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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
MARCKS MACS, PRKCSL
Sequence Length (AA) Molecular Weight (Da)
332 31555
Protein Name
Myristoylated alanine-rich C-kinase substrate
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MGAQFSKTAA KGEAAAERPG EAAVASSPSK ANGQENGHVK VNGDASPAAA
60 70 80 90 100
ESGAKEELQA NGSAPAADKE EPAAAGSGAA SPSAAEKGEP AAAAAPEAGA
110 120 130 140 150
SPVEKEAPAE GEAAEPGSPT AAEGEAASAA SSTSSPKAED GATPSPSNET
160 170 180 190 200
PKKKKKRFSF KKSFKLSGFS FKKNKKEAGE GGEAEAPAAE GGKDEAAGGA
210 220 230 240 250
AAAAAEAGAA SGEQAAAPGE EAAAGEEGAA GGDPQEAKPQ EAAVAPEKPP
260 270 280 290 300
ASDETKAAEE PSKVEEKKAE EAGASAAACE APSAAGPGAP PEQEAAPAEE
310 320 330 332
PAAAAASSAC AAPSQEAQPE CSPEAPPAEA AE

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

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Assay Details for CPTAC-976 Collapse assay details

Data source: Panorama

Official Gene Symbol
MARCKS
Peptide Modified Sequence
GEPAAAAAPEAGAS[+80.0]PVEK
Modification Type
Phospho (ST)
Protein - Site of Modification
101
Peptide - Site of Modification
14
Peptide Start
88
Peptide End
105
CPTAC ID
CPTAC-976
Peptide Molecular Mass
1,701.7611
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTrap 5500 (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
nanoLC-2D (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
75 µm x 15cm
Flow Rate
300 nL/min

Chromatograms

Data source: Panorama


Response Curves

Data source: Panorama

Retrieving Data

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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
y16 (2+) 28 10.7 11.3 17.3 10.6 12.6 32.9 15.1 16.9 15 24 15
y10 (1+) 22.7 11.8 11.5 22.9 13.6 15.5 32.2 18 19.3 15 24 15
y11 (1+) 29.8 9.7 14.9 39.8 13.5 18 49.7 16.6 23.4 15 24 15
sum 22.9 10.5 11.2 22.3 11.9 14.2 32 15.9 18.1 15 24 15


Additional Resources and Comments


Assay Details for non-CPTAC-4045 Collapse assay details

Data source: Panorama

Official Gene Symbol
Marcks
Peptide Sequence
EEPASGSAATPAAAEK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
70
Peptide End
85
CPTAC ID
non-CPTAC-4045
Peptide Molecular Mass
1,485.6947
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
>80%
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
y14 (2+) 6.8 4.4 4 10.8 7.2 6.5 12.8 8.4 7.6 15 15 15
y6 (1+) 18.5 10.5 9.2 18.7 13.9 15.3 26.3 17.4 17.9 15 15 15
y8 (1+) 41.6 13 14.7 46.8 14.6 15.8 62.6 19.5 21.6 15 15 15
y11 (1+) 13.5 10.1 10 14.5 9.7 9.6 19.8 14 13.9 15 15 15
y12 (1+) 31.2 7.3 4.5 31.6 11.7 10.3 44.4 13.8 11.2 15 15 15
sum 5.5 4 2.8 9.8 6.3 6.3 11.2 7.5 6.9 15 15 15


Additional Resources and Comments


'); all_in_one_graph.append('
Sequence Domains
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Isoforms
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SNPs
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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}, "MARCKS, 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-976/#!' + 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":"GEPAAAAAPEAGASPVEK","manage":976},{"peptide_sequence":"EEPASGSAATPAAAEK","manage":4045}]'); 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}, "MARCKS, 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-976/#!' + 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 .976'); $(details_div_id).show(); //loadDisqus($('#comments_container_976'), 'GEPAAAAAPEAGASPVEK', 'http://assays.cancer.gov/CPTAC-976/#!GEPAAAAAPEAGASPVEK'); // 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

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