And if we figure out what it is (or not, and just search for it anyway) I can use the new ptmRS to get confident site localization of the mod! Is it the next -ome that we have never looked at that is disregulated in tumors? We won't know until we take a look. Interestingly, there really isn't anything of that mass in Unimod. In the case of this file, the Excel sheet pointed out that I should definitely search for methionine oxidation AND it pointed out a slew of peptides that have a +128 Da mass shift. You get several other HTML pages generated with more details AND you get an Excel sheet with potential wild card results. You can use that data to fine tune how you set up your real search. It gives you your top scoring proteins and your potential m/z errors. This sweet overview of the file opens in your default browser. My poor personal desktop is about to burst into flames. PS, ignore the "Low memory warning" above. Now, its supported by this nice GUI so now these claims can be scrutinized by me (when I finish the next previous 10 things on my list) or by you!
PEPTIDESHAKER PTM COLOR CODE
Now, thats interesting all on its own, but I've never seen a link to download this magic code before. In the introduction paper for MS-GF+, the authors showed that on virtually every MS and fragmentation mode, their algorithm produced more and better IDs than Mascot running Percolator. Namely, using p values to accurately gauge the efficiency of peptide identifications. What's that? It is a program written a few years ago that took a good hard swing at something people ask about a lot. Not only do you get a nice (and interesting themed) GUI, but there is a big reason that you might want to check it out now if you haven't before. Heard of it, but I never went out of my way to check it out. Y'all are always coming up with so much cool stuff! Peptide Shaker isn't exactly new, but its mostly new to me. Imagine that it had to look at every amino acid possibility and up to 600 Da heavier! What are the combination? It took a few hours. I just said "do a wildcard search up to 600 Da".
PEPTIDESHAKER PTM COLOR MOD
What are the chances that Byonic could find a mod like this? So, I gave Byonic this file and didn't tell it about the mod. So, I took a file that was treated this way and ran it. You can then use the Mass tags function on the Orbitraps to, basically, do a gas phase enrichment for the low abundance crosslinked counterparts. They are exactly 8.00 (I forget) Da apart. The crosslinks come in two types, the heavy and the light, but otherwise completely identical. The idea is that when two proteins are in association, you crosslink them with this compound. Proof? You know those crosslinkers that were developed at the University of Victoria Protein Centre? ( Described in this paper).
And not to poo on anybody, but this works. Wildcard search! Fully customizable wild card search! Wooooohoooo! Okay, so you are thinking "big deal, right? We can wildcard search in Mascot and some other software." Sure. The sounds of the CPU fans in this room, lol!
PEPTIDESHAKER PTM COLOR UPDATE
I have some glycopeptide files here now that I may process and update you on, but my sample queue is loaded for at least the next 3 days. Specific focuses are available for glycopeptides! What else does glycopeptide analysis? Sure, there are some packages out there, but my dog, this is EASY. Simple to set up, just like a SequestHT or MSAmanda search (Advanced parameters are hidden because it has too many options for a screenshot on this laptop!)
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