Help with remote working and Progenesis

As we get to grips with our new lives in the presence of COVID-19, lots of you will now find yourselves working from home. We at Waters and Nonlinear want to ease a least a bit of the burden by offering a solution to accessing your Progenesis software installed at the lab or office.  

You may have found that if you try to use a local dongle over remote desktop (RDP) you will find that you will be taken to the licencing screen because the dongle will not be recognised, leaving you with no ability to access the software or your analysis. 

As a workaround for this, we will issue 2 month licence codes to those of you who find yourselves in this predicament whilst working from home. If the lockdown is still in effect after this, or if you require more runs, we will issue more codes as and when it’s needed.

Licence codes are a way to licence your runs without using the dongle – This will not affect your dongle. How they work is explained in this FAQ: http://www.nonlinear.com/progenesis/qi/v2.4/faq/sample-licensing.aspx  

If you require one of these whilst working from home, please contact support@nonlinear.com – This applies to any of you with a local dongle, regardless of current contractual status (whether in support or out of support).

Stay safe and please let us know if there is anything else we can do to help.

CEO Update on COVID-19

Dear Customers and Partners, 

At Waters, our purpose has always been centered on enhancing human health and well-being. Today, that purpose is more important than ever. As we continue to monitor the global Coronavirus pandemic, our top priority remains the health, safety and well-being of our employees, customers and partners while continuing to serve our customers and other stakeholders. We are committed to staying ahead of the curve on safety measures, while also continuing to deliver the technology, service, support and expertise you rely on Waters to provide. To that end, I would like to share a few key measures we have put in place: 

First, due to restrictions placed on travel and onsite visits, we have increased our bandwidth, capability and technology to support you remotely. At Waters we have extended our non-essential global travel restrictions until May 1 and will continually revisit this policy as time progresses.  

Second, we are limiting visitors to all our facilities and offices worldwide until April 1. While many visits can be turned into virtual meetings, we understand others need physical access to our facilities. All visitors that do come to our offices will need to fill out a screening form before being admitted.  

Third, given the technology we have at our disposal, many of us are readily able to work remotely. We have asked many of our employees around the world to work remotely until April 1. This proactive approach will help reduce risk in our facilities by protecting those that need to be in laboratories, manufacturing facilities and other capacities where remote work is not an option.  

Last, I want to reassure you we have a global business continuity team in place addressing every aspect of this dynamic situation. This team meets with me daily to ensure we are making data-driven decisions with speed and communicating with transparency.   

To all of our customers, partners and employees working day and night to manage through this pandemic, I thank you sincerely. I am truly humbled by the personal commitment, dedication and expertise all aimed at keeping us safe and healthy, especially those most vulnerable in our populations. It gives me a great sense of pride to participate in this innovative field and support each of you in your missions.  

We are all in this together, and my door is always open to you. 

Thank you,  

Chris O’Connell

Chairman and CEO at Waters Corporation

Happy New Year

It’s that time of year when we make resolutions for the coming year.  We look at ourselves with a fresh pair of eyes, we are honest with ourselves and we decide what we would like to change.  Here are mine for 2020:

New Year Resolutions

Do we achieve our resolutions?  Sometimes…  One year I vowed not to miss a birthday and get cards for all my friends and family.  I managed that one.  Another year I vowed to do a handstand every day.  I lasted until mid-February.

We can make resolutions at work too.  We want to be more effective, especially in technically demanding Omics.  How can we do this?  Where are we less than effective?

A fresh pair of eyes in Omics… the problem

As described during a lively presentation, Prof Don Jones cites the ‘Valley of Death’.  The slide below questions how effective we are in producing clinical success, considering our extensive research efforts in plasma proteomics.

There are some successes, although not many considering the amount of research funding that has gone into Biomarker Discovery.  You can click on the image to get his full presentation.

Proteomics biomarker discovery doesn’t work??

