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 - kevincho

1
METLIN / Re: Generation of theoretical fragment structures
Hi Kirsten,

1. We update the fragmentation prediction once every a couple of week, so yes it's manually updated.

2. Some of the peaks, we can't generate the predicted structure due to the rearrangement or we do not have enough information to predict the suitable fragments.

3. We do not offer downloadable MSMS data, but we do offer SOAP service where you can query METLIN's tandem MS data based on your data.

Thanks for using METLIN :D

-Kevin
3
METLIN / METLIN SOAP API
Hi all,

We now launched SOAP API for METLIN (http://http://metlin.scripps.edu/soap/), currently there are 2 major features (Batch search and Spectrum Match for MS/MS data) that you can use for this.
Please feel free to use it, and let us know if there are any issues or suggestions.

By the way, don't forget to register to receive token for this service

Thank you,
Kevin
4
metaXCMS / Re: problem with installation of metaXCMS on MAC
Hi Koen,

I've been trying to find the right solution for your issues, but not successful.  Please try to update your OS X, and delete everything named gtk+ from your finder (But not sure whether this will help or not.)
I can't really reproduce this problem here, can't help you too much though.  I would recommend you to reinstall OS X from scratch, which is the optimal solution for this problem since you didn't find the same error on other Mac

Let me know if you still need help.
Kevin
5
metaXCMS / Re: problem with installation of metaXCMS on MAC
Hi Koen,

I have tried on 3 different Mac Computers here, and everything works fine if you follow the description.
I believe it might be your Mac Issues.  How much memory do you have on your computer? which version do you have? and have you tried to delete R from 'Applications' and reinstall it?

I tested R 64bit on iMac, MacBook Pro, and MacBook (all of them have version 10.6.8), and at least 4GB of RAM.

I am not sure why it keep crashes, but you may want to try it with a fresh installation, and may not run other softwares during installation(?)

I suggest you to try on different Mac if it's available, and if not you want to contact R-Project.

I found a couple of FAQ from their website... Please refer following.

Kevin
______________
4.8 R.app Bugs

On Unix systems a bug report can be generated using the function bug.report(). This automatically includes the version information and sends the bug to the correct address. Alternatively the bug report can be emailed to http://bugs.R-project.org/.

Before you fill a bug report, please try to reproduce it using both R.app and the console version of R (if applicable). If the bug if R.app-specific, please report the bug to http://r.research.att.com/tools/.

CRAN binaries of R versions 2.3.0 to 2.4.1 supplied their own complier (gcc 4.0.3 in /usr/local/gcc4.0), overriding the Apple-supplied compiler. The system compiler was kept in place, but R used the new compiler for compiling packages instead. The main reason for this was that the compiler supplied by Apple contained several fatal bugs that lead to crashes of R due to incorrectly generated code, especially for the Intel Macs. This has been fixed in Xcode 2.4.0 so we switched back to Apple's compilers for R 2.5.0 and later.

12.16 R.app GUI crashes on startup!

If your R.app GUI crashes on startup, there are usually two major causes for this: saved workspace or corrupted history

Saved workspaces can contain commands that implicitly load packages which in turn can trigger bugs in packages or feed R with incorrect starting values (especially if it was saved using another R). Try removing or renaming your workspace – it's called .RData. If you did not change your startup settings, you can e.g. use

    mv ~/.RData ~/workspace.RData
to move it aside and load later manually for inspection using load("~/workspace.RData").

Second most common cause of crashes on startup is a history file that was not created using the R.app GUI. Again, move it aside to see if that's the issue:

    mv ~/.Rhistory ~/history.txt
Although we are trying to recover from invalid history files, they can still crash R.app due to issues in the internal handling of strings in Mac OS X. We are currently working on preventing this issue.

