SIRIUS+CSI:FingerID — CANOPUS — ZODIAC — BCD Supertrees — EPoS — Gecko3 — COCONUT

### Passatutto

Passatutto enables the assessment of confidence in a match for metabolomics mass spectral library search. The tool allows both, to use either an empirical Bayes or a target-decoy approach. Different methods to construct the decoy database can be used, all of them avoiding to construct “decoy metabolite structures”. In addition, passatutto can be used for noise-filtering reference spectra based on fragmentation trees. Passatutto is now available through SIRIUS 4.4 and never.

Cite: K. Scheubert, F. Hufsky, D. Petras, M. Wang, L.-F. Nothias, K. Dührkop, N. Bandeira, P. C. Dorrestein, and S. Böcker. Significance estimation for large scale metabolomics annotations by spectral matching. *Nat Commun*, 8:1494, 2017.

### MSICorrect

**MSICorrect** is a Java-based commandline tool that performs recalibration of mass spectrometry imaging datasets without the need of specifying a lock-mass value. The computational approach implemented in the tool generates a reference spectrum, termed here as a *consensus spectrum*, using all the spectra present in the dataset. This *consensus spectrum* is used as a reference spectrum to recalibrate the input mass spectra. More…

### PLUMS

PLUMS is a software that analyses tandem mass spectra of synthetic polymers. It helps to identify monomer repeating units and fragmentation series of homopolymers. The end groups of the fragment ions are determined without any further knowledge of the polymer class or the fragmentation mechanism. More…

### MoLE

**MoLE** is a tool for estimating heavy isotope incorporations of molecules based on mass spectrometry data. The program comes with an easy-to-use graphical user interface, and allows for batch processing of mass spectra. More…

### PEACE

PEACE (Parameterized and Exact Algorithms for Cluster Editing) is a project for clustering experimental data using a weighted graph derived from pairwise similarity information.

The underlying mathematical model is the NP-complete Cluster Editing problem. Similar models are used in the clustering algorithms CLICK and CAST. Advantages are that you do not have to specify cluster centers, the number of clusters need not be given in advance, and solutions are definite. We compute exact solutions for this model, mainly with fixed-parameter algorithms. These algorithms employ both parameter-independent and parameter-dependent reduction rules to cut down the size of the instance initially and inside the search tree. PEACE is implemented in C++. More…

### Bond order assignment

Bond order information is essential for many applications in chemistry. Unfortunately, this information is omitted in many data formats of molecule graphs. We have developed a Java-based program that computes bond order assignments of molecule graphs using a penalty function as suggested by Wang *et al.* (2006). This program implements our tree decomposition-based dynamic programming algorithm introduced in Böcker *et al.,* 2009. More…

### Decomp

Decomp is a tool that computes the sum formula of all molecules whose mass equals the input mass. This problem arises in mass spectrometry when we know the molecular mass of a protein, DNA, or metabolite fragment but have no other information. Decomp employs efficient algorithms for computing such decompositions. Decomp is supplied with an easy-to-use web interface that allows users to modify all important parameters. Results can be used either independently or as a starting point for further evaluations in the identification pipeline of unknown sample fragments.