With SIRIUS 4.4.0 we finalized and released the SIRIUS project-space, the file based persistence layer and output format of SIRIUS. Both, CLI and GUI store the computed results as SIRIUS project-space (see the Figure below) which in turn can also be an input for the GUI or the CLI. This allows the user to review results in the GUI that have been computed with an automated workflow using the CLI.


Mass spectra


The input of SIRIUS are MS and MS/MS spectra as simple peak lists. SIRIUS can read CSV files which contain on each line a m/z and an intensity value separated by either a whitespace, a comma or a TAB character. For example:

85.041199 4034.674316 
203.052597 12382.624023 
245.063171 50792.085938
275.073975 124088.046875 
305.084106 441539.125 
335.094238 4754.061035
347.09494 13674.210938 
365.105103 55487.472656

The intensity values can be arbitrary floating point values. SIRIUS will transform the intensities into relative intensities, so only the ratio between the intensity values is important.


SIRIUS also supports the MGF (Mascot Generic Format). This file format was developed for peptide spectra for the mascot search engine. Each spectrum in a MGF file can contain many spectra each starting with and ending with . Peaks are again written as pairs of m/z and intensity values separated by whitespaces with one peak per line. Further meta information can be given as NAME=VALUE pairs. SIRIUS recognizes the following meta information:

  • PEPMASS: contains the measured mass of the ion (e.g. the parent peak)

  • CHARGE: contains the charge of the ion. As SIRIUS supports only single charged ions, this value can be either 1+ or 1-.

  • MSLEVEL: should be 1 for MS spectra and 2 for MS/MS spectra. SIRIUS will treat higher values automatically as MS/MS spectra, although, it might be that it supports MSn spectra in future versions.

This is an example for a MGF file:

185.041199 4034.674316
203.052597 12382.624023 245.063171 50792.085938 275.073975 124088.046875
305.084106 441539.125 335.094238 4754.061035 347.09494 13674.210938
365.105103 55487.472656 

See also the GNPS database for other examples of MGF files.


[ms file needs update]

A disadvantage of these data formats is that they do not contain all information necessary for SIRIUS to perform the computation. Missing meta information have to be provided via the commandline. Therefore, SIRIUS supports also an own file format very similar to the MGF format above. The file ending of this format is .ms. Each file contains one measured compound (but arbitrary many spectra). Each line may contain a peak (given as m/z and intensity separated by a whitespace), meta information (starting with the > symbol followed by the information type, a whitespace and the value) or comments (starting with the # symbol). The following fields are recognized by SIRIUS:

  • >compound: The name of the measured compound (or any placeholder). This field is mandatory.

  • >parentmass: the mass of the parent peak

  • >formula: The molecular formula of the compound. This information is helpful if you already know the correct molecular formula and just want to compute a fragmentation tree or recalibrate the spectrum

  • >ion: the ionization mode. See for the format of ion modes.

  • >charge: is redundant if you already provided the ion mode. Otherwise, it gives the charge of the ion (1 or -1).

  • >ms1: All peaks after this line are interpreted as MS peaks

  • >ms2: All peaks after this line are interpreted as MS/MS peaks

  • >collision: The same as >ms2 with the difference that you can provide a collision energy

An example for a .ms file:

>compound Gentiobiose
>formula C12H22O11 
>ionization \[M+Na\]+ 
>parentmass 365.10544

365.10543 85.63 366.10887 11.69 367.11041 2.67

>collision 20 
185.041199 4034.674316 
203.052597 12382.624023 
245.063171 50792.085938 
275.073975 124088.046875 
305.084106 441539.125 
335.094238 4754.061035 
347.09494 13674.210938 
365.105103 55487.472656

Note: The .ms file format is SIRIUS’ internal format and might change with as same speed as the SIRIUS developend went forward. Nevertheless we try to provide backward compatibilty where possible. A more detailed and commented but also WIP example of the an .ms file can be found here


SIRIUS can import full LCMS-Runs in (mzML/mzXML) format via the prepossessing tool . [todo: describe lcms-align]


SIRIUS project-space

The SIRIUS project-space is a standardized directory structure that is organized in a three hierarchy levels, namely, the project level, the compound level and the method level (see Figure below for details).

Schema of the SIRIUS project-space.

