LC-MSsim specifications


Unique identifier OMICS_25823
Name LC-MSsim
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data The simulated LC-MS map and the list of peptides and contaminants with m/z and retention time.
Operating system Unix/Linux, Windows
Programming languages C++
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes


No version available



  • person_outline Oliver Kohlbacher
  • person_outline Ole Schulz-Trieglaff
  • person_outline Nico Pfeifer
  • person_outline Clemens Gröpl
  • person_outline Knut Reinert

Publication for LC-MSsim

LC-MSsim citations


An Ultra Fast Metabolite Prediction Algorithm

PLoS One
PMCID: 3380062
PMID: 22745711
DOI: 10.1371/journal.pone.0039158

[…] be revised when “correct” features are scanned later , . Many alignment tools, both commercial ones and freeware, belong to this type e.g. MetAlign , MSFACTs , OPenMS . Binbase , MathDAMP , ChromA , LC-MSsim , XCMS , SpecAlign , MET-IDEA .In order to increase alignment accuracy we recently developed PAD (Peak Alignment via Density maximisation), which adopted a global merge strategy using a conc […]


Statistical quality assessment and outlier detection for liquid chromatography mass spectrometry experiments

BioData Min
PMCID: 2678124
PMID: 19351414
DOI: 10.1186/1756-0381-2-4

[…] To provide a sanity check of our method, we simulated a mixture of standard peptides using our software LC-MSsim []. This software simulates an entire LC-MS experiment, including protein digestion, retention time prediction, isotopic pattern and elution peak models. It produces a realistic LC-MS map and […]

LC-MSsim institution(s)
International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany; Department Computer Science and Mathematics, Free University of Berlin, Berlin, Germany; Wilhelm Schickard Institute for Computer Science, Tübingen University, Tübingen, Germany
LC-MSsim funding source(s)
Supported by the International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC) and by a grant of the German Federal Ministry for Education and Research (BMBF), grant no. 031369C.

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