Skip to main content ↑ ↓

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - Jan Stanstrup

138
XCMS / Re: Targeted (and consistent) peak detection with XCMS
Any chance to get this into XCMS? XCMS is currently being overhauled so perhaps now is the right time...

EDIT: I wonder if benjie still reads this? Seems it is a few years since he logged in.
EDIT2: Anyone else has a good idea of how to use XCMS for targeted peak picking? Right now there doesn't seem to be any straight forward method apart for picking all peaks and filtering afterwards. Eventually findmzROI can be used and ROI.list supplied directly but that seems rather convoluted...
139
XCMS / Re: Peak filling - an example of strange results
I would start by troubleshooting the group step. It can be either the m/z or the rt dimension that goes wrong. If the peaks have long tails or your parameters are bad the peaks could get cut up. Or you could have small peaks you don't see without zooming specifically.
It would be easier if you posted parameters for your processing.
You can possibly use a function I have written to understand better what is going on: http://www.metabolomics-forum.com/index.php?topic=577.msg1789#msg1789

Another problem with orbitrap data is that you can get so-called shoulder peaks or satellite peaks in the m/z dimension. If you are affected by that (look at the mass peak and zoom at low intensity around the peak. Do you see some very small noise-like mass peaks around the real peak?) you can use xcmsRaw.orbifilter from https://github.com/stanstrup/chemhelper to filter the raw data before analysis. But I don't think it is that. that usually creates a lot of peaks in the table with slightly different masses.

It looks strange that you say there is a peak at 140 s and the closest it finds is 130 sec...

I am not sure what output table you are talking about. What function generates it? If you use the one that calculates statistics I think it is ordered by p-value (not sure, never use it).
141
Compound identification / Re: A list of common neutral losses
The tsv files? I think you can treat them as csv for all practical purposes. Just that opening csv in excel seems to be system dependant (expecting different separators depending on the locale). With tsv it is explicit what to expect.
142
Compound identification / Re: A list of common neutral losses
I have created a github and added the Keller list as separate tsv files: https://github.com/stanstrup/common_mz
I have opened issues from some of the other possible sources that were mentioned here: https://github.com/stanstrup/common_mz/issues

It would be cool if we could collaborate on this.
One thing I have been thinking about is how to handle fragments of contaminants. For example can you think of a nice way to add all known masses originating from a specific PEG?
If you think it should be organized differently please speak up.
144
Site related / Re: Logo needed for @MetSoc-Forums
Btw.: would it be possible to upload a vector version so we have that here for safe keeping?
I think we could use your version of the MetSoc logo for the favicon too (somehow cropped to a square).
146
Site related / Re: Logo needed for @MetSoc-Forums
I think it should be based on the MetSoc logo. Nothing fancy or very time consuming should be needed.

We could also use a favicon version of the logo for the forum.
147
Compound identification / Re: A list of common neutral losses
Hi Ville.

There are a couple of good resources. The best is the supplementary material from:
Keller BO, Sui J, Young AB, Whittal RM. Anal Chim Acta. 2008;627(1):71–81.

There is also the book "Pretsch, Buļhlmann & Badertscher. Structure Determination of Organic Compounds: Tables of Spectral Data." with more fragments. Your might have access online through your library.

Then there is the list I compiled for CAMERA annotation: https://github.com/stanstrup/chemhelper/tree/master/inst/extdata (beware that the mz difference is to the monoisotopic +/- H peak in that list)

I have some additions to the Keller list. Perhaps I can put that on github and we can expand from that. Or perhaps google docs etc might be easier. What do you think? I know Keller wouldn't mind (I wrote with him recently) and as far as I know the publisher, Elsevier in this case, doesn't have copyright on the data itself (can someone confirm this?).
149
Publication Committee / Re: New Metabolomics Society Journal - Your Input Needed!
Wish list:

  • Open access at sane prices
  • Double blind review
  • free color figures. no need to spend money on print
  • Require description of the identification of each compound (beyond MSI)
  • Require reprodudible data analysis (i.e. no black box in house methods)
  • Require raw data available
  • Description of data analysis methods uninteresting without available implementation

EDIT: I think @Reza Salek intended to put it in this forum so I moved it here.
150
Announcements / Re: Announcing new forum
Portal
We are introducing a new portal front page, which shows you the latest posts together with a section of the latest announcements below. At the top of the front page, you will find a navigation bar that can take you to all the forums sections as well as to your private messages. On the right hand side you will find the links to your accounts/profile settings.

(click to enlarge the image)
[attachimg=1 width=800]


New Forum organization
Due to the merger, unavoidably, some forums sections became redundant. Section that were rarely used have now been merged with similar sections under new heading. Click the "Forum" link in the upper navigation bar to see all the current forum sections.
We have organized the forum in categories and sections and sub-sections.

(click to enlarge the image)
[attachimg=8 width=800]


Follow topic and specific forums sections
Below each forum and at the end of each topic you will find a "notify" button. If you enable this you will receive email notifications of new replies.

You can change how you get replies in the account settings. Click "My Account" in the upper right corner --> Account settings. Then hover over "Modify profile" and select "Notifications".


Reply by email
We are also happy to announce that you can now reply to a topic using your email. It works in this way: You go to a forum section you are interested and click “notify”. You will receive an email each time a new posts arrives in that forum section. You can then reply using your registered email and your reply will appear on the forum under the topic you are replying to.

If you do use this feature please remove the quote of the previous post that your email client likely added. Otherwise the quote will appear in the forum too. However be sure to include the key that looks something like "[dceacc6034782277a456839acaa6cdeb-m2937]"; otherwise the post will not be added.

For this feature you work you need to change how you receive notifications to include the whole post and not just a notification of a new post.
Click "My Account" in the upper right corner --> Account settings. Then hover over "Modify profile" and select "Notifications".
We suggest the following settings:

(click to enlarge the image)
[attachimg=7 width=800]

Note: Starting a new topic by email is not allowed.


Mentions
You can now “mention” other users in your posts, if you want to direct a certain comment at a specific user. You can do this by using the “@” sign followed by the user name; for example write @example_user_name and example_user_name will be notified that you have mentioned him/her.


Post and Member likes
One of the new features that we have added is the ability to like a post or give credit to a user for solving a problem. This way our users can get credit for the time they put into making useful posts.

Hover over a user and you can click "applaud" or "smite":

[attachimg=5 width=327]


Below and to the right of each post you will find the "Like" button:

[attachimg=6 width=307]


Twitter integration
We added to ability to integrated with twitter. @MetSoc-Forums you will find new topics posted with a link to the forum thread. Please use the "follow topic" option to get email notification of new replies to the topics.



Solved topics
You can now mark topics as solved:
[attachimg=3 width=492]


In the list of topics it then appears as:
[attachimg=2 width=335]


RSS feed
You can get an RSS feed for all the forums using:

Code: [Select]
http://www.metabolomics-forum.com/index.php?action=.xml;type=rss2;limit=50

If you want an RSS feed for specific forums you need to browse to each specific forum. You will see that for example the XCMS forum has the URL:

Code: [Select]
http://www.metabolomics-forum.com/index.php?board=8.0

That means that the XCMS forum is board number 8. You can then build your RSS URL like this where I have selected board 8 and 51:

Code: [Select]
http://metabolomics-forum.com/index.php?action=.xml;sa=news;boards=8,51;limit=5


WYSIWYG editor
Now you can format your post with an intuitive editor instead of using codes.
[attachimg=4 width=854]

[attachment deleted by admin]