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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.

Pam

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
Pam N/A
Sequence Length (AA) Molecular Weight (Da)
979 108963
Protein Name
Peptidyl-glycine alpha-amidating monooxygenase
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MAGRARSRLL LLLGLLALQS SCLAFRSPLS VFKRFKETTR SFSNECLGTT
60 70 80 90 100
RPITPIDSSD FTLDIRMPGV TPKESDTYFC MSMRLPVDEE AFVIDFKPRA
110 120 130 140 150
SMDTVHHMLL FGCNMPSSTG SYWFCDEGTC TDKANILYAW ARNAPPTRLP
160 170 180 190 200
KGVGFRVGGE TGSKYFVLQV HYGDISAFRD NHKDCSGVSL HLTRVPQPLI
210 220 230 240 250
AGMYLMMSVN TVIPPGEKVV NSDISCHYKM YPMHVFAYRV HTHHLGKVVS
260 270 280 290 300
GYRVRNGQWT LIGRQSPQLP QAFYPVEHPV DVAFGDILAA RCVFTGEGRT
310 320 330 340 350
EATHIGGTSS DEMCNLYIMY YMEAKHAVSF MTCTQNVAPD MFRTIPEEAN
360 370 380 390 400
IPIPVKSDMV MIHGHHKETE NKEKSALIQQ PKQGEEEAFE QGDFYSLLSK
410 420 430 440 450
LLGEREDVVH VHKYNPTEKT ESGSDLVAEI ANVVQKKDLG RSDAREGAEH
460 470 480 490 500
EEGGNAILVR DRIHKFHRLE STLRPAESRA LSFQQPGEGP WEPELAGDFH
510 520 530 540 550
VEEALEWPGV YLLPGQVSGV ALDSKNNLVI FHRGDHVWDG NSFDSKFVYQ
560 570 580 590 600
QRGLGPIEED TILVIDPNKA EILQSSGKNL FYLPHGLSID TDGNYWVTDV
610 620 630 640 650
ALHQVFKLEP RSKEGPLLVL GRSMQPGSDQ NHFCQPTDVA VEPSTGAVFV
660 670 680 690 700
SDGYCNSRIV QFSPSGKFIT QWGEESSGSS PKPGQFSVPH SLALVPHLNQ
710 720 730 740 750
LCVADRENGR IQCFKTDTKE FVREIKHASF GRNVFAISYI PGFLFAVNGK
760 770 780 790 800
PYFGDQEPVQ GFVMNFSSGE IIDVFKPVRK HFDMPHDIVA SEDGTVYIGD
810 820 830 840 850
AHTNTVWKFT LTESRLEVEH RSVKKAGIEV PEIKEAEAVV EPKVKNKPTS
860 870 880 890 900
SELQKMQEKK KLIKDPGSGV PVVLITTLLV IPVVVLLAIA MFIRWKKSRA
910 920 930 940 950
FGDHDRKLES SSGRVLGRLR GKGSSGLNLG NFFASRKGYS RKGFDRVSTE
960 970 979
GSDQEKDEDD GSESEEEYSA PLPTPAPSS

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 non-CPTAC-3445 Collapse assay details

Data source: Panorama

Official Gene Symbol
Pam
Peptide Sequence
EGPLLVLGR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
614
Peptide End
622
CPTAC ID
non-CPTAC-3445
Peptide Molecular Mass
952.5706
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
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
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

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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
y6 (1+) 33.8 11 10.8 36.3 15 11 49.6 18.6 15.4 15 15 15
y5 (1+) 13.3 5.8 4.9 15.7 6.9 5.5 20.6 9 7.4 15 15 15
y4 (1+) 8.7 5.5 5.2 10.4 5.7 6.1 13.6 7.9 8 15 15 15
y3 (1+) 6.5 7.8 4.9 8.8 6.8 6.2 10.9 10.3 7.9 15 15 15
y2 (1+) 9.2 5.5 5 10.1 6.9 6.1 13.7 8.8 7.9 15 15 15
sum 5.2 3 2.3 7.1 3.4 3.7 8.8 4.5 4.4 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments
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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}, "Pam, 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/non-CPTAC-3445/#!' + 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":"EGPLLVLGR","manage":3445}]'); 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}, "Pam, 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/non-CPTAC-3445/#!' + 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 .3445'); $(details_div_id).show(); //loadDisqus($('#comments_container_3445'), 'EGPLLVLGR', 'http://assays.cancer.gov/non-CPTAC-3445/#!EGPLLVLGR'); // 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

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