Guide to generate mzIdentML files


  1. Introduction
  2. Tools to export mzIdentML v1.1

1. Introduction

mzIdentML is the HUPO-PSI standard for protein/peptide identifications coming from MS-based proteomics approaches. The stable version is 1.1, which is supported for Complete ProteomeXchange Submissions via PRIDE, please see our Submission Guidelines.

It is important to highlight that mzIdentML does not contain the mass spectra, which must be provided in external files referenced from the mzIdentML files (XML based files like mzML, mzXML or mzData, or peak lists like mgf, dta, ms2, apl or pkl).

mzIdentML files version 1.0 are not supported. 


2. Tools to export mzIdentML v1.1

Currently this is the list of software that can export mzIdentML v1.1 (see an updated list):

1- Mascot from Matrix Science. From version 2.4. See the screenshots from Mascot with export options and details of the user interface.

2- Scaffold by Proteome Software. From version 4.0. See the tutorial with screenshots from Proteome Software with export options and the details of the user interface.

3- MS-GF+ from Computational Mass Spectrometry Group at UC San Diego. The default output option is mzid 1.1, see the documentation on how to set up a search an specify the parameters on the command line.

4. ProteinPilot from AB SCIEX. See the screenshots with explanation.

5- ProCon from The Medical Proteomics Center at the Ruhr-Universität Bochum can be used for converting Sequest .out, ProteomeDiscoverer (Thermo)  v1.2/1.3/1.4 .msf files and ProteinScape 2.1 (Bruker) database content. See the ProCon documentation for details.

6- Trans-Proteomic Pipeline (TPP) (pep.xml and prot.xml files) from The Seattle Proteome Center: The idConvert tool from can be downloaded from ProteoWizard, or is bundled with the TPP directly starting with version 4.6.3.

7- mzidLibrary for X!Tandem and OMSSA output files developed by the Post-genomic Bioinformatics Group at the University of Liverpool.

8- OpenMS

9- MIAPE MSI Extractor from ProteoRed.

10- PAnalyzer: Tool to perform protein inference analysis, accepts mzIdentML files as input and generates mzIdentML files as output. 

11- Software tools from D. Tabb lab: MyriMatch, Pepitome (spectral library search) , TagRecon and IDPicker.

12- PeptideShaker (from the Compomics group). If the open source analysis tool PeptideShaker is used, the output of additional open source search engines are fully supported via the PeptideShaker mzIdentML export functionality: X!Tandem, MS Amanda, OMSSA, Tide and Comet.

13- X!Tandem supports in beta mzIdentML export since April 2015 (PILEDRIVER version). The export still needs to be tested.

14- PEAKS (BSI).

15- IP2 (Integrated Proteomics Pipeline).

16- Progenesis QI by Nonlinear Dynamics, owned by Waters. Please see instructions.