Virscidian’s advanced baselining algorithm (AsLS2) quantifiably gives higher quality and more accurate results than one of the older generation algorithms which we retain in the software. We found that the maximum deviation of the automatically calculated (AsLS2) Area% from an ideal result; ie: manually reviewed and integrated peak(s), gave no more than 0.5 % deviation in the returned Area% results. When compared with another more commonly used baseline algorithm, we found that the maximum deviation was as generally within 2% but had one data point which was almost 22% different. The results are shown graphically below in Figure 1

Figure 1: Plot of normalized Area% deviation for two different baseline algorithms that are included in Virscidian’s Analytical Studio Professional – Compund QC product. The key baseline of interest is the AsLS2 baseliner.

The supporting detail

Sometime back we promised to explore more on quality of results processing in our blog post “Does the physical task of having someone review the results of purity and concentration output for substance confirmation make a difference?”. As we can all see time passed, lots due to project, travel and other commitments, but mostly because to do the type of analysis we had planned was either going to be a bear of a manual project or required us to develop some tools to help us do the job properly. Needless to say we went the second route, but this we had to put a little on the back burner whilst we attended to other pressing business needs. While I might be prepared to delve hour after hour into the depths of numbers and manual data review {and have done on many occasions}, we have better things to do and thus waited until we could automate much of the data gathering.

So armed with an experimental implementation of a data collection package, which we have embedded into our Analytical Studio Professional – Compound QC and Analytical Studio Reviewer, we set about trying to quantify the performance of some aspects of our software, which we share here as a forerunner of more detailed studies we intend on performing over time and publishing here and in other appropriate venues.

Customers have told us anecdotally that “they are extremely happy and impressed with the accuracy of the results we produce for our Compound QC substance analysis” by LC/MS/UV/ELSD, CLND (or CAD), which is all well and good but is entirely unquantified.

Experimental summary

For Compound QC or substance analysis in support of library management or Medicinal Chemistry – synthetic chemists or purification of crude substance, the calculated Area% of the target substance is used as a powerful indicator of the implied purity of the substance using some chosen detector and some extracted channel of data for the 3D type detectors that are available (DAD/PDA or LC/MS). In this case we chose the DAD 310 nm extracted wavelength chromatogram.

These results are based on a pilot small scale study of 70 samples of varying complexity from relatively clean to crude mixtures with lots of closely eluting chromatographic peaks, which we wanted to share and get feedback on. The final results are based on 52 extracted target substance peaks on a subset of the original 70 samples. This was because there were a number of samples where the target substance was not found or was identified as maybe.

The same data (UV310) were processed firstly with the Peak Picker baseliner, then the AsLS2 baseliner and then finally all results were reviewed manually and reintegrated to produce our gold standard result. The peak area% of the target substance for each sample was then extracted from each of the three series of results. The Area% values for the peak picker algorithm were then differenced from the manually reviewed results, as were the AsLS2 results. The two final sets of data were then plotted as we see in figure 1, though for ease of visualization the outlier point of 21.9% deviation for the Peak Picker algorithm was excluded from display, so that the fine detail of the graph could be observed. No other changes were made to how the data were processed or reviewed. Nothing fancy in the overall treatment and presentation of the data and results.

Results

We can see that the maximum deviation from our graph above is 0.5% for the AsLS2 baseline and was actually 21.9% for one data point using the Peak Picker algorithm {though this was excluded from the graph above}. We can also observe that there is a much tighter cluster for the AsLS2 algorithm than for the Peak Picker as shown below in Table 1.

 

Table 1:- Summary of results for the comparison of AsLS2 and Peak Picker algorithm against a series of manually reviewed gold standard results

Figure 2:- Summary of results for the comparison of AsLS2 and Peak Picker algorithm against a manually reviewed gold standard results

Conclusions

Using a development statistical data gathering approach, it is now possible to capture important data features, which can then be used to design performance evaluation studies within Analytical Studio Professional – Compound QC and Analytical Studio Reviewer, and as a consequence we are now able to start quantifying the performance of our software and further allow us to quantify improvements we make to our processing algorithms.

We hope you find this short investigation interesting and welcome feedback on our results, approach and new experiments that would further help quantify the performance of our software.

Observation

Small or large, our organizations are having their marketing budgets squeezed and we are globally being asked to find new ways to market ourselves and our products. Traditional marketing is arguably becoming replaced by on-demand viral marketing though social media forums such as Blogs, You tube, Face Book, and community groups on professional sites such as LinkedIn and Plaxo. So while these forums do have a role to play how should we best leverage their power and influence when the market we promote too may often be niche?

In search of the constructive input

So how should we best market ourselves and our products in a way that gets us to the people that may want our products that maybe never heard of who we are and all of this in niche industries?

That really is the crux of the question that I’d like to get feedback on. Comments are most welcomed…

We are in the final straight preparing for the Release of Analytical Studio Professional Version 1.1 – Compound QC workflow due to be released at the end of June.

Our foci for this release

• Getting you closer to a quality and reliable result requiring as little additional manual manipulation as possible.
• Providing you a richer, more streamlined results review experience for speed scanning through large volumes of results at a glance.

Quality and reliability of your results

Getting a software processing method optimized to produce the perfect result is one that many of us know can be a time consuming and tedious process, especially when you have to repeat this for every analytical detector stream that you are using/ {MS – Positive and Negative Ionization, CLND, ELSD, UV and so on…}. With this release we are delivering a fully interactive data processing tuning tool where you can visually see the impact of the processing settings and data filters in real time. You might call this the WYSIWYG of analytical data. Our experiences during testing have resulted in methods being developed from scratch to ideal processing method in less than half the original time using early implementations of our software. At the same time, we have also found it is much easier to get a processing method that produces more reliable and consistent results which in turn increases the trust in the result and reduces the time to quality control review the results.

Richness of information and streamlined data review

Results interpretation and evaluation can often be a tedious process, requiring lots of individual pieces of information, extracted spectra, chromatograms and feedback messages from processing, in order to perform results QC quickly and efficiently. Consider the impact of what one mouse button click can do for your results evaluation when you have 1000 or 10,000 samples to review. So, with this release we have redesigned our sample summary information page to bring together all important facets of sample results, processing warnings, and other important information in a single visual concise color coded summary page. At the same time diagnostic information has been made more readily available to ensure that the time to result is reduced as much as possible.

Our aims for your research

As a company focused on giving you 100% of what you want, our commitment is to continue to strive to improve what we offer as our different workflows, and make them deliver what you want from your data, at the highest possible level of accuracy, maximum level of precision, maximum level of relevant information, maximum flexibility of reporting and minimum amount of time for review.

About Virscidian Inc.

For those not familiar with Virscidian Inc., our products, services and solutions: we are an analytical chemistry software company founded as a spin out from an Analytical Clinical Research Organization (CRO), offering software products and implementations that support a number of different tailored workflows. Two examples of what we do include High Throughput LC/MS Compound QC Screening (HTS) and HTS Biomarker Validation and Quantitation. Our software is built on our proprietary development software framework, which in turn allows us to build completely customized workflows that encompass only functionality that is required to deliver the workflow. Results may be viewed using our Analytical Studio Reviewer (ASR) which has also been licensed by Agilent Corporation for sale. Our development, customization and business analysis services are available by request.

There are just some events in business that really make a difference to the industry – I expect this to be one of those events. On the 11^th May the Royal Society of Chemistry (UK) acquired Chