[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-1-en-105":3,"doc-seo-573272-105":53,"doc-detail-573272-en":126},{"code":4,"msg":5,"data":6},0,"success",[7,14,19,24,29,34,39,44,49],{"id":8,"doc_module":9,"doc_module_name":10,"category_name":11,"show_sort_weight":12,"slug":13},11,1,"Template","Presentations",90,"presentations",{"id":15,"doc_module":9,"doc_module_name":10,"category_name":16,"show_sort_weight":17,"slug":18},12,"Resumes",80,"resumes",{"id":20,"doc_module":9,"doc_module_name":10,"category_name":21,"show_sort_weight":22,"slug":23},14,"Invoices",70,"invoices",{"id":25,"doc_module":9,"doc_module_name":10,"category_name":26,"show_sort_weight":27,"slug":28},15,"Posters",60,"posters",{"id":30,"doc_module":9,"doc_module_name":10,"category_name":31,"show_sort_weight":32,"slug":33},16,"Social Media",50,"social-media",{"id":35,"doc_module":9,"doc_module_name":10,"category_name":36,"show_sort_weight":37,"slug":38},17,"Forms",40,"forms",{"id":40,"doc_module":9,"doc_module_name":10,"category_name":41,"show_sort_weight":42,"slug":43},18,"Letters",30,"letters",{"id":45,"doc_module":9,"doc_module_name":10,"category_name":46,"show_sort_weight":47,"slug":48},21,"Paper Templates",5,"papers-templates",{"id":50,"doc_module":9,"doc_module_name":10,"category_name":51,"show_sort_weight":4,"slug":52},158,"General","general-158",{"code":4,"msg":54,"data":55},"ok",{"site_id":56,"language":57,"slug":58,"title":59,"keywords":60,"description":61,"schema_data":62,"social_meta":119,"head_meta":121,"extra_data":123,"updated_unix":125},105,"en","proteomediscoverer-mascot-1424-cheat-sheet-v1","ProteomeDiscoverer Mascot 1.4/2.4 Cheat Sheet - v1","","ProteomeDiscoverer/Mascot LC-MS/MS results cheat sheet for interpreting matched proteins and peptides in an Excel-style report. It explains protein confidence scoring, peptide and protein “area” based on the three most intense peptides, and quantitative use of peptide spectrum matches (PSMs). It also covers peptide/protein match counts, sequence coverage, protein MW, optional annotations, and key quality controls including PEP and false discovery rate group thresholds (High/Medium/Low).",{"@graph":63,"@context":118},[64,80,101],{"@type":65,"itemListElement":66},"BreadcrumbList",[67,71,74,77],{"item":68,"name":69,"@type":70,"position":9},"https://docshare.wps.com","Home","ListItem",{"item":72,"name":10,"@type":70,"position":73},"https://docshare.wps.com/template/",2,{"item":75,"name":51,"@type":70,"position":76},"https://docshare.wps.com/template/general/",3,{"item":78,"name":59,"@type":70,"position":79},"https://docshare.wps.com/template/proteomediscoverer-mascot-1424-cheat-sheet-v1/573272/",4,{"url":78,"name":59,"@type":81,"image":82,"author":87,"headline":59,"publisher":90,"fileFormat":93,"inLanguage":57,"description":61,"dateModified":94,"datePublished":95,"encodingFormat":93,"isAccessibleForFree":96,"interactionStatistic":97},"DigitalDocument",{"url":83,"@type":84,"width":85,"height":86},"https://docshare.wps.com/thumbnails/proteomediscoverer-mascot-1424-cheat-sheet-v1/573272.png","ImageObject",442,249,{"name":88,"@type":89},"McGucket","Person",{"url":68,"name":91,"@type":92},"DocShare","Organization","application/pdf","2026-10-17","2026-10-14",true,{"@type":98,"interactionType":99,"userInteractionCount":79},"InteractionCounter",{"@type":100},"ViewAction",{"@type":102,"mainEntity":103},"FAQPage",[104,110,114],{"name":105,"@type":106,"acceptedAnswer":107},"What does a higher Mascot protein or peptide score indicate?","Question",{"text":108,"@type":109},"Higher scores indicate higher confidence in the match. Protein scores and best-scored PSM peptide scores are intended as confidence metrics.","Answer",{"name":111,"@type":106,"acceptedAnswer":112},"How is the protein “area” metric calculated?",{"text":113,"@type":109},"Protein areas are calculated as the average area of the three most intense peptide signals. Peptide uniqueness is not considered in this area assignment.",{"name":115,"@type":106,"acceptedAnswer":116},"How are PEP and FDR used to judge match quality?",{"text":117,"@type":109},"Posterior Error Probability (PEP) estimates the chance a PSM is incorrect (lower is better). False discovery rate (FDR) groups classify confidence as High (\u003C1%), Medium (1–5%), and Low (>5%).","https://schema.org",{"og:url":78,"og:type":120,"og:title":59,"og:site_name":91,"og:description":61},"article",{"robots":122,"canonical":78},"index,follow",{"doc_id":124,"site_id":56},573272,1792109494,{"code":4,"msg":5,"data":127},{"doc_id":124,"user_id":128,"nickname":88,"user_avatar":129,"doc_module":9,"category_id":50,"category_name":51,"doc_title":59,"doc_description":61,"doc_content":130,"file_id":131,"file_url":132,"file_type":133,"file_size":134,"view_count":79,"is_deleted":4,"is_public":9,"is_downloadable":9,"audit_status":9,"page_count":9,"language":135,"language_code":57,"site_id":56,"html_lang":57,"table_of_contents":136,"faqs":137,"seo_title":138,"seo_description":61,"update_tm":139,"read_time":4},1236954412713,"https://us-avatar.wpscdn.com/davatar_29158cc5080c5b710cf443261637dec0","Average area of the 3 most intense peptides for a protein group per sample.  \nMascot protein score for sample A. Higher score => higher confidence in match.  \nClick + to see peptide details.  \nSpecific to Sample A  \nSpecific to Sample B.  \nArea of peptide in Sample A  \nArea of peptide in Sample B  \nModification(s) included in search and matched to peptide.  \n\\# of proteins that the peptide matches.  \nB B B  \nA guide to ProteomeDiscoverer (1 .4)/Mascot (2 .4) based LC‐MS/MS data analysis (Excel format) .  \nThis report format presents qualitative and quantitative details of matched proteins and peptides  \nA B  \nA A A A B  \nPoPrtentoteil contaminating proteins are marked CON_ .  \nTotal \\# of peptides.  \n% protein sequence coverage for sample A.  \nA  \nA  \nBA  \nB  \nB  \nTotal \\# of Peptide Spectrum Matches.  \n\\# of peptides matched to the protein in sample A.  \nPosterior Error Probability (PEP) is the probability that the observed PSM is incorrect. Lower is better.  \nB A  \nMascot peptide score for best scored PSM for the particular peptide. Higher score, higher confidence.  \nTotal \\# of Peptide Spectrum Matches in Sample A.  \nMaster  \nprotein MW.  \nOptional protein annotations.  \nSample B: False Discovery  \nRate group: High: \u003C1% or  \nbetter, Medium: 1‐5%, Low: >5% .  \nSingly charged mass of peptide.  \n\\# of missed cleavages. in the peptide.  \noin3 0 6.   \nGood to know ● Unique (Σ\\# Unique Peptides) and all peptides (Σ\\# Peptides) together with sequence coverage (Σ Coverage) are used to understand sequence representation of the particular protein. ● Peptide Spectrum Matches (Σ\\# PSMs) indicates how many MS/MS spectra that were matched to a particular protein or peptides. PSMs can be used as a quantitative metric. When comparing same protein, higher number is an indication of higher abundance. The robustness of this metric increases with greater numbers. ● Areas assigned to proteins is calculated as the average‐area‐of‐the‐3‐most‐intense‐peptides‐signal. Uniqueness or not of a peptide is not taken into account. The ability to gauge changes increases with increased with fold difference and signal. A peptide or protein assigned an ‘area’ of 0 was either not matched or could not be quantified. ● A peptide match False Discovery Rate (FDR) is calculated per searched data set. Peptides can be assigned as High (FDR \u003C 1%), Medium (FDR: 1%‐5%) or Low (FDR >5%) confidence based on statistical calculations.","cbCaikrtrkmRvWwP","https://ap.wps.com/l/cbCaikrtrkmRvWwP","pdf",248614,"English","# Protein and peptide scoring\n## Mascot scores and match counts\n# Quantitative metrics\n## Area, PSMs, and sequence coverage\n# Confidence and error estimates\n## PEP and FDR groups","[{\"question\":\"What does a higher Mascot protein or peptide score indicate?\",\"answer\":\"Higher scores indicate higher confidence in the match. Protein scores and best-scored PSM peptide scores are intended as confidence metrics.\"},{\"question\":\"How is the protein “area” metric calculated?\",\"answer\":\"Protein areas are calculated as the average area of the three most intense peptide signals. Peptide uniqueness is not considered in this area assignment.\"},{\"question\":\"How are PEP and FDR used to judge match quality?\",\"answer\":\"Posterior Error Probability (PEP) estimates the chance a PSM is incorrect (lower is better). False discovery rate (FDR) groups classify confidence as High (\\u003c1%), Medium (1–5%), and Low (\\u003e5%).\"}]","ProteomeDiscoverer Mascot 1.4/2.4 Cheat Sheet - v1 | PDF",1791936296]