General FAQ
COMPASS is designed to work with complex biological samples. It can analyze mass spec data regardless of instrument, chromatography methods employed, sample type (lipids, peptides, small molecules and metabolites, or others), sample preparation (proteolytic cleavage, chemical modification).
It is focused on LC-MS or LC-MS/MS experiments with a single sample corresponding to one or more output files. It is not configured to handle any multiplexing, where the instrument generated data from multiple samples in a single convolved file.
COMPASS works with MS level 1 scan information, the initial scans for any ion signal entering the mass spec from each sample along with the signal intensity (abundance). In some LC-MS experiments there is only MS1 information, which experiments are often referred to as feature-first mass spec studies.
MS1 data contains no molecular identity information. In LC-MS/MS experiments, the MS1 scan information is used by instrument software to pick specific MS1 features for subsequent mass spectrometry, the MS2 scan.
In the MS2 scan, the precursor ion (the MS1 peak) is fragmented and the MS2 scan analyzes the pieces. MS2 scan information can be used to ascertain molecular identity. Only a small percentage of MS1 scan features are selected for MS2 fragmentation and analysis, and instrument software has biases in their selection.
In files generated in LC-MS/MS experiments, 90% of the instrument time is used generating MS2 scan data. MS1 scan information is still generated and available for analysis, though seldom used.
COMPASS can use the molecular identity information generated from MS2 scan data in your experiments. COMPASS does not perform analysis of the MS2 scans (yet!), but rather uses the molecular identities generated using any of the many other software packages designed expressly for this purpose.
Once other software has generated molecular identifying information, you can supply COMPASS a dictionary file (see Q14) that links the molecular identity information to the precursor ion feature location in the MS1 scan data. This will allow you to see which, and how many, MS1 scan datapoints are associated with MS2 molecular identity information. Molecular identity information associated with any MS1 scan datapoint is provided in COMPASS’ analysis.
Yes. COMPASS will operate on any operating system that can run a browser (Chrome is preferred) and can access the server location where COMPASS is installed. Note that you do not need a huge server. Even a laptop or small desktop can run a server internally and its own browser can then point at that server port, so you can run COMPASS easily on a single machine.
COMPASS is designed for a Windows or LINUX servers. Note that a ‘server’ just means that it runs on one machine (a laptop or desktop can do this) and that any machine that can access the server machine’s server port can operate COMPASS through a browser window.
COMPASS is optimized for Chrome. Other browsers may work, but you may run into trouble with some (Safari, in particular).
Once COMPASS has been downloaded and installed, it can be activated with a token that you should receive in an email. Access COMPAS using your browser and click on the license information line, which will reveal a field where a license token can be entered. Just copy the token and paste it into the license field. Make sure to copy the entire token, including the lines that contain “BEGIN” and END.”
This also works to renew the software or for yearly software license updates and expanding you data usage. If you want to see how to activate the software, please watch the first instructional video. The expiration of your COMPASS license, as well as its data limits, are reported on the license line.
Your COMPASS download comes with a data limitation that allows processing and analysis of 20 mass spec files. To analyze additional files you will have increase your data limit (please contact us for a quote here). One credit allows the processing and analysis of one mass spec file.
When you increase your COMPASS data limit, you will receive an email with a license token code. Copy and paste that code into the license entry field, just as for activating the license (see Q7). Your data limit and usage is reported on the license summary line.
The COMPASS interface allows you to drag and drop your mass spec and other files into specific fields within the browser window. They will automatically populate into the correct location. Make sure the files are in the correct format. Also, it is important to note that the server administrator will need to ensure there is sufficient storage if you plan on analyzing large numbers of files.
COMPASS (currently!) works with mzML files. The files should be stripped of data from MS level 2 and above, such that they contain MS1 data only.
ProteoWizard’s free open source msconvert tool can convert mass spec files in almost all file types to mzML.
During conversion, msconvert has filters that can be applied to extract MS1 data only and to reduce file sizes. Instrument software can often export files in mzML format, but may or may not be able to extract MS1 scan information only.
Export by instrument software may generate the most error-free mzML files, but msconvert may be needed to extract MS1 scan data. ProteoWizard’s msconvert is available at proteowizard.sourceforge.io/doc_users.html
The Assembly File is a spreadsheet that connects the file names of the mass spec files to the specific sample and its associated information. It needs a column containing a unique identifier for the example, one or more columns for the file names (one column for each preparation, one or more columns for outcomes, and as many other columns as needed to include all of the sample information you would like to consider. This file should be saved as a .csv file. Please watch the first instructional video and help file to see an example.
A Dictionary File is a spreadsheet, saved as a .csv file, that contains molecular identify information and connects it to the MS1 scan coordinates, meaning the m/z and retention time of the precursor ion subjected to identification. This file may be generated from analysis of MS2 scan information by other software packages and exported. It may be generated from library files. It can contain multiple columns of molecular identify information (COMPASS allows three to be selected for reporting in its analytics), columns for the MS1 scan coordinates, and a column detailing which preparation this entry refers to . Please watch the Molecular Dictionary instructional video and support page to see an example.
COMPASS is designed with this in mind. Whether you have proteomics and metabolomics datasets for the same set of examples, or if you have run the instrument in different configurations (ion mode, for example) for the same sample, these datasets can be integrated for seamless and unbiased analysis. We refer to these as different preparations. As described in FAQ entries 13 and 14, there simply needs to be distinct columns for the corresponding file names in the assembly file for each preparation and the dictionary file uses a column to indicate the preparation connected with each dictionary file entry. Please see the instructional video and help file on this topic.
COMPASS can include data entries in the assembly file as datapoints in its analysis. If you have as assay score or categorization associated with each of your examples, you can indicate so as you set up your COMPASS analysis.
Not yet. Check back with us as we build out COMPASS’ capabilities for seamless, parallel, and unbiased analysis of sequencing- and mass spec-based omics.