{"id":2856,"date":"2019-10-07T00:00:00","date_gmt":"2019-10-07T00:00:00","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/analyteguru\/don-t-hide-from-the-unknown-part-3\/"},"modified":"2026-02-17T22:05:30","modified_gmt":"2026-02-17T22:05:30","slug":"access-unknown-compound-analysis-tools-and-mass-spectral-libraries","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/analyteguru\/access-unknown-compound-analysis-tools-and-mass-spectral-libraries\/","title":{"rendered":"Unknown Compound Analysis Tools and Mass Spectral Libraries to Harness the Power"},"content":{"rendered":"

This is Part 3 in a series.<\/em><\/p>\n

So, we’ve come on a journey from ensuring that we can completely profile (MSn<\/sup> analysis) all of the small molecule components within a complex sample (I WANT MY CAKE — Part 1<\/a>), through to taking all of this extensive and high-quality MS and MSn<\/sup> data and determining the identity of the many components using wide-ranging mass spectral libraries (From Cake to Cloud, Data to Knowledge: Part 2<\/a>).<\/p>\n

\"unknown\"

Don’t be in the dark about unknown compounds.<\/p><\/div>\n

Well, true unknowns, i.e., unknown unknowns, would indeed take a lot of manual work to even begin to stand a chance of any degree of confidence in structural assignments. Thankfully, with high-quality accurate mass data, and with multiple levels of fragmentation providing what we could call a “spectral tree” of data, we have a lot of information available to us to start this process.<\/p>\n

Now this spectral data contains the information that we need to determine a structure, but the information is effectively buried or coded within the mass spectral data and are products of potentially complex and numerous fragmentation reactions.<\/p>\n

Fear not — we’ve got your back!<\/strong><\/p>\n

Yes, that’s right — even if you have an extensive list of compounds that were not present within the mzCloud library<\/a>, the more than 5,000,000 spectra* contains extensive fragmentation information (up to MS9<\/sup>) for a structurally diverse range of over 17,000 compounds* (* at the time of writing) means that there is likely some structural overlap between your unknowns and the many fragments contained within the spectral library.<\/p>\n

How do we identify unknowns then?<\/h3>\n

Glad you asked.<\/p>\n

With mzLogic Data Analysis Algorithm<\/a>, you can take your confident elemental compositions (based upon excellent mass accuracy combined with high resolution, for isotopic clarity) and search many on-line structural databases such as ChemSpider,<\/a> which has over 73,000,000* chemical structures to see how many hits you get for these unknown elemental compositions. For example, let’s take the elemental composition C16<\/sub>H24<\/sub>N2<\/sub>O2<\/sub> and search multiple online databases — we get 1,468 possible candidates. That is a lot!<\/strong> What happens next is easier to explain with a picture:<\/p>\n

mzLogic reduction of putative candidates. a) Searching online databases with an elemental composition can return many hundreds of possible candidates. b) mzLogic uses the extensive high-quality fragmentation information from mzCloud to identify fragments which are similar. c) Structurally similar fragments are rapidly identified using forward and reverse searches and then d) ranked based upon their measure of similarity. e) The ranking reduces the many hundreds of potential candidates to a significantly smaller list of putative structures. Visualization tools provide explanations for the ranking.<\/p>\n

Great! So in short, mzLogic compares mzCloud similarity matches against database hits, looking for maximum common substructure. mzLogic ranks database hits based on structure overlap, leveraging real fragmentation information to rank structure candidates for true unknowns.<\/p>\n

Thankfully, for those who want to know more information, there is this handy mzLogic Smart Note, <\/a>which details everything in a lot more detail!<\/p>\n

How do we get to access this mzLogic?<\/h3>\n

Well, mzLogic is integral to both Thermo Scientific Compound Discoverer<\/a> and Thermo Scientific Mass Frontier software<\/a>. Once you have your reduced list of putative candidates, if you really need to interrogate things further, then greater insights can be found through Mass Frontier’s in-depth visualization and understanding of fragmentation pathways, as well as more unique ways to search the fragmentation spectra of mzCloud. For example, Mass Frontier software provides a rational understanding of fragmentation schemes using the proprietary mass spectral interpretation algorithms of the HighChem Fragmentation Library. Mass Frontier software includes the fragmentation mechanisms published in more than 95% of all peer-reviewed scientific journals.<\/p>\n

Discover confidence in unknown identification<\/h3>\n

Discover for yourself how Compound Discoverer software<\/a> and Mass Frontier software<\/a> can harness the power of mass spectral libraries and unknown compound analysis tools, as well as numerous other valuable tools to get the most out of your data.<\/p>\n

Also, there is more information for you here:<\/p>\n

Mass Spectral Libraries ><\/a><\/p>\n

Compound Discoverer Brochure ><\/a><\/p>\n

Mass Frontier Brochure ><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

So, we\u00e2\u0080\u0099ve come on a journey from ensuring that we can completely profile (MS n analysis) all of the small molecule components within a complex sample<\/p>\n","protected":false},"author":1327,"featured_media":2858,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[1809],"tags":[1810],"division":[],"class_list":{"0":"post-2856","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-mass-spectral-libraries","8":"tag-mass-spectral-libraries","9":"entry"},"_selected_authors":[],"_selected_reviewers":[],"acf":[],"yoast_head":"\nUnknown 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