Progenesis plugins: gotta catch ’em all!

Data import plugin options in Progenesis QIHere at Nonlinear Dynamics, we’ve always strived to keep Progenesis QI and Progenesis QI for proteomics vendor agnostic.

This allows our users to utilise a single software package to analyse data from all of their instruments, and interface with a wide range of search methods and pathways tools.

We achieve this through our plugin architecture, which allows you to install and update your supported data formats, search methods, and pathways tools independently of Progenesis.

What are the advantages of the plugin system?

Distributing vendor specific functionality as plugins confers a number of advantages. Progenesis users can:

  • interface with multiple vendors using a single piece of software – a key distinguishing feature versus other analysis software.
  • remain up to date with new file formats and/or changes to existing file formats, without having to install a new version of Progenesis.
  • apply novel search methods and pathways tools to their existing data analyses, thus staying up to date with developments in the scientific community.

What plugins are available?

Data import plugins

Progenesis allows you to import raw data from a number of different vendors and machines. All imported data is converted to Progenesis’s unique internal peak models, so all types of data can be analysed using a consistent workflow. You can even combine data from different vendors in the same experiment (although this isn’t recommended as you may have trouble aligning the data).

Data file format Plugin FAQs Availability
Waters (.raw) QI
QI for proteomics
Provided as standard
Thermo (.raw) QI
QI for proteomics
Provided as standard
UNIFI Export Packages (.uep) QI Provided as standard (only available in QI)
AB SCIEX (.wiff) QI
QI for proteomics
Provided as standard
Agilent (.d) QI
QI for proteomics
Free download
Bruker Daltronics (.d) QI
QI for proteomics
Free download
mzXML files QI
QI for proteomics
Provided as standard
NetCDF files QI
QI for proteomics
Provided as standard in QI for proteomics
Free download for QI

Search plugins (QI)

These plugins allow you to search for small molecules or lipids in your data set, using a wide variety of data sources. Elemental composition even enables you to elucidate compound composition without the use of a dedicated compound database. Progenesis MetaScope allows you to search SDF and MSP files from any source you choose, e.g. HMDB or PubChem.

Search method Availability
Progenesis MetaScope Provided as standard
METLIN batch metabolite search Provided as standard
LipidBlast Provided as standard
Elemental composition Provided as standard
ChemSpider Provided as standard
NIST MS/MS Library Contact us for access

Search plugins (QI for proteomics)

Progenesis QI for proteomics can perform peptide search and protein inference using a number of different plugins. These encompass both database search methods like Mascot, and de novo sequencing methods such as PEAKS Studio.

Search method Alternative versions Availability
Scaffold v3.0 and v4.0 Free download
Mascot Provided as standard
Phenyx Provided as standard
SEQUEST dta and out files
dta and pepXml files
sqt and ms2 files
Dta plugins provided as standard
Free download for sqt plugin
PLGS v2.4 and v2.5
v2.3 and v3.0
Free download
Proteome Discoverer v1.3 (.xls)
pepXml
Free download
ProteinPilot Free download
Spectrum Mill Free download
PEAKS Studio pepXml import only Free download
EasyProt Free download
Byonic Free download

Inclusion list plugins

Inclusion list plugins in both QI and QI for proteomics allow you to target your ms/ms data collection for greater ms/ms coverage. Importantly, you can import new LC/MS runs into an existing experiment without having to replace peak picking and other analysis steps. This makes the use of an inclusion list workflow a powerful tool to increase ms/ms coverage in DDA experiments.

Inclusion list format Plugin FAQs Availability
AB SCIEX QI
QI for proteomics
Provided as standard in QI for proteomics
Free download in QI
MassLynx QI
QI for proteomics
Provided as standard
Thermo Finnigan QI
QI for proteomics
Provided as standard
Thermo Finnigan (4 d.p.) QI
QI for proteomics
Free download
Thermo Q exactive QI
QI for proteomics
Free download
Agilent preferred MSMS table QI
QI for proteomics
Free download
Agilent targeted MSMS table QI
QI for proteomics
Free download
Bruker Maxis QI
QI for proteomics
Free download

Pathways plugins

Progenesis provides reliable quantitative information about the changes in your experimental conditions. A number of pathways tools exist to translate such quantitative results into biologically relevant conclusions. Progenesis supports the following pathways tools, including the widely used IPA, and the multi-omics approach of IMPaLA.

Inclusion list format Plugin FAQs Availability
IMPaLA QI
QI for proteomics
Provided as standard
PANTHER classification system QI for proteomics Provided as standard (only available in QI for proteomics)
IPA QI
QI for proteomics
Provided as standard

Recent plugin updates

These are just a few examples of recent plugin releases we have made. As you can see, we regularly produce updates to Progenesis plugins, and develop new plugins when requested by customers.Progenesis web panel plugin update notification

  • In April 2016 we released an updated version of the mzML reader for Progenesis QI, introducing the ability to read indexed mzML files, as requested by our customers.
  • In January 2016 we released the IPA plugin for Progenesis QI for proteomics, giving users of Progenesis QI for proteomics v2.0 easy integration with this widely used pathway tool.
  • In November 2015 we released a new version of the Proteome Discoverer plugin, to support the newly released Proteome Discoverer v2.0 and v2.1.
  • In November 2015 we also released a brand new Thermo Q Exactive inclusion list plugin for both QI and QI for proteomics, since the Q Exactive machine uses a different inclusion list format to other Thermo machines.

Future plugins

Here at Nonlinear Dynamics we are committed to ensuring Progenesis remains vendor agnostic and supports the widest range of third party integrations possible.

As such, we’re always happy to hear from customers if they wish to use Progenesis with a third party piece of software for which a plugin does not exist. Please get in touch if you have any ideas for new plugins, or improvements to existing plugins.

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