SuperHirn protocols

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SuperHirn specifications


Unique identifier OMICS_02395
Name SuperHirn
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Lukas Mueller <>

Publication for SuperHirn

SuperHirn in pipelines

PMCID: 5547443
PMID: 28673088
DOI: 10.1021/acs.jproteome.7b00248

[…] in what we call the “de novo” approach to feature detection (illustrated in , top). this classical approach is used by many important software tools for label-free quantification, including superhirn, maxquant, and openms (e.g., featurefindercentroided). however, decoupling feature detection from peptide identification in the “de novo” approach leads to a common problem: some peptides […]

PMCID: 4423578
PMID: 25952148
DOI: 10.1186/1471-2105-16-S7-S2

[…] signal to compare analyte quantities. ideally, solutions would focus on one of the several complex individual steps for data processing []. however, most are released as end-to-end solutions (e.g., superhirn [], maxquant [], xcms [], and skyline []). this makes comparison to other competing algorithms virtually impossible, and is at least partially responsible for the lack of critical […]

PMCID: 4252003
PMID: 25420746
DOI: 10.1186/s12859-014-0376-0

[…] test our algorithm, practical applications of ab3d for lc-ms data sets were evaluated using 3 datasets. comparisons were then carried out between widely used software tools such as mzmine 2, msight, superhirn, openms and our algorithm ab3d, using the same lc-ms datasets. all quantitative results were confirmed manually, and we found that ab3d could properly identify and quantify known peptides […]

PMCID: 4252003
PMID: 25420746
DOI: 10.1186/s12859-014-0376-0

[…] replicates of prepared samples were conducted for each bsa peptide concentration and all acquired raw ms1 and ms/ms data were input into all the peak detection algorithms (ab3d, mzmine 2, msight, superhirn and openms) to produce peak lists for each peptide spectrum. peaks identified as peptides of bsa or four standard proteins by either mascot [] or x! tandem [] from multiple samples […]

PMCID: 4252003
PMID: 25420746
DOI: 10.1186/s12859-014-0376-0

[…] in the literature were set as tp in our study. raw (.wiff) data was converted to mzxml format files by using proteowizard [], then the peak lists were produced using ab3d, mzmine 2, msight, superhirn and openms algorithms, respectively. parameter tuning was conducted 9-26 times for each algorithm and the best result was used for comparison finally. the different times of parameter […]

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SuperHirn in publications

PMCID: 4632119
PMID: 26629404
DOI: 10.1016/j.molmet.2015.08.003

[…] were filtered to a false-discovery rate of ≤1%. for ms1 based label-free quantification of the identified peptides, ms1 ions signals corresponding to peptide features were extracted with the superhirn (version 03) software. after intensity normalization, peptide signal intensities belonging to the same protein were summarized followed by statistical analysis of the data., fractionation […]

PMCID: 4252003
PMID: 25420746
DOI: 10.1186/s12859-014-0376-0

[…] the following criteria, which have a similar concept as ab3d; 1) label-free quantitation using ms1; 2) widely used and freely available; 3) run on windows os, therefore, mzmine 2 [], msight [], superhirn [] and openms [] were chosen finally for comparison in this study. mzmine 2 is java-based label-free software package using ms1 data for quantitation and has capabilities for gui and batch […]

PMCID: 3878627
PMID: 24341404
DOI: 10.1186/1471-2105-14-364

[…] advantage of existing ms/ms peptide identifications. more recent alignment methods by tang et al. [] and zhang et al. [] utilize peptide intensity along with mass-to-charge ratio and retention time. superhirn [] indirectly incorporates intensity information during multiple alignments by performing pairwise alignments in a specific order based on lc-ms similarity and intensity correlations., […]

PMCID: 3853187
PMID: 24324795
DOI: 10.1371/journal.pone.0082473

[…] 2.2.04 software (matrix science, uk) against the wormbase ws228 protein sequence database. subsequently, label-free feature extraction and alignment were performed using a customized version of superhirn 0.03. data normalization and peptide-level anova were performed using danter false discovery rates were calculated at three stages: at the level of peptide identifications, […]

PMCID: 3792097
PMID: 24115998
DOI: 10.1371/journal.pone.0072951

[…] detection especially on crowded extracted ion chromatograms (xics): quil and proteinquant determine lc peak boundary by the apex and the full-width-half-maximum (fwhm) of a peak; msinspect and superhirn use thresholds; asapratio and mapquant use peak apex and fwhm; and maxquant uses local minima after xic smoothing. these algorithms cannot guarantee the exclusion of noise […]

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SuperHirn institution(s)
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

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