If you did both of the above and R.app still crashes, please select `1' in the menu after the crash (if you get the crash menu in the console) and send us the resulting crash report (see see R.app Bugs above).
6
metaXCMS / Re: problem with installation of metaXCMS on MAC
Hi Koen,

Please follow the following steps to install metaXCMS

1. Copy and Paste the following 3 lines in R console.
    install.packages(c("cairoDevice","RGtk2","gstat","RANN","xlsx"))
    source("http://bioconductor.org/biocLite.R")
    biocLite(c("Biobase","xcms"), dep=T)

2. Go to 'Packages & Data' and open 'Package Manager'
    if 'cairoDevice' is not loaded please check the status box to be loaded, which will take a few seconds to few minutes to load the package and ask you to install GTK+.
    Please install GTK+

3. Download metaXCMS source package (metaXCMS_0.1.19.tar.gz) at http://metlin.scripps.edu/metaxcms/download.php

4. Go to 'Packages & Data' and open 'Package Installer'
    Select 'Local Source Package'
    For Install Location, select 'At System Level (in R framework)'
    and click 'Install'
    then select the 'metaXCMS_0.1.19.tar.gz' from where your downloaded file is located

5. You may want to run the following line (If not working you may want to restart the R Gui)
    library(metaXCMS)

Please let me know if this doesn't work for you.

Kevin
7
metaXCMS / metaXCMS Protocol
Hi XCMS users,

As many of you aware of this, the metaXCMS protocol is published.  The usage of metaXCMS software is thoroughly described on the paper, so please review the paper at Nature Protocols

Thank you,
Kevin
8
METLIN / Re: MS/MS Spectrum Match is available now
Hi Laura,

Thank you for using METLIN, and I am very glad that you like the tool :)
Answering your questions,
- I am working on creating a manual for users, which will be available on the web shortly.  Please visit the site frequently :)
- You are correct, the upper half of the spectrum is what you submitted, and the bottom half of the spectrum is from the METLIN MS/MS data of the standard compound analysis, the blue line(s) indicate(s) the matching peaks between your data vs. METLIN's data, and black lines are the rest of peaks that you submitted or our data that do not match with your peaks.
- The length of the peak is a relative intensity from your data and METLIN's data.  We recalculate your maximum intensity peak as 100%, and then other peaks are relative to the strongest intensity peak.

So, based on your data and our data, we compute the possible matching score, and display it in the METLIN score column.

Please feel free to contact me if you have further questions, and leave me comments if you have advices.

Regards,
Kevin
9
METLIN / MS/MS Spectrum Match is available now
Hi METLIN users,

I'm very glad to announce that we recently launched a new tool for MS/MS Spectrum Match, which allows users to ID known/unknown compound with a score (based on the modified X-Rank Algorithm).  The current version requires to enter m/z, intensity (of the user's MS/MS data) with a few parameters to search against METLIN's MS/MS database (currently ~5400 LC MS/MS data).

Please feel free to use the new feature, and give us some feedbacks regarding the tool.

You can check the awesome feature at http://http://metlin.scripps.edu/spec_search.php

-Kevin
10
METLIN / Re: Install METLIN locally
Hi Chris,

SOAP Interface is not available at the moment, we will announce the service when it will be available.  Please check the website occasionally.

Thank you,
Kevin
11
METLIN / Re: Install METLIN locally
We are currently updating and improving the database. The recent modifications are not reflected in the SOAP interface yet. We are hoping to bring it back online once the update process is complete.
12
METLIN / Re: Install METLIN locally
Dear Panos,

First of all, thank you for using METLIN as one of your metabolomic data search.  Unfortunately, we do not offer any downloadable database nor local installation.  However, we offer a batch search that allows you to search many distinct masses at the same time with multiple adducts as targets.  Hopefully, this resolves your issues.  Please do not hesitate to contact me if you have any questions.
13
XCMS / Re: METLIN information extraction
Hi Ricca,

You can use METLIN Batch Search (http://metlin.scripps.edu/metabo_batch.php) to find the metabolites that you are interested with.  You can simply enters masses (up to 500 unique masses), select adducts as targets, and set tolerance (either ppm or Da).  Please let me know if you have further questions using METLIN DB.

Cheers
14
METLIN / Welcome to METLIN online forum
Hi all METLIN users,

Welcome everyone, we would like to hear from you to make METLIN better for your research and for Metabolomics community

Please report any bugs, suggestions, errors on this forum. 

- If you report bugs, please also mention the operating system (e.g. Windows XP, Mac OS X 10.6.7, Ubuntu 10.04) and the web-browser (e.g. Internet Explorer 8, Firefox 3.6.17) that you are using.

- If you suggest new ideas or features (contains sensitive information), please email me details at kevincho [at] scripps [dot] edu

- If you report some errors on METLIN, please provide me MID(METLIN ID) and fields information(NAME, MASS, and etc) for correction.

Thank you,
Kevin