NYEPLAK

Re analysis of the great Gomez Baena et al dataset They arent messing around! Yesterday I made a short post on this new study in Open Reports.  Ill be honest, I thought it was a seriously impressive sample set, but I was a little skeptical about the results. Not that I didnt believe the authors could find the bacterial proteins, but I was skeptical that the results could be that clean cut. Ive seen a few "identification of digested bacterial proteins in body fluid" studies and even with high resolution data the matrix is complex enough that there is noise there. These results just seemed a little too good to be true. Shoutout to ProteomeXchange/PRIDE and these authors for making this data extremely easy to obtain, sort and reprocess overnight!! For my re-analysis, I threw all the files into PD 2.2 and used the default processing workflow for LTQ-Orbitrap LFQ and LFQ concensus with enhanced annotation.  I made a 77MB FASTA in PD by parsing a UniProt TrembL I downloaded in July...

Proteomic analysis of human cells grown in bacterial cellulose A LOT of biological studies of human cells occurs with cells grown in culture. And we can thank cell culture techniques for a huge amount of what we know of how cells work, but it has been no secret that there are some limitations to cell culture techniques. This is a nice open review on limitations -- with a strong title. Over the last 15 years or so there have been numerous ideas put forward to bridge the gap between cells growing in monolayers in cell culture and cells as they actually exist in human tissues and organs. Growing cells in 3 dimensions is something that has been discussed for years, but -- so far hasnt yielded much in the way of new understandings in biology. Please dont take this as a criticism, I know two great people working hard on this stuff right now who will have stuff out soon, but these complex bioreactors seem to come with their own bevy of complications -- which better technology may soon fix. In...

RIG Exploit Kit Shellcode analysis Brad published a traffic analysis exercise which I had a quick look at and felt that I wanted to take it to the next level so I started looking at how to decode the payload delivered by the exploit kit. I get the shellcode from the Flash exploit as its provided as a hex-encoded string starting with "90909090" (NOP): An easy way to go is to create an executable from the shellcode utilizing Shellcode2Exe to be able to step through it in OllyDbg. Taking the step into shellcode Loading it up in Olly, it will start with a loop which decodes the payload URL using XOR as seen below. The key can be found by inspecting ESI when first hitting the loop and the encoded data can be found by inspecting EDI. After decoding: The decoding loop will continue until the decoded byte is "!" (0x21), the reason will be explained later in the post under "Multiple payloads". The shellcode uses URLDownloadToCacheFileA to download the payload. Shou...

Prosight Lite! Free top down analysis of single proteins Now that 20 papers are out that have cited the use of Prosight Lite it may be time that actually link the paper on the blog -- as a partial thank you for how often I use this awesome free resource! Im too lazy to search the blog for some of the older posts on the software and Im too busy with work to write a real post for Tuesday, so here is the paper for Prosight Lite! download  file  now