Blog Archives

GPM Tip of the Day

Ron Beavis recently reminded me that the the GPM has several very useful graphs that are automatically created when you search your data using theGPM The Graph below plots the fraction of identified spectra (Green) plotted against the predicted retention time in

Posted in Proteomics Blog

We can charge you more if you want!

True story, had a potential customer tell us that they did not want to send us samples because our turn around time was too good and are charges were reasonable. When asked why, they said they were trying to justify purchasing their own

Posted in Proteomics Blog

Scaffold FDR Calculations

Ever wonder why Scaffold calculates the FDR’s the way it does? Here is a good primer on how FDR’s are calculated Scaffold Calculates FDR’s a bit differently Here is the inside scoop From Brian Searl from proteome software “When you calculate

Posted in Proteomics Blog

Minor Updates

We updated our FAQ’s on Co-authorship and number of replicates needed . Please leave comments if you have any. We like to read them Also updated the Proteomics Profiling Page to add info about our data independent analysis

Posted in Proteomics Blog

Journal Club

Starting next week we will be having a monthly Proteomics Journal Club. Everyone is welcome to come and join our monthly rotation. The First Journal club will be Wed July 16th at 3 pm Room 1414. We will be discussing

Posted in Proteomics Blog

Protein Decoy FDR’s?

There was a lot of discussion of the utility of protein decoy FDR’s at ASMS. Especially in light of the two Nature human proteme papers that only calculated peptide decoy fdr’s on the spectra level. I assume it was spectra

Posted in Proteomics Blog

ASMS 2014

Our ASMS poster will be posted soon in the poster section . Still trying to recover from the excellent meeting. Hopefully I’ll get those up soon and provide a wrap up of the interesting things I learned at ASMS 2014

Posted in Proteomics Blog

Simple wins the day

So it’s often temping to use the newest and the latest technologies for separating proteins and peptides prior to LC-MS/MS, but it’s often the case that tried and true technologies often win the day. For example in this recent paper

Posted in Proteomics Blog

2014 Summer short Course

Our Summer short Course will be Aug 4 -> Aug 8th this year (2014).  Head over to our Short Course page for more information. I will update the page as we finalize what we are going to cover this year.

Posted in Proteomics Blog

New Web site

Welcome to our new web site. Please let us know if we forgot to move something over or some of the links are not working. Moving a website to a new platform (SquareSpace to WordPress ) is a lot of

Posted in Uncategorized