The LipidXte web application provides automatic correction for lipid HCD MS/MS spectra from Orbitrap instruments and is dedicated to supporting accurate quantification of molecular lipid species. The application is specifically designed to support easy access to established correction functions with minimum interference requirements.

Kai Schuhmann, HongKee Moon, Henrik Thomas, Jacobo Miranda Ackerman, Michael Groessl, Nicolai Wagner, Markus Kellmann, Ian Henry, André Nadler, and Andrej Shevchenko.
Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics.
Analytical Chemistry 2019 91 (18), 12085-12093
DOI: 10.1021/acs.analchem.9b03270

Reference validator for mzTab 2.0-M

mzTab-m 2.0 structure

mzTab 2.0 for metabolomics is a data exchange format for mass-spectrometry-based experimental data from the "omics" and neighboring sciences, focusing on small molecules like metabolites and lipids.

  • It is hierarchically organized, from metadata to summary information to ms features and evidence,
  • captures quantitative and qualitative information about reported molecules for individual ms runs and aggregated across study variables,
  • follows minimum recommended reporting guidelines for omics experiments, and
  • provides structural, logical and semantic (controlled vocabulary terms) validation.

This application provides a web-based validator for mzTab 2.0-M and the prior mzTab version 1.0 (mainly for proteomics) below, and a REST API for programmatic validation against mzTab 2.0-M.

It is based on the jmzTab-M reference implementation.

The spectral comparison score (SCS) algorithm provides a well-defined quality control approach for PRM based quantitation of lipid mediators. The score is based on the correlation between structural similarity and MS/MS fragmentation profile. All fragment ions above a user defined threshold are considered to calculate a score based on matching m/z and Spearman’s rank correlation between fragment intensities. SpeCS was developed to

1) process raw peak lists,

2) generate customized spectral libraries,

3) perform SCS calculations, and

4) help to identify quantifier ions.

A set of filters can be employed to delete background signals and/or select only fragments that fit the user-defined compositional constraints.

Release Note: Database Expansion

March 28th, 2019: A new version of a spectral library for the Thermo Fisher Scientific Q Exactive mass spectrometer with new lipid mediators is now available. For detailed information:

QExactive Mediator Library

Download SpeCS v.0.7.

The new version enables now to utilize XReport (Xcalibur, Thermo) generated peak lists as import into SpeCS. Such generated peak lists can directly be used as Query in SpeCS without any modification (see also Readme-File).

Additionally, this release contains an updated library of LMs for the Q Exactive with 13 new lipid mediators.



GUI for the calculation of the Spectra Comparison Score (SCS). SpeCS is able to automatically filter peak lists by matching with a library of background or target mass lists. Peak lists are compared considering user definable settings for mass accuracy and intensity threshold settings. The calculation of the score is based on Spearman's rank correlation of matched signals.


Adam Wutkowski, Matthias Krajewski, Navratan Bagwan, Mathias Schäfer, Bhesh R.Paudyal, Ulrich E. Schaible, Dominik Schwudke,

Software-aided quality control of parallel reaction monitoring based quantitation of lipid mediators,

Analytica Chimica Acta (2018),doi:10.1016/j.aca.2018.01.044.   originally published SpeCS version:  v0.6 for Windows 

Bioanalytical Chemistry - Research Center Borstel

Dr. Domink Schwudke - Research group leader
Dr. Adam Wutkowski - Research Center Borstel