10/02/14
Customer contacts us via online chat, and asks about pathway analysis for proteomics data. Although our current Lead Bioinformaticians are not particularly experienced with spectrum-level proteomics data (Note - we are trying to identify proteomics analysis experts to join our Lead Bioinformatician team), following spectrum analysis, we are capable of analyzing and interpreting peptide sequence and protein level data. Customer asks about pathway analysis, in particular, she says she is considering an option without having to purchase a MetaCore license. She forwards a number of papers in her domain after the chat session.
Fri, 10/03/2014 at 12:00 PM
AccuraScience LB: I have got chance to quickly browse through the papers you sent. Work related to pathway analysis would include GO-based analysis identifying significantly enriched GO terms among differentially expressed proteins using DAVID, a similar analysis using the UniProt resource (http://www.uniprot.org/), and MetaCore.
We can handle most parts of this work without problem. The only part that involves higher level of uncertainty is related to MetaCore: there are a number of free tools that might be considered as potential substitute for MetaCore, and these tools include: Cognoscente, StarNet, Ariadne Pathway Studio (free trial), iPathwayGuide, Moksiskaan, Pathwaycommons, GeneMANIA, HumanCyc plus, and Reactome pathway analysis tool. The thing is, although they are generally considered the same category of tools, none is exactly the same as MetaCore, and most were developed to suit RNA-level analysis, thus it will take some digging to find out how they work with proteomics data. Therefore, if you would want us to do this for you, the first project is expected to involve a lot of exploration, and might turn out to be less cost-effective than purchasing a MetaCore license (which costs $4900 in the U.S.). But this option will offer longer term benefit, because the expensive exploration will happen only once.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer’s privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.