10/11/14
Sat, 10/11/2014 at 11:17 AM
Customer: I have attached a spreadsheet showing the type of data I have after doing PAGE and MS on tissue samples of uterine lining of two types. I wish to compare the proteins from one group B with group to see preliminary differences in protein expression in two groups - here I have only attached results of B but I also have comparable dataset for P. I want to see any differences in protein/peptides between two groups.
Sun, 10/12/2014 at 3:17 PM
AccuraScience LB: The file you sent came out of a typical label-free identification and quantification experiment. We might not able to evaluate the false discovery rate (FDR) and other accurate quantification measurements, if we only work on these files. If you could check with the proteomics lab to see if they could provide the mascot searching "*.dat" file - which are the raw searching results with decoy database setup, it would be best. But if not, any proteomics raw file , for instance, "*.mgf" file with required database ( *.fasta), would help for the precise analysis.
Wed, 10/22/2014 at 2:00 AM
Customer: Unfortunately the proteomics unit at the university has been reorganised due to funding issues. I have therefore found it difficult to get the original files which you suggested would be required.
Thu, 10/23/2014 at 11:13 AM
AccuraScience LB: I took another look at the search result file you provided. Your data had FDR < 1%, the ION score is 20, and protein probability is 0.05. The data quality should be good enough to use label-free spectral counts to do quantification in multiple samples. We could proceed the analysis based on the search result file, though some additional coding would be needed.
Another piece of information that is required for the analysis is the "meta-data" about the samples, i.e., the sample amount information when the proteomics experiments were performed. If you or your associate handed the sample for the proteomics unit, then I am sure you have the sample amount information recorded somewhere. When they did the experiments, they should have basic information about the volumes injected to the equipment (e.g., 3 ug or 5 ug). This information is required for the "differential expression" analysis, because, apparently, if sample amounts used in the experiments were different across samples, this difference needs to be accounted for in the analysis.
Back to Other Selected Recent Inquiries
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.