Slide from Novel strategies for discovery of cardiovascular biomarkers in human plasma – Donald JL Jones, Leicester Cancer Research Centre, RKCSB, University of Leicester, UK

Pre-analytical variation (or biological variance) is a huge problem with clinical data and can make it very difficult to find biomarkers even from large scale discovery Omics experiments. However, the powerful co-detection workflow of Progenesis eliminates missing values, maximising the statistical power of the experiment and increasing the ability to find the real biomarkers.

It’s interesting to see poor experimental design in there, we can do something about that!  Progenesis helps you to understand the power needed in your experiment and easily lets you alter your experimental design so that you can compare the same ions in many different ways.

Don also mentions how Progenesis QI for proteomics has made a huge difference to the Department’s research.  Nice to hear!

A fresh pair of eyes in Omics…  part of the solution

This is where the New Year’s Resolution comes in…

Progenesis can truly make a difference to the success of your research project.  This is because it analyses ALL of your data – no ‘holes’, no missing values messing up your statistical conclusion.

We are seeing it being used in success stories, such as this Nature Scientific report, discussing how dietary modification using a snack made from Eurotium cristatum fermented okara (ECO) can help reduce Type 2 diabetes mellitus (T2DM).

It’s a really neat piece of work done at the International Food and Water Research Centre, IFWRC, which was opened by Waters in Singapore to advance innovative research in the food and water industries by creating a collaborative laboratory facility for both industry and academia to solve their mutual challenges.

So, have you made your work New Year’s resolutions yet?  Why not make one to try out Progenesis QI or QI for proteomics and boost your project’s chances of success?

30 years of Nonlinear Dynamics

30 years logo

Nonlinear Dynamics celebrates 30 years of being in business this year end.  We thought it would be interesting to take a trip down Memory Lane and see what was happening around the world while founder, Will Dracup, was starting his embryonic company.

1989 was an interesting time to be around, especially in Eastern European countries.  There was huge hope and optimism in the air as these countries opted for democracy.  Here are just some of the Global events that took place in December 1989:

  • USSR President Mikhail Gorbachev meets Pope John Paul II at the Vatican
  • V. P. Singh sworn in as the 8th Prime Minister of India
  • Soviet President Mikhail Gorbachev and US President George H. W. Bush, declare the Cold War over
  • France TGV train reaches world record speed of 482.4 kph
  • President Gustav Husak of Czechoslovakia, resigns
  • “The Simpsons” created by Matt Groening, premieres on Fox TV as a full animated series with the episode, “Simpsons Roasting on an Open Fire”
  • After 23 years in power, Romania ousts Nicolae Ceausescu
  • Japanese scientist achieves -271.8°C, coldest temperature ever recorded
  • Alexander Dubček elected Chairman of the Federal Assembly (Parliament) of Czechslovakia
  • Václav Havel is selected to be president of Czechoslovakia by the Federal Assembly shortly after the Velvet Revolution
  • Wayne Gretzky and Martina Navratilova, named athletes of decade by the Associated Press

After setting the scene of what was going on in 1989, we then decided to talk to Will about his motivations and ambitions when starting his company.  Here’s what he told us:

“I’d been working as an employee for a scientific company when two scientists inspired me that the time was right to set up a 2D gel analysis company.  Back then my main aim was to make enough money so I could take summers off work and spend time by the river.”  It didn’t quite work out that way, Will and his colleague, Dr David Bramwell have established a pioneering research company, Biosignatures, whose ultimate aim is to be able to analyse a single sample of blood and provide an early diagnosis for as many as 20 or 30 life changing diseases.

At our ASMS breakfast seminar this year, Nonlinear’s Jonathan McSayles, gave a brief history of Nonlinear Dynamics that we’d like to share with you. It shows the growth of the products and how we adapted to the changing market to continue to serve our customers.

Landmarks of the early years of Nonlinear

Nonlinear Dynamics was established in 1989 and launched the first product in 1991 which was Phoretix 2D gel analysis software. Two years later in 1993, a second product for 1D Gel analysis was released. Not long after, came the Phoretix Array and TotalLab software products.

In 2000 there came a major leap for Nonlinear – opening an office in the US and the following year launching the first Progenesis product for 2D gel analysis.  After the success of Progenesis Discovery we continued development with the launch of Progenesis SameSpots in 2005.

