After upload of .mzXML files the window doesn't close

Topic: After upload of .mzXML files the window doesn't close (Read 5482 times) previous topic - next topic

After upload of .mzXML files the window doesn't close

November 16, 2015, 09:00:12 AM

Dear All,

I'm trying to convert lipidomic (Thermo) .RAW files (acquired in (+) and (-) ion modes simultaneously) into mzXML format through Proteowizard using the conversion settings as suggested by XCMS team.

Apparently conversion step runs fine, but upon upload of .mzXML files on XCMS platform the window (after which is supposed the window to automatically close once the files are reassembled and md5 checked) doesn't close. Upon inspection of datasets in XCMS platform they show 0 files on the dataset. The upload is being carried out with internet explorer browser (with google Chrome and firefox browsers I don't see the filetree).

I've tried this a couple of times, with no success.
I'm now wondering whether I should use different settings for acquisition (+)/(-) acquisition files - if so, which ones?

Any suggestions are highly appreciated.

Thanks,

Re: After upload of .mzXML files the window doesn't close

Reply #1 – November 17, 2015, 03:43:58 AM

Dear All,

following my latest post I've tried a different approach which involved converting LCMS .raw files using R package which went on smoothly and tried uploading again on the XCMS platform.
Unfortunately got the same result, after uploading converted files the window doesn't close automatically and datasets show 0 files on the XCMS platform.
I've tried the same route using google chrome browser but Java requires a NPAPI plugins which is no longer active on google chrome.

I'm running out of ideas on what the problem may be - any suggestions out there?

Thanks in advance,

Re: After upload of .mzXML files the window doesn't close

Reply #2 – December 10, 2015, 12:30:35 PM

Dear Ana,

I also have the same problem. I am also unable to upload data files into the DataSet. I am using .mzXML files which are dragged to the "Drop Files Here" area and zipped automatically. However, when I press the "Upload" button, it appears the icon "Failed" in front of each file (yellow triangular icon with a black exclamation marker).
I am using the latest Java, and added https://xcmsonline.scripps.edu to the exception site list in the Security tab in Java Control Panel.

I have also tried converting to .cdf and apparently uploads (an green icon with a white right sign appears on the side of each file), but the window doesn't close automatically and when I want to select the dataset I don't see any files uploaded...

Does anybody knows what might be the cause?

Regards,
João Sá

Re: After upload of .mzXML files the window doesn't close

Reply #3 – January 25, 2016, 08:17:12 AM

Hi Joao,

Gave up on the data analysis task for a while and just saw your reply. Have you had any success following Seshu sugestions?
I'll give it a go otherwise I'll try to contact the XCMS team again for suggestions.

Best regards,
Ana

Re: After upload of .mzXML files the window doesn't close

Reply #4 – March 03, 2016, 10:37:05 AM

Hi Joao
I'm a new user in xcms. I have a problem to upload data same you. I'm not sure now you can solve this problem or not. If you already solved this problem, please you suggest me to do it.

Best regards,
Tongchai

Re: After upload of .mzXML files the window doesn't close

Reply #5 – March 10, 2016, 05:35:27 PM

Dear all,

Unfortunately, browser support for java is being phased out. With this and the added security issues with java we are developing a new uploader which is still in beta at the moment but is being set to high priority.
For the time being I recommend using the HTML5 uploader. You can see a video on how to change your uploader type via the XCMS Institute videos here: https://xcmsonline.scripps.edu/landing_ ... =institute and direct link to the video here: https://www.youtube.com/watch?v=qaCv-Q9hVFk

I hope this helps questions are answered the fastest via our direct email on contact page.

Cheers,

Paul

~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page