On the project level, each compound corresponds to one sub-directory (compound level) storing the input data, parameters and results of the different analysis methods. These data is continuously written to the project-space, so that it represents the actual progress of a SIRIUS analysis. Further, the .progress file gives an overview about the progress of the ongoing analysis. On the compound level, each method provided by SIRIUS stores its results in its own sub-directory (method level). This allows the user to redo one analysis step without having to recompute the intermediate results it depends on. Further, SIRIUS is able to transfer intermediate results to a new project-space, so different parameters can easily be evaluated without having to recompute intermediate results. Since a project-space can be imported into the GUI, the user is able to judge intermediate results using the GUI before executing further analysis steps. Project-spaces can be read and written as an uncompressed directory or a compressed zip archive when using the .sirius file extension.

Summary files

In addition to the method level results, the project-space contains summaries of these results on the project level and the compound level. These summaries are in tsv (tab-separated-values) format (summary_<NAME>.tsv) to provide easy access to the results for further downstream analysis, data sharing and data visualization. The summaries are not imported into SIRIUS but are (re-)created based on the actual results every time a project-space is exported.

Molecular formula results summary

formula_identifications.tsv contains the top-ranked formula result of each compound as determined by the SIRIUS score, or the ZODIAC if available. However, different adduct candidates with the same precursor ion molecular formula will have identical score (e.g. [C20H14O6 + NH4]+ and [C20H19NO7 - H2O + H]+). In such cases, the the top-ranked candidate in formula_identifications.tsv is resolved to [C20H17NO6 + H]+ only considering the ion type but ignoring adduct types. formula_identifications_adducts.tsv contains all top-ranked adducts (in this case [C20H14O6 + NH4]+ and [C20H19NO7 - H2O + H]+).

Molecular structure results summary

compound_identifications.tsv contains the top-ranked structure result of each compound as determined using the CSI:FingerID score; the molecular formula of the top structure does not have to be the top-ranked molecular formula of this compound. compound_identifications_adducts.tsv contains the top structure for each considered adduct of the top molecular formula.

CANOPUS results summary

canopus_summary.tsv contains compound classes predicted to be present by CANOPUS for the top-ranked molecular formula of each compound. most specific class denotes the most specific compound class for this compound. The columns level 5, subclass, class, and superclass refer to the ancestors of this most specific class. The column all classifications contains all classes predicted for this compound with probability above 50%.

If there are multiple molecular formulas with same score (which should happen only for adducts, see the molecular formula results summary) then the canopus_summary.tsv will decide for one molecular formula for each compound. We always choose the molecular formula for which the CANOPUS probability of the most specific class is maximal.

compound_identifications_adducts.tsv contains the classifications for the other top-scoring adduct formulas, too.

Standardized project-space summary with mzTab-M

The project-space is a SIRIUS-specific format that allows the user to access all results and analysis details, but may not be optimal for sharing this data with third party tools or data archives. For this purpose, SIRIUS provides an analysis report (analysis_report.mztab) in the standardized mzTab-M format. All results summarized in this report are linked to the results in the corresponding SIRIUS project-space, allowing the user to share summarized results using mzTab-M without losing the connection to the detailed results provided in the project-space. Furthermore, SIRIUS passes meta information (if available in the input) such as scan numbers and ids of the input data into this analysis report. This allows for an easy combination of the SIRIUS results with the results of other analyses such as MS1-based quantification.

Parameter formats

Ion modes

Whenever SIRIUS requires the ion mode, it should be given in the following format:

[M+ADDUCT]+ for positive ions
[M+ADDUCT]- for negative ions
[M-ADDUCT]+/[M-ADDUCT]- for losses 
[M]+/[M]- for instrinsically charged compounds
[M+?]+ for positive ions with unknown adduct
[M+?]- for negative ions with unknown adduct

ADDUCT is the molecular formula of the adduct. The most common ionization modes are [M+H]+, [M+Na]+,[M-H]-, [M+Cl]-. Currently, SIRIUS supports only single-charged compounds, so [M+2H]2+ is not valid and will be skipped during import. Further dimers are also not yet supported so that everything containing [2M] will be skipped during import.

Molecular formulas

Molecular Formulas in SIRIUS must not contain brackets. Hence, 2(C2H2) is not a valid molecular formula; write C4H4 instead. Furthermore, all molecular formulas in SIRIUS are always neutral, and there is no possibility to add a charge on a molecular formula (instead, charges are given separately). Hence, CH3+ is not a valid molecular formula. Write CH3 instead, and provide the charge separately via commandline option.

Chemical alphabets

Whenever SIRIUS requires the chemical alphabet, you have to provide which elements should be considered and what is the maximum amount for each element. Chemical alphabets are written like molecular formulas. The maximum amount of an element is written in square brackets behind the element. If no square brackets are given, the element might occur arbitrary often. The standard alphabet is CHNOP[5]S, allowing the elements C, H, N O and S as well as up to five times the element P.