Author Archives: Steve Anderson

Progenesis plugins: gotta catch ’em all!

Here 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, […]

Identification scoring in Progenesis QI

One of the advantages of using Progenesis QI is its ability to combine results from multiple search methods and databases. Progenesis QI uses a common scale to score results from all the databases and search methods it supports, so you can compare search results obtained from different search methods. This post explains the scoring method […]

Hi-N Quantitation For Clinical Discovery Proteomics

Progenesis QI for proteomics provides untargeted absolute quantitation of all identified proteins via the Hi-N method. This post explains the method and how it can be a useful tool for discovery proteomics in a clinical setting. What is Hi-N? Hi-N is a label-free quantitation method allowing absolute quantitation of all identified proteins in a sample, […]

5 key steps to peak picking that make Progenesis QI better

Nonlinear Dynamics were at MetSoc2015 this year, talking to attendees about our small molecule software Progenesis QI. One common confusion we discovered was our use of the term peak picking. In the minds of many, this simply refers to detecting MS peaks in profiled LC-MS data. In Progenesis QI, we use this term a lot […]

Creating custom fragmentation databases using Progenesis QI

One of the major new features in Progenesis QI (the successor to Progenesis CoMet) is the ability to create fragmentation databases from your experimental data, which can subsequently be used to assist identification. This blog post will show you how to start building your own. Identification phase The first step in creating a fragmentation database […]

Latest developments in fragmentation support for Progenesis CoMet

This post refers to Progenesis CoMet, which has since been superseded by Progenesis QI. While all of the features described remain relevant, we’ve now extended the software’s capabilities beyond what’s here. A fuller description of the new product can be found here. Thanks! The Nonlinear Support Team Here on the Nonlinear development team, we’re busy […]

Support for AB SCIEX WIFF files in Progenesis and wider search engine support

We’re always looking to improve our support for vendor specific data formats, and we are pleased to announce that Progenesis LC‑MS and Progenesis CoMet now support direct loading of AB SCIEX WIFF files. Previously, we recommended users of AB SCIEX machines convert their WIFF files to mzML prior to importing into Progenesis. The release of […]