Stay in the fast lane with Progenesis at ASMS 500, Indianapolis, 2017

The ASMS 2017 meeting follows the Indianapolis 500 – if you’re there, maybe you can still smell the burning rubber in the air. Comparisons can be drawn between the intense Indy 500 race and the jam-packed annual ASMS meeting… instead of IndyCars battling through the pack to secure their winnings, scientists race between the convention center and hospitality suites to ensure they’re knowledgeable about the best tech investments to enable their teams to keep on winning.

The Waters suite, ready to roll, at ASMS 2017
The Waters suite, ready to roll, at ASMS 2017, Indianapolis.

We had some of our own exciting tech presentations at the Waters breakfast seminar on Monday:

  1. Dr. Martha Stapels, Principal Scientist of the Bioanalytics Characterization Group of Sanofi Corporation, presented some host cell proteins (HCP) data analysis using new spectral library function which resulted in more efficient use of time and improved confidence.
  2. Dr. Andrew Collins, lead developer at Omic Analytics presented an interesting SILAC study of Phospho-Proteomes analyzed using Proteolabels software, which extends Progenesis QI for proteomics (QI·P) capabilities beyond just label-free proteomics.

In this post, I’d like to convince you that Progenesis is a winning brand worth investing in and will do that by firstly recapping the research value enabled by the traditional Progenesis Quantify then Identify approach. Secondly, I’d like to highlight how Progenesis QI has been evolving with user feedback.

Progenesis trusted to keep you in the fast lane

Let me strengthen your confidence in Progenesis with some key stats. Waters Corporation saw high value in the Nonlinear Dynamics team after working closely on projects, ultimately, resulting in the decision to invest in Progenesis. Nonlinear Dynamics has 28 years of experience on the discovery software circuit and although now a part of Waters, the Progenesis team continues to serve the wider community with data analysis capability for all major MS vendors. To date, there are over 850 groups invested in Progenesis QI technology – for their small molecules or proteomics research.

The Progenesis team year on year draws in crowds of curious scientists to the Waters suite at ASMS (and other meetings), wowing them with the easy to use software and visual workflow.

It’s easy to lose sight of the finish line with all of the interesting ‘new tech’ when you’re racing around the Indiana Convention Center. Make sure you take a pit stop at the Waters booth [#501] where the Progenesis team will provide you the tech updates to get your data analysis in the fast lane. Meaning you can secure the winnings from good research.

Progenesis QI: the difference engine you can rely on

Built on a solid foundation, the Progenesis QI alignment and co-detection engine ensures no missing values in your data matrix so you can draw conclusions based on a complete data matrix and resultant solid statistics. This means your research is going to tell the truth about your experiment, allowing you to create better-controlled experiments. You will see the important change with greatly increased sensitivity, ensuring you’re a winner in the race to progress your research, your teams’ objectives and your career.

At acquisition Waters Corp. identified Progenesis as a well-recognised and strong brand, so they kept this branding and added a core aspect of the Progenesis workflow, Quantity then Identify, hence Progenesis QI. This quantify then identify approach enables a comparative analysis free from the bias of identification challenges. Meaning you are able to focus your identification efforts after you know what is worth further investigation. The achieved clarity and confidence prior to the identification stage means you can spend your time positively on the features that matter.

Build your own spectral libraries in Progenesis QI·P v4.0

Screenshot from Progenesis QI for proteomics software showing search result from a spectral library search.
A screenshot from the Progenesis QI for proteomics software, showing search results and their fragment matching from a spectral library search.

Progenesis QI for proteomics has numerous options for database searching, interfacing with 14 different search engines. Version 4.0 brings further flexibility with the functions of spectral library creation and searching. You now have the facility to use and build spectral libraries such as NIST.msp, Mascot.msp and SWATH Atlas sptxt files. This feature enables improved specificity and time saving when searching proteomics and HCP data.

At Monday’s breakfast seminar Dr. Stapels presented a study in which the new spectral library functionality in Progenesis QI·P was used to analyze HCPs resulting in reduced false positive IDs, greatly reduced time taken for data analysis, and improved confidence in selection of peptides used for HCP quantification.

Proteolabels: a solution for label-based proteomics quantification

The peak co-detection feature in Progenesis QI for proteomics gives a 75% gain in the number of peptides quantified and a 39% gain in the number of proteins in that sample, via a Proteolabels analysis of public data set PXD003284.The peak co-detection feature in Progenesis QI for proteomics gives a 75% gain in the number of peptides quantified and a 39% gain in the number of proteins in that sample, via a Proteolabels analysis of public data set PXD003284. (htttp://

Dr. Andrew Collins of Omic Analytics presented his talk entitled ‘Application of Novel SILAC Analysis Software Proteolabels for Large-Scale Meta-Analysis of Phospho-Proteomes’ at Monday’s breakfast seminar. The team from the Liverpool University spin out [Omic Analytics] wanted to leverage the benefits gained in sensitivity from Progenesis co-detection and the various QC steps to analyze labeled data and so developed Proteolabels as a plugin to Progenesis.

Proteolabels is for quantitative proteomics, supporting studies involving stable isotope labels. Workflows include SILAC (two and three channels) and dimethyl (two and three channels).

Progenesis QI·P v4.0

With the imminent release of a new proteomics version of Progenesis, this post has focussed more on the large molecules workflow. So to conclude this thread it is worth mentioning Progenesis support for SONAR data. SONAR is a new data independent acquisition mode which is also being promoted at ASMS. SONAR provides additional specificity and clarity to DIA experiments.

Not all of the new capabilities of Progenesis QI·P v4.0 have been covered in this post as I’m racing to get it to you before the 500 miles have been covered. To find out more simply get in touch with us either at the Waters booth or via email.

Waters adds METLIN MS/MS Library to Progenesis QI Software

Progenesis demo station in Waters booth
Offline searching of the METLIN MS/MS database brings convenience and efficiency

For those of you that have been to the Progenesis station in the Waters booth or you looked carefully at the image on the left, you can see that METLIN MSMS is mentioned above one of the visible screens. Click here to read technology networks news release on this from March this year.

We are excited to be able to have METLIN integrated with the Progenesis QI software.

To summarize, Progenesis QI is enabling both small molecules and proteomics researchers to stay in the fast lane with a workflow built on the solid foundations of ‘Analyse ALL of your data’ followed by ‘Quantify then Identify’. Specific to proteomic research workflows Progenesis QI·P v4.0 is now geared up to give you an efficient and accurate HCP analysis with the addition of spectral library building and searching. You can now even analyze your MS1 labeled data with Proteolabels!

Again, if you’d like more information, simply skid into the ASMS Waters booth or send us an email.