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Description:
This group provides news and support for users of Crux, a program for identifying peptides from MS/MS data.
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Crux error when searching huge space
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Dear Colleagues, I'm a new user of Curx. I'm doing an experiment on searching an expanded database by specifying PTM on all amino acids. The parameters are set as follows: -------- precursor-window=5 precursor-window-type=ppm isotopic-mass=mono fragment-mass=mono mz-bin-width=0.36 mz-bin-offset=0.11... more »
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Crux sequest-search for qexactive data
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Hello,
I have used Crux sequest-search with the parameters below to search a
sample run on a qexactive instrument.
precursor-window=10
precursor-window-type=ppm
isotopic-mass=mono
enzyme=trypsin
missed-cleavages=TRUE
num-decoys-per-target=0
Everything worked fine, but after post-processing with percolator I... more »
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Error in NSAF calculation?
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Hi All,
I was looking closely at the NSAF values of some data and was noticing
that the NSAF values are all very tiny (most abundant protein has
NSAF : P69905 = 0.00021868. However, the unnormalized score (spectral
count I assume) is P69905 = 1137.0. Well, P69905 is 142 aa long, so
the numerator of the NSAF (as its described on... more »
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percolator error
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Hi,
I have been getting an error in percolator on a good number of files,
and was wondering if anyone knows what might be going on.
The command I am running is:
/usr/local/bin/crux percolator --output-dir perc --fileroot
OCI_AML3_070111_2 uniprot-taxonomy_human_reviewe d_020612 search
I get the following error:... more »
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deltaCn
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This email was not sent to the Google group, but I'm replying here in case others have this question: Dear Prof. William Stafford Noble This is Naiping Dong, a doctoral student in Central South University in China. When I used Crux to learn the XCorr scores, I found that in some results, the deltaCn scores would be as large as more than 100.... more »
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Tide
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Hi Johannes and Christine, This question has come up a few times recently, so it's clearly important to some users. I'd suggest as a temporary workaround to convert to ms2 and from that to convert to spectrumrecords, since both those conversions seem to work. (Please report whether this two-step process works for your data.) Bear in mind, Tide is still a... more »
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tide setup questions
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First of all, thanks for all the work you've put into this project!
I'm trying out tide with an eye to replacing or at least supplementing
our Proteome Discoverer 1.3 installation. I've successfully (I think!)
put together a workflow from Orbi .raw as input through pep.xml
or .sqt as output, but I've run across a few things I'm hoping to get... more »
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search-for-matches, SQT files, and new version of q-ranker
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Forwarded message:
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The new version of crux contains a rework for the q-ranker, which
requires a .sqt file. This was different from the previous version
which did not. As I can see, only "sequest-search" provides a sqt
file, so is there any converter for the 'search-for-matches' results?
Many thanks,... more »
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crux 1.37 minor bug
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Hello Crux Users, I'm writing to inform you of a bug that was recently discovered. (Many thanks to the user who reported it.) The results for crux search-for-matches and crux sequest-search may be off if you change the --bin-width parameter. The default value still works. The bug will be fixed in the next release coming out later this month.... more »
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