Also See the Tranche FAQ

For how long will my data be hosted?

The intention is to host data indefinitely. Currently the project is funded by the Phil Andrews Lab at The University of Michigan and through various other collaborators with different grant and funding sources and will continue to operate for the foreseeable future.

What kinds of data can I upload?

Any type of file can be uploaded. There are several instances where data may be removed:

• You did not have the legal right to upload the data.
• The data is not relevant to proteomics.

How do I structure my files for upload?

Uploads to the Tranche network can be structured in any manner that you would like; however, in order to facilitate locating the exact information you are looking for, it is recommended that an upload is structured in a manner similar to the following: Create a readme file to be placed in the folder with the data to be uploaded. This file would contain information regarding who you are, and information as to what the rest of the uploaded folder contains. Within this main folder it is recommended that subdirectories be created for peak lists, spectra, or for any other images/annotations that you would like to publish.

Is it faster if I compress my files first?

As of right now compressing a file does not make the process faster. Tranche will auto compress the files for you and it is best to let it do that.

How does Tranche make collaborations easier?

Tranche allows collaborators to share data and research data regardless of file size, the number of files, or the file types. Tranche can also securely share data in pre-review before publication. Files can be encrypted and the passphrase is only available to the original uploader and whomever they share it with. In this way researchers can work in various locations all sharing data without worry about the security of the data being compromised.

If my data are password protected, how can I be sure only my collaborators have access?

The ability to decrypt data is only available to those with whom the passphrase has been shared. When data is uploaded with encryption the only individual that has access to the passphrase is the original uploader; thus, only the original uploader has the ability to allow others access to data by sharing the passphrase with them. Tranche uses the same encryption standards as modern e-commerce websites, e.g. your online bank, and it is unlikely that anyone will break these standards anytime in the near furture.

When I am ready, how do I publicly release my data?

1. Sign in
2. Navigate to your My Data page (Data > My Data)
3. Click on the title of the data set you want to make public. This will take you to the data page.
4. In the left menu, click the link Make Public

How will other investigators and funding agencies know my lab produced the data?

Data can be documented and provenance shown in several different ways. The best formal way is to publish the Tranche hash within any manuscript in which you publish. Not only does this formally prove where the data comes from, Tranche can also be used to verify the completeness of data uploads.

How do I annotate my data sets?

1. Sign in
2. Navigate to your My Data page (Data > My Data)
3. Click on the title of the data set you want to annotate. This will take you to the data page.
4. In the left menu, click the link Annotate.

How do I find my data sets after I have uploaded them?

There are many ways to access data sets.

You can browse or search data sets. This will only show your visible data sets. You can launch Tranche and browse the data sets from the tool as long as the data sets are visible. You can launch Tranche and use the Tranche hash to download or look at the project. Note that the last option is the only way to access private data sets, which is why it is important to save your upload hash or receipt. Also, if the project is encrypted (which it will be if it is private), you will need the passphrase.

Can I upload multiple versions of my data sets?

Yes, multiple versions of a data set can be uploaded. Most often this manifests itself with users first uploading a complete directory with all raw data, spectra, and any images and/or annotations. Then the data is uploaded as an individually, returning its own hash, and the spectra is uploaded individually returning its own hash; etc. Because Tranche is intelligently designed and all of these files have already been uploaded, Tranche will not duplicate an these files with another upload, thus saving time, while allowing for greater organization.

How do I retract/delete data?

You can delete any of your data sets from Tranche provided that you have not given up control of that data set. Please note that we will not be able to recover a data set once you have deleted it.

1. Sign in
2. Navigate to your My Data page (Data > My Data)
3. Click on the title of the data set you want to delete. This will take you to the data page.
4. In the left menu, click the link Delete.