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I've been trying to download some of the mzML files used to build MassIVE-KB, but it seems there seems to be a consistent problem for files in the ccms_peak directories. For example, here I try to download an mzML file from MSV000088407:

$ wget ftp://massive.ucsd.edu/x01/MSV000088407/ccms_peak/RAW/AD02_BA46_INSOLUBLE_01.mzML
--2024-04-24 10:01:14--  ftp://massive.ucsd.edu/x01/MSV000088407/ccms_peak/RAW/AD02_BA46_INSOLUBLE_01.mzML
           => ‘AD02_BA46_INSOLUBLE_01.mzML’
Resolving massive.ucsd.edu (massive.ucsd.edu)... 132.249.211.16
Connecting to massive.ucsd.edu (massive.ucsd.edu)|132.249.211.16|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /x01/MSV000088407/ccms_peak/RAW ...
No such directory ‘x01/MSV000088407/ccms_peak/RAW’.

If instead I try a different file outside of the ccms_peak directory, it works without issue:

$ wget ftp://massive.ucsd.edu/x01/MSV000088407/ccms_parameters/params.xml
--2024-04-24 10:07:03--  ftp://massive.ucsd.edu/x01/MSV000088407/ccms_parameters/params.xml
           => ‘params.xml.1’
Resolving massive.ucsd.edu (massive.ucsd.edu)... 132.249.211.16
Connecting to massive.ucsd.edu (massive.ucsd.edu)|132.249.211.16|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /x01/MSV000088407/ccms_parameters ... done.
==> SIZE params.xml ... 16688
==> PASV ... done.    ==> RETR params.xml ... done.
Length: 16688 (16K) (unauthoritative)

params.xml.1           100%[===========================>]  16.30K  --.-KB/s    in 0.04s

2024-04-24 10:07:03 (374 KB/s) - ‘params.xml.1’ saved [16688]

Please note that the mzML file I'm trying to download is also shown on the webpage, but must be downloaded over FTP:

Thanks for your help!

I noticed that MassIVE reanalyses (RMSV*) projects don't seem to be supported by the PROXI API. For example, the following returns a 404 error:

https://massive.ucsd.edu/ProteoSAFe/proxi/v0.1/datasets/RMSV000000253

Is there another API endpoint for reanalyses that I've missed? Thanks!

Line 51 in docs/access_public_datasets.md has a broken anchor.

Filling in docs/convert_tsv_to_mztab.md (linked to from submission workflow page). Old link is https://bix-lab.ucsd.edu/display/PS/Tab-Separated+Result+File+to+mzTab+Conversion.

Julie

Not sure if this is the best repository to submit this issue, but I am planning to contribute MSMS data collected on an Agilent 6545 QTOF, which has not been added to the instrument list on the MassIVE data submission workflow.

According to the existing pattern of nomenclature for MassIVE I would suggest: 6545 Quadrupole Time-of-Flight LC/MS (Agilent instrument model)

Accepted nomenclature found for ReDU at https://www.ebi.ac.uk/ols/search?q=6545+&ontology=ms should be:
6545 Q-TOF LC/MS|MS:1002791. (which has already been updated)

Hi folks 👋

Recent changes to the MassIVE FTP site organization broke the functionality of my project, ppx (wfondrie/ppx#30), which strives to make it easy to programmatically access datasets. It seems that projects are now distributed among multiple version subdirectories (currently, I see v0[1-7] and x01).

Is there an API endpoint or similar from which I can retrieve the correct FTP URL for a given dataset? I spot checked a few using the PROXY API (http://massive.ucsd.edu/ProteoSAFe/proxi/v0.1/datasets/<accession>), but they were incorrect.

For example:

https://massive.ucsd.edu/ProteoSAFe/proxi/v0.1/datasets/MSV000094236

Returns an FTP link of ftp://massive.ucsd.edu/MSV000094236 when it is actually ftp://massive.ucsd.edu/v07/MSV000094236.

Thanks!