At that time, we also signed a co-marketing agreement with Waters Corporation, and this set the stage for Nonlinear to diversify.


Landmarks of the later years of Nonlinear, now a Waters Company

In the mid 2000’s the 2D gel market changed, but we were already on the path to move our development into the emerging label-free mass spec market. 

Progenesis MALDI was launched in 2008 followed by Progenesis LC-MS, and many of our customers had moved from 2D based techniques to mass spec-based analysis. We moved into the metabolomics field in 2011 with the launch of Progenesis CoMet.

In 2012 another significant milestone was made with the Co-development agreement with Waters Corporation. The Waters Corporation branded LC-MS product TransOmics Informatics was born. The success of that partnership and product development led to the acquisition of Nonlinear by Waters in 2013, followed by the fully integrated products we have today – Progenesis QI and Progenesis QI for proteomics.

We hope you have enjoyed the brief history of Nonlinear Dynamics.  Before we close out the year, we’d like to wish you Season’s Greetings and a very successful New Year.  Stay tuned for our first blog post in 2020 to see how Progenesis can help you achieve success in your research. As always, if you would like to download or learn more about the software then don’t hesitate to get in touch. We will be more than happy to help you.

New release of the Progenesis QI for proteomics software

Nonlinear Dynamics, a Waters Company, is proud to announce a new release of the Progenesis QI for proteomics software. Version 4.2 has now been released and is available to download. If you are working in the area of Host Cell Proteins (HCP), this release is the one for you.

While many of our customers are using the software for HCP analysis already, this latest release has a quantitation method that has been specifically designed for HCP analysis. If you choose to use the HCP quantitation method, then a new column has been added for greater understanding of your HCP data.

Screenshot of the HCP quantitation workflow option
Screenshot of the HCP quantitation workflow option

Not to be overshadowed by the HCP content, we are excited to let you know that we now integrate with Metacore, a Cortellis solution for pathway analysis. MetaCore is one solution in the Cortellis™ suite of intelligence solutions that enables precise, actionable answers to specific questions across the R&D lifecycle. MetaCore delivers high-quality systems biology content in the context of comprehensive pathway-based analytics, molecular network building and insightful visualizations. This plug-in now comes as standard with the software, but you must be on this new version in order to take advantage of it.

For existing users, you can update through the software or download the update here. To help you get the most out of the new features, we’ve updated our list of FAQs.

This update will also require you to update your plugins, which can be downloaded from the relevant FAQ pages:

As always if you aren’t currently using it and are looking to make a difference in your lab, then Progenesis QI for proteomics could be the change you are looking for. We can set you up with an evaluation so you can see what difference it can make to your workflow. We offer online and in-person walkthroughs of the software so get in touch now, you could be writing the next review of Progenesis QI for proteomics, like the one below.

Progenesis QI for proteomics 5-star review

How was Progenesis QI used in an untargeted lipidomics workflow?

Following on from last month’s blog post, I’d like to continue with the other exciting video presentation from ASMS 2019. Dr. Jace Jones from the University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences in Baltimore, Maryland gave a very interesting talk on how the Progenesis QI software was used effectively and robustly to process a variety of lipidomic datasets from a traumatic brain injury model. His talk was entitled: The Use of Progenesis QI to Efficiently Process Lipidomic Data: Application to Traumatic Brain Injury

At a first glance, people only see what they want to see as we are preprogrammed to view things from our own perspective. The same can happen in science where we look at what we know over and above what we don’t. Dr. Jones highlighted the fact that the Progenesis QI software facilitates a process for them to be able to see what is not always visible at first so they could focus on groups that may not have been obvious.

After using the Progenesis QI software in his discovery workflow he then went on to do his quantitation workflow which corresponded well with the discovery results. This gave him great confidence that his workflows were robust in that he could go back and forth between discovery and quantitation.

The abstract for the talk Dr. Jones gave is below, but I again highly recommend you watch the video as the work they are doing can have a big impact on how we treat traumatic brain injuries moving forward.   

