); }); // FUNCTIONS /////////////// function scrollToAnchor(aid) { var aTag = $("a[name='" + aid + "']"); $('html,body').animate({scrollTop: aTag.offset().top}, 'slow'); } function showTooltip(x, y, contents) { $("
" + contents + "
").css({ position: "absolute", display: "none", top: y - 28, left: x + 8, border: "1px solid #000", padding: "4px", "background-color": "#000", opacity: 0.80, color: "#fff" }).appendTo("body").fadeIn(200); } function get_plots_table_data(genes) { // If we're using an element repededly, let's create variables var response_curve_message = '

Table data unavailable

'; // Display the preloaders $.each(genes, function (index, gene) { $('div.span12.' + gene.peptide_sequence + '_' + gene.laboratory_abbreviation + ' .loc_lloq_preloader_loading').show(); }); // Send the request via AJAX $.ajax({ url: "/assays/get_plots_table_data" , dataType: "json" , type: "post" , data: {genes: JSON.stringify(genes)} , success: function (data) { if (data) { $.each(data, function (index, single_gene_data) { /* * Build out the LOC/LOQ data table */ if (single_gene_data.lod_loq_comparison_data[0].length) { var crude = (single_gene_data.peptide_standard_purity_types_id == 3) ? true : false; var peptide_sequence = single_gene_data.lod_loq_comparison_data[0][0].peptide; var lod_loq_units = single_gene_data.lod_loq_comparison_data[0][0].lod_loq_units; var crude_style = (crude) ? 'class="crude-header"' : ''; var lod_loq_units_note = (crude) ? '
Estimated based on crude peptide concentration' : ''; // Strip brackets from the modified peptide sequence. var peptide_sequence_stripped = peptide_sequence.replace(/[\[\+\d+\]]/g, ''); var table = $('
').addClass('table table-bordered table-striped table-condensed').attr('id', single_gene_data.manage_id + '_loc_loq'); var table_header_row = $(''); var table_headers = $(' LOD (' + lod_loq_units + ')' + lod_loq_units_note + 'LLOQ (' + lod_loq_units + ')' + lod_loq_units_note + ''); table_header_row.append(table_headers); table.append(table_header_row); var table_top_row = $(""); var labels = [ "Peptide" , "Transition" , "blank only" , "blank+low-conc" , "rsd limit" , "blank only" , "blank+low-conc" , "rsd limit" ]; // Stitch together the table headers row $.each(labels, function (index, label) { table_top_row.append('' + label + ''); }); table.append(table_top_row); $.each(single_gene_data.lod_loq_comparison_data, function (index, single_data) { var lod_loq_rowspan = single_data.length; $.each(single_data, function (idx, single) { var transition_id = (single.transition_id == '.Sum.tr.') ? 'Sum' : single.transition_id; var table_row = $(""); table.append(table_row); var a = (single.blank_only_LOD != 'NA') ? Number(single.blank_only_LOD).toExponential(1) : single.blank_only_LOD; var b = (single.blank_low_conc_LOD != 'NA') ? Number(single.blank_low_conc_LOD).toExponential(1) : single.blank_low_conc_LOD; var c = (single.rsd_limit_LOD != 'NA') ? Number(single.rsd_limit_LOD).toExponential(1) : single.rsd_limit_LOD; var d = (single.blank_only_LOQ != 'NA') ? Number(single.blank_only_LOQ).toExponential(1) : single.blank_only_LOQ; var e = (single.blank_low_conc_LOQ != 'NA') ? Number(single.blank_low_conc_LOQ).toExponential(1) : single.blank_low_conc_LOQ; var f = (single.rsd_limit_LOQ != 'NA') ? Number(single.rsd_limit_LOQ).toExponential(1) : single.rsd_limit_LOQ; var peptide_sequence_label = (index == 0) ? peptide_sequence : ''; if (idx == 0) { table_row.append('' + peptide_sequence_label + ''); } table_row.append('' + transition_id + ''); table_row.append('' + a + ''); table_row.append('' + b + ''); table_row.append('' + c + ''); table_row.append('' + d + ''); table_row.append('' + e + ''); table_row.append('' + f + ''); }); }); // Remove preloader $('div.span12.' + single_gene_data.manage_id + '_' + single_gene_data.laboratory_abbreviation + '_' + single_gene_data.manage_id + ' .loc_lloq_preloader_loading').remove(); // Load the table $('div.span12.' + single_gene_data.manage_id + '_' + single_gene_data.laboratory_abbreviation + '_' + single_gene_data.manage_id).append(table); } if (single_gene_data.response_curves_data[0].length) { /* * Build out the Curve Fit table */ var peptide_sequence = single_gene_data.response_curves_data[0][0].peptide; // Strip brackets from the modified peptide sequence. var peptide_sequence_stripped = peptide_sequence.replace(/[\[\+\d+\]]/g, ''); var table = $('
').addClass('table table-bordered table-striped table-condensed') .attr('id', peptide_sequence_stripped + '_response_curves') .attr('style', 'margin-top:40px;'); var table_header_row = $(""); var table_headers = $(' Curve Fit'); table_header_row.append(table_headers); table.append(table_header_row); // Response curves data table var table_top_row = $(""); var labels = [ "Peptide" , "Transition" , "slope" , "intercept" , "r squared" ]; // Stitch together the table headers row $.each(labels, function (index, label) { table_top_row.append('' + label + ''); }); table.append(table_top_row); $.each(single_gene_data.response_curves_data, function (index, single_data) { var curve_fit_rowspan = single_data.length; $.each(single_data, function (idx, single) { var transition_id = (single.transition_id == '.Sum.tr.') ? 'Sum' : single.transition_id; var table_row = $(""); table.append(table_row); if (idx == 0) { table_row.append('' + single.peptide + ''); } table_row.append('' + transition_id + ''); table_row.append('' + single.Slope + ''); table_row.append('' + single.Intercept + ''); table_row.append('' + single.RSquare + ''); }); }); // Remove preloader $('div.span12.' + single_gene_data.manage_id + '_' + single_gene_data.laboratory_abbreviation + '_' + single_gene_data.manage_id + ' .loc_lloq_preloader_loading').remove(); // Load the table $('div.span12.' + single_gene_data.manage_id + '_' + single_gene_data.laboratory_abbreviation + '_' + single_gene_data.manage_id).append(table); // Response Curves LLOQ header notice var high_values = $('#' + single_gene_data.manage_id + '_validation_sample_data_' + single_gene_data.manage_id + ' tbody tr td').find('.red'); if (high_values.length) { // try to prevent duplicates $('#outer-wrapper #' + single_gene_data.manage_id + '_loc_loq .lloq_header .icon-exclamation-sign').remove(); $('#outer-wrapper #' + single_gene_data.manage_id + '_loc_loq .lloq_header').append(' '); $('.icon-exclamation-sign').tooltip(); } } if ((single_gene_data.lod_loq_comparison_data[0] == 0) && (single_gene_data.response_curves_data[0].length == 0)) { $.each(genes, function (index, gene) { var div_wrapper = $('div.span12.' + single_gene_data.peptide_sequence + '_' + single_gene_data.laboratory_abbreviation); // Remove preloader $('.loc_lloq_preloader_loading').remove(); $(div_wrapper).append('

Response Curves Data Unavailable

'); }); } }); } } }); }