Fragments Report Null modifications Carboxymethyl (C) Acetyl (N-term) Carbamidomethyl (C) Oxidation (M) Phospho (ST) Or in bar form…. Null modifications Carboxymethyl (C) Acetyl (N-term) Carbamidomethyl (C) Oxidation (M) Phospho (ST) Read More
The trick with problem sets so sparsely filled with noteworthy information is skipping as many processing steps as possible without marring the final results by skipping something important. I have made some modifications to GFS and am testing those now: If MSMSFit goes through all of the y-ions and finds less than 12% match then [...] Read More
“Tandem mass data hash,” try to say that five times fast. To get a better feel for how MS/MS data will be represented as a hash I wrote a quick visualizer. How the MSMS data is hashed: an NxM bin matrix is computed where N is the number of bins to store mass and M [...] Read More
This was confusing the hell out of me. I’d have an fprintf call that would say something like “loading spectra…” and a breakpoint before that and in the console it would still print “loading spectra…” and continue on its merry way like the breakpoint didn’t even exist. So what’s the real problem? I don’t know [...] Read More
I’m curious if a job on one DTA/PKL file with N spectra will run faster than a job that processes the exact same data broken into N different files. I just wrote a quick java app to take OutputFile2.dta which has 112 spectra and split it into 112 different dta files. At the moment I [...] Read More
…and sits down in the barber’s chair awaiting his hair cut. “That’ll be eight dollars, please,” says the barber. “What about my hair cut?” “I gave you one. It’s a null hair cut.” haha. Read More
Some example intensity data of MS/MS data. My thought is that perhaps selecting local maxima may be a good way to cull the peaks in our PKL and DTA files. The basic algorithm: Select a peak if its intensity is greater than both the previous peak and the next peak. Peaks that would be selected [...] Read More
Of course he doesn’t read this blog, so he won’t know until this afternoon that I’ve already created the visualizer for his first set of data: (Larger View) Read More
This assuages my performance fears of porting to a MySQL database. The MEMORY (HEAP) Storage Engine Read More
in Spectrum.m. It’s a minor retooling of readPKL. Working on combining the two…. Read More
The one everyone thinks is useful, the one on SourceForge, is out of date. Google Code has a more recent fork of the project HERE. Usage: Google on MCPConnection. In general I’m surprised at the low amount of MySQL support in OS X. Read More
Grand Central Dispatch: Wikipedia Apple PDF Read More
For a basic database which holds peptides from in silico digestion of a genome, I think these fields will be helpful: peptide – the chain sequence of amino acids location – This will probably be many fields which will track location information mass – (theoretical) size – the number of amino acids cleavage – number [...] Read More
It looks like finding mass list files goes on in runListsWithParams in ClientManager loadTandemData in FHMSMSCategory. tandemFilesContainedInDirectory in ClientManager At first glance it looks like the code in runListsWithParams in ClientManager is useless… this is also where a bug is popping up. Read More
Jainab and I have discussed this before, but I want to get it down: Taking your peak list, sorting by intensity, then selecting the top X of them can be detrimental for this reason: Some locations where fragments are very likely to occur and with high intensities can act as intensity hogs. They will be [...] Read More
For my reference more than for yours: frenchbroad:gfs.git risk2$ git cvsimport -v -d :local:/Volumes/LabShare/cvsroot GFS-Vec-V2 Initialized empty Git repository in /Users/risk2/Documents/gfs.git/.git/ Running cvsps... cvs_direct initialized to CVSROOT /Volumes/LabShare/cvsroot cvs [rlog aborted]: -t/-f wrappers not supported by this version of CVS A legacy version of cvs with -t/-f wrapper support is available as: /usr/bin/ocvs. Read More
You probably don’t need to. If you have the Git tool installed it is probably one of the tools that comes with it. To check try this on the command line: git help -a | grep cvsimport I got that from this site on how to import CVS into Git. The official Git page on [...] Read More
need to work on getting this method (if that is what it is called) to work. Right now we are having to convert from DTA to PKL. NOTE: reference readPKL — it works with all newline characters. Read More
So MSMSFit may be a good replacement for seqtagscore, but it doesn’t solve the redundant overhead processing that comes with comparing a directory of fasta files to a directory of pkl files. The way we are doing it now is like an individual job for each comparison; that means that if there are 100 pkl [...] Read More