Presentation of the lipidomics talk presented by Dr. Jace Jones

Abstract

The Use of Progenesis QI to Efficiently Process Lipidomic Data: Application to Traumatic Brain Injury

Jace W. Jones, Ph.D.

University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD

Lipids have significant potential to inform on disease and injury due to the pivotal role they play in many biological processes including cellular integrity and permeability, energy storage and metabolism, and signaling pathways. Heightened interest in the mechanism by which disruption of lipid metabolism and homeostasis contributes to a variety of human diseases and injuries (e.g., cancer, diabetes, neurodegenerative disorders, infectious diseases, and pulmonary conditions) has led to a substantial increase in lipidomic research. The field of lipidomics, broadly described as the comprehensive biochemical characterization of “all” lipids (referred to as the lipidome) within a cell, tissue, or organism presents a variety of analytical and data processing challenges. The analytical challenges result primarily from the dynamic range, vast structural diversity, and sheer number of biological lipids. These challenges have been commonly addressed using liquid chromatography coupled to high resolution tandem mass spectrometry. This workflow results in an information-rich data matrix that must be processed for retention time alignment, peak picking, adduct deconvolution, abundance, identification, and statistical analysis. Successful implementation of the aforementioned lipidomic workflow in a model system where two appropriate cohorts (e.g., disease vs control) are comparatively analyzed yields differential expression data delineating lipid profiles between the two groups and abundance of individual lipids.

The data processing challenges associated with efficiently and properly handling lipidomic data is not trivial and has been meet with a variety of software solutions. One such software solution is Progenesis QI from Nonlinear Dynamics (Waters). Progenesis QI offers a comprehensive workflow for efficiently processing LC-MS/MS generated lipidomic datasets. Progenesis QI is streamlined to handle multidimensional data in the form of chromatographic retention time, ion mobility, accurate mass, and data-independent acquisition. Data will be presented detailing the use of Progenesis QI to effectively and robustly process a variety of lipidomic datasets from a traumatic brain injury model.  

Try it for yourself

Now you can see how our Progenesis QI users are having success with the software in their research, why don’t you see how the software can help you in your research? The Progenesis QI team are more than willing to work with you to see how you can transform your results. We would like to help you see results in your workflows that you may not already be seeing. Please get in touch or comment below.

Are you missing out on how Progenesis QI can help your research?

ASMS 2019 has come and gone but the research continues. Nonlinear and Waters were lucky to have speakers at ASMS 2019 who shared their research with us and explained how the Progenesis QI software was an integral part of their work.

If you didn’t get to attend the talk by David W. Gaul, PhD., from the Georgia Institute of Technology or would like to hear the presentation again then we have the video for you. The title of his talk was “Preoperative Metabolomic Signature of Prostate Cancer Recurrence” To get an idea of what the presentation entails, you can read the abstract below, but I highly recommend you watch the video so you can see how important the work David and his group are doing with regards to giving people more information on how they can change their treatment decisions moving forward from a simple blood test.

Abstract

Up to 50% of prostate cancer surgical patients will suffer from biochemical recurrence manifested by detectable serum prostate specific antigen levels even after prostate removal. Currently available pre-operative information has not yielded adequate prognosis to guide a patient’s treatment decision.  More clinical data is needed to improve prognosis. New biomarkers can arise from metabolome analysis of patient serum to aid physicians and patients in developing a treatment plan. We applied a multiplatform (NMR + LC−MS) metabolomics approach to the study of preoperative metabolic alterations associated with prostate cancer recurrence.

If you would like to trial the Progenesis QI software in your lab to see how it can impact your research, then please get in touch.

Why are reviews important?

The internet is a huge resource at our fingertips that enables us to find lots of information about any product that’s of interest to us, but how can we be confident the information is accurate, unbiased and a true representation of the product? 

That’s where reviews come in. If a real live person has used a product and given a review, then you can be more confident about that product and its capabilities and the choice you are making.

