MS muddle made manageable by mulitplierz software

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  • Published: Sep 6, 2017
  • Author: Ryan De Vooght-Johnson
  • Channels: Laboratory Informatics / Chemometrics & Informatics
thumbnail image: MS muddle made manageable by mulitplierz software

Diverse proteomic mass spectrometry data creates problems

Modern mass spectrometry employs a number of different types of instrument. These typically produce data in a format specific to the instrument manufacturer, thus making comparison of the results from different instruments a challenge. In the field of proteomics, mass spectrometry is usually carried out on peptide fragments produced via protein hydrolysis (the peptides may be labelled in some manner before or after hydrolysis). There are many software packages, such as Mascot, MassMatrix, Comet and X! Tandem, that can be used to match the mass spectra with peptide sequences. In addition, there are large-scale libraries of proteomic mass spectral data, such as PRIDE (run by EBI, the European Bioinformatics Institute) and PeptideAtlas (run by the Institute of Systems Biology in Seattle). These comprise data obtained from various research groups from around the world.

The Boston researchers have developed an open-source software package called ‘multiplierz’ for proteomic mass spectrum data analysis. The package is coded in Python and employs an API (application programming interface) called mzAPI to extract data from binary files of spectral output. The current paper describes the updated version of the software, multiplierz v2.0.

Updated multiplierz software enables acquisition of data from multiple sources

The updated software is accessed through a desktop GUI (graphical user interface) called mzDesktop. The use of the GUI makes the software functions accessible to those with no experience of Python. It can be used to produce high-quality graphics. Another submodule, mzReport, can be used to generate reports and can output data to various other packages, such as Excel.

The mzAPI interface can handle LC-MS/MS data from a number of manufacturers’ instruments, such as files from Thermo Fisher (.RAW), Agilent (.D) and Danaher/Sciex (.WIFF). The capability to handle MALDI (matrix-assisted laser desorption/ionisation) runs has been added.

A new function, mzSearch, is used to send the data to protein identification software. The user has a choice of three different packages: Comet, Mascot or X! Tandem. Further manipulation of the data can be carried out using the mzTools submodule. This can be used to link peptides to proteins, and proteins to the relevant gene. It also can implement peptide quantification when required.

The use of the software was demonstrated by the analysis of a HeLa cell protein (a protein from ‘immortal’ human cancer cells). The protein was hydrolysed giving a mixture of peptides, some of which were labelled with TMT or iTRAQ labels (standing for ‘tandem mass tags’ and ‘isobaric tags for relative and absolute quantitation’, respectively). The mixed peptides were analysed by a 3D RP-SAX-RP-MS/MS set-up (i.e. reverse phase HPLC, strong anion exchange, reverse phase HPLC and tandem MS). The mzAPI submodule was used to access the output data, which were in the form of Thermo Fisher ‘.RAW’ files. The data was displayed in a series of two dimensional plots, showing the effects of labelling on HPLC column retention, the latter been shown by means of the percentage of eluting solvent in the gradient elution.

New proteomic mass spectral software has powerful capabilities

The updated multiplierz software can be used to obtain and manipulate proteomic data from a number of manufacturers’ instruments and run it through a choice of three different protein identification engines. The system will appeal to those with experience in Python programming, although such knowledge is not essential to its use. However, the field of mass spectrometry proteomic software is a crowded one, and only time will tell whether the multiplierz software is ultimately widely used.

Related Links

Proteomics, 2017, Early View paper. Alexander et al. multiplierz v2.0: a Python-based ecosystem for shared access and analysis of native mass spectrometry data.

BMC Bioinformatics, 2015, 10, 364. Parikh et al. multiplierz: an extensible API based desktop environment for proteomics data analysis.

Wikipedia, List of Mass Spectrometry Software

Article by Ryan De Vooght-Johnson

The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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