In reply to Felipe's point 3, I created a custom database for positive mode and
negative mode with all common adducts.
Here is an example of the format I used for our positive database.. (first 5
entries only)
ID m/z Retention Time Identity
Fo
Hi Martin,
I too wanted to be able to add together scans, or even better subtract one from
another. This would have been a good way to remove background peaks by
subtracting blank runs for example.
However when you sit down and think about this it becomes very problematic for
accurate mass dat
Dear mzMine users,
I will be talking at the EMBL-EBI Industry Programme and MetaboLights Project
meeting next week on 22nd May.
The first session at 16:45 will show the features added during the Syngenta
sponsored development and at 17:15 I will lead a hands on tutorial session in
mzMine.
I w
Hi William and Ye-Soon,
Firstly regarding the baseline correction. We have this working on a number of
PC's here and it works fine. The lowest spec machine is a Pentium Dual core 2.6
GHz with 4GB RAM
The developer who wrote this module is on holiday currently but I will ask when
he is back if h
Dear Yee-soon,
I have recently had the task of installing a number of copies of mzMine 2.6 and
have a few modifications to the official setup instructions. It may be worth me
reproducing them here to make sure you have not missed anything.
It's also worth noting that you need a good deal of mem
Hi Chris,
How about some string parsing routine, i.e like what we did in Excel
So split the string by spaces into subsrings
Sort on nth substing
?
Cheers,
Mark
-Original Message-
From: mzmine-devel-requ...@lists.sourceforge.net
[mailto:mzmine-devel-requ...@lists.sourceforge.net]
Sent
Dear fellow mzMine users,
We have discovered a subtle problem with using the Gap-Fill function for
aligned peak lists.
The average mass is calculated after gap-filling and this appears to often be
different than the true exact mass, presumably due to gap filled peaks with
slightly different ma
Dear All,
I have been installing a fresh mzMine installation on 64 bit Windows 7 and I
tried to use Thermo's MSFileReader 2.2 dated 12/19/2011. This refuses to work
resulting in a "java.io.IOException Unable to Initialise RAW file object, have
you installed MSFilereader" message. I tried both
Hi David,
I am also using orbitrap and the biggest collection of files I have used is 220
!
I have a Win7 64 bit system with 8GB RAM and I have set the Heap Size to 4GB
One thing is that I don't convert to mzML I read the .RAW files directly which
can be done if you install the Thermo MS Filer
Hi Tomas,
Another observation - what happened to the "Close Project" on the file menu?
Why has it been removed - I thought it was useful !
Thanks,
Mark
-- -
Mark Earll
Research Leader - Metabolomics
Analytical Sciences (Office 102/65)
[cid:image001.jpg@
Hi Thomas,
I have noticed that when I select batch mode in mzMine 2.3 I get a message "At
least 1 raw data file must be selected" then if I select a raw data file I get
the message "At least one peak list must be selected" so basically I can't
access Batch mode at all
Previously in version 2.x
Hi Chiarina and Tomas,
I am using 64bit Windows 7 and reading Thermo .RAW files directly. The Thermo
File Reader is installed in ProgramFiles(x86) on my PC. I think your problem
hinges around the failed registration:
Error 1904.Module "C:\Program Files
> (x86)\Thermo\MSFileReader\XRawfile2.dll"
Hi Tomas,
Of course I've just realised the reason for the CSV issue is because you have
commas in the chemical names when they are brought back from the external
database..
i.e 3-Amino-1,2,4,-triazole
Not sure how this can be overcome
Cheers
Mark
-- -
Hi Sandra, Tomas,
Firstly thanks for the comments . As my file is some 15GB I don't think sending
it to you is an option ;-) However I have played around with the data and by
using the row filter I have filtered out peaks with fewer than 50 instances.
This is probably where the program was stru
Hi Tomas,
I have left my PC running for 4 days and the gap filling is still only 48%
complete. Since it was only 32% complete after one day it seems to be getting
slower with time.
Is there any reason this is so computationally intensive or is there a bug?
Many thanks,
Mark
-- --
Dear Tomas,
I am finding the gap filling algorithm very slow in mzmine. Its been running
all day on my 210 samples and only 32% complete. Considering the RANSAC
alignment only took 20 mins or so on the same data, this seems surprising. I
would have though the RANSAC routine would be more comput
Hi Tomas,
Thanks for the info. Does the mzXML format preserve ms2 spectra?
Last night I successfully loaded 210 .RAW files totalling around 15GB using the
XP virtual machine. Its slow but it does seem to cope OK.
Yesterday I discovered another ms format (YAFMS) which is meant to be smalle
Hi Tomas and fellow mzmine users,
I have found a workaround that allows me to read in Thermo .RAW files in mzMine
on Windows 7. Its a bit of a 'kerfuffle' but it does work:
Install the Windows 7 XP Mode virtual machine
Install Thermo Xcalibur 2.1 and accompanying files in the VM
Install Java an
Hi Tomas and mzmine users,
Now I have successfully installed mzmine on Windows 7 64 bit I have run into
another hiccup.
Thermo Xcalibur software does not run on Windows 7 but I have managed to
install it using the "Windows XP mode" which is an XP virtual machine.
Unfortunately this does not al
Hi Tomas,
My colleague Chris Pudney has found the solution to the 3D plot not working in
Windows7 64bit
I had installed the early access (EA - update 23) version from
http://download.java.net/jdk6/
jre-6u23-ea-bin-b03-windows-amd64-18_oct_2010.exe but Chris informs me the
current official r
Hi Tomas,
There is a problem when downloading Java for 64bit windows as the java website
just gives you the 32 bit version regardless. See the webpage which explains it
here: http://windows7themes.net/windows-7-java-64-bit-download.html
So I went to the site http://download.java.net/jdk6/ and
Hi Tomas,
I have installed mzmine 2.1 on windows 7 64 bit with Java 6 and Java 3D
installed. I have verified that Java 3D works by visiting the java 3d test page
at .downloadjava3d.com/java3dtest.php and indeed I do see a 3D spinning
image. (The hardware is an Intel Xeon 8 core processor wi
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