Here at the Progenesis QI team, we want you to be happy with your mass spec software so we’ve been working with SelectScience for a while now to generate informative reviews of Progenesis QI and Progenesis QI for proteomics software that will be a valuable resource for our potential users.

Who are SelectScience?

Image of the SelectScience logo celebrating their 20 year anniversary
SelectScience an independent product review website

I’d be surprised if you haven’t heard of SelectScience already but if you haven’t, they are a trusted, independent website for laboratory scientists to find impartial reviews written by their peers, as well as application notes and videos. They work with scientists to inform them about the best products and applications. Google recognizes them as a trusted review site for independent product reviews and they have won the Queen’s Award for International Excellence.

two images. One showing the logo for the Queens Award for Enterprise and the other shows the five star trusted review image.

As a Progenesis QI or Progenesis QI for proteomics user, you’ll be receiving an email shortly with a link to enter a prize drawing for the chance to win an *iPad® or a $400 *Amazon® gift card in return for simply writing a review and sharing information about Progenesis QI or Progenesis QI for proteomics software with your peers.  If you don’t receive the email, then let me know and I can send you the link. You will have to act quickly as the option to enter the draw will only be available for a limited time.

If you have used the software in the past then you also have the option to write a review here or you can access the review form direct from our website.

You can see below some of the reviews we currently have for both the Progenesis QI and the Progenesis QI for proteomics software. As more and more people use it, we hope many of them will share their experiences.

Image of the review from SelectScience for the Progenesis QI for proteomics software.

Review for the Progenesis QI for proteomics software
Image of a review from SelectScience for the Progenesis QI software

Review for the Progenesis QI for proteomics software

If you haven’t tried the software yet and would like to talk further, don’t hesitate to get in touch.

*iPad® and Amazon® are not affiliated with this drawing and are independently owned and operated.


Identification scoring in Progenesis QI

With the amount of information available today, important and helpful information can easily get lost and overlooked. I’d like to take this opportunity to repost this blog post about identification scoring in Progenesis QI of as many of our customers find this very useful in their research and still refer to it today.

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 we use in Progenesis QI, and how you can improve your search scores by searching additional dimensions of your data.

Progenesis QI search methods

At the time of writing, Progenesis QI supports these search methods and databases:

Progenesis MetaScope

Searches SDF and MSP files from any source. Supports retention time, CCS, theoretical fragmentation and spectral libraries.

METLIN™  MS/MS Library (requires purchase)

The Waters® METLIN™ MS/MS Library for Progenesis QI contains a local copy of the METLIN database and allows you to search this copy rapidly.

LipidBlast

Searches the LipidBlast MS/MS database provided by Metabolomics Fiehn Lab.

Elemental composition

Produces putative formulae for compounds based on mass, isotope profile, and the Seven Golden Rules.

ChemSpider

Searches the ChemSpider structure database. Supports theoretical fragmentation, isotope similarity filtering, and elemental composition filtering.

NIST MS/MS Library (requires purchase)

Searches the NIST MS/MS library for spectral matches.

You can find out more about each of these search methods in the search methods and databases FAQ. This blog post, however, will focus on how we calculate scores so that identifications from different search methods can be compared.

The Progenesis scoring method

For any given search, there are a possible five properties that can contribute to the overall score:

  1. Mass error
  2. Isotope distribution similarity
  3. Retention time error
  4. CCS error
  5. Fragmentation score

Each of these individual scores is on a scale from 0-100. If your search criteria do not include a given piece of data, the score for that piece of data is 0. The overall score is the mean of these 5 scores.

Note that the more search criteria you use, the higher the maximum possible score becomes, as described in the following example.

Example

Suppose we have searched ChemSpider using theoretical fragmentation. For a given compound we find Identification A, with these scores:

Note that the scores for retention time and CCS errors are 0, because ChemSpider does not support searching those properties.

If we then perform a MetaScope search, this time including a CCS constraint, we might obtain the following scores for Identification B:

We have identical scores for the mass error, isotope distribution, and fragmentation. However, we also have an extra piece of information in the CCS score. This provides additional evidence for Identification B, so it is given a higher score than Identification A.

Note that in the ChemSpider case, if an identification scores 100 on all 3 items, it obtains a score of 60. In the MetaScope case, if an identification scores 100 on all items, it obtains a score of 80. So, for each additional piece of data we include in our search, the maximum score increases by 20.

The component scores

Here we’ll briefly describe how the five component scores that make the final score are calculated.

Mass error, retention time error, and CCS error

These are all functions of the magnitude of the relative error, Δ:

The score profile for mass error, retention time error and CCS error.
Figure 1: The score profile for mass error, retention time error and CCS error.

For the mass error, Δ is the ppm mass error and N = 4000. For the retention time and CCS errors, Δ is the percentage error, and N = 20.

Isotope distribution similarity score

This compares the intensities of each isotope between observed and theoretical distributions. A total intensity difference of 0 gives a score of 100, which falls linearly to 0 when the total intensity difference is equal to the maximum isotope intensity.

Fragmentation score

The fragmentation score is more complicated and depends on the fragmentation method used. The FAQs describe how scoring works for theoretical fragmentation and database fragmentation.

Improving identification scores

The best way to improve the scores of your identifications and your confidence in them is to use more search constraints.

37.9/100

In general, most searches will be able to produce a mass error score and an isotope similarity score. With just these two pieces of information, the maximum score for any identification is only 40/100. In this example we’ve identified Warfarin using only mass error and isotope similarity.

55.4/100

By including fragmentation data in your search criteria (either theoretical fragmentation or a fragmentation database), this increases the possible score for identifications to 60/100. Here we’ve added theoretical fragmentation to our search parameters.

70.8/80

Finally, if you use an appropriate data source (e.g. an SDF and additional properties file) you can add search constraints for retention time and CCS, giving a maximum score of 100/100. Here we don’t have CCS information but have added retention time to our search parameters for a maximum of 80/100.

Future improvements

Currently Progenesis gives equal weight to the five component scores – mass error, isotope similarity, fragmentation score, retention time error, and CCS error. In some cases, this might not be ideal, so if you have any suggestions for different weightings we’d love to hear from you in the comments section below.

As always, if you have any further questions, check our FAQ or get in touch.

How do you know your raw materials are as they should be?

Agnès Corbin of Nonlinear Dynamics gives us an overview of what’s needed to maintain high manufacturing standards.

Agnes Corbin

We all know it, reproducibility is one of the key parameters to master for maintaining a product’s quality. As a customer, we all like our favorite products of a consistent high quality; as a manufacturer, we want to preserve our quality and customers’ satisfaction

That starts with the supply chain of the raw materials and ingredients used to manufacture a finished product.

A non-conformity, be it a cross-contamination, adulteration or degradation, can have huge economic, clinical and sanitary consequences, especially with high cost raw materials.

With this in mind, you might be interested in the below application note, produced in collaboration with Robertet Group, the world leader in sustainable natural raw materials for fragrance and flavor.

Click on the image to download the Vetiver essential oils application note
Vetiver essential oils application note

It describes how Progenesis QI was used, to spot an ‘out-of-the-blue’ potential non-conformity in Vetiver essential oil, using an Untargeted Metabolomics Profiling approach with LC-HRMS and a variety of Ionization techniques.

Progenesis QI helped to detect and identify adulteration with Castor Oil, a non-volatile compound, in a new batch of Vetiver Essential Oil. It would have been missed with the use of classical and common GC-MS techniques applied on volatile compounds.

The combination of LC separation equipment UPC² and UPLC (with different ionization sources ESI, APCI, ASAP) were used to get a better understanding of the product’s composition. Suppliers of natural raw materials must increase their phytochemistry knowledge of their products, as per the recent change in the REACH regulation based on the Natural Complexes Substances (NCS).

The easy-to-set-up LC-MS techniques for non-volatile compounds, can be considered as complementary to GC-MS for volatile compounds QC.

Robertet could have missed out if they hadn’t used the Progenesis QI software.

Are you missing out by not using it?

Please contact us for an evaluation today and we can help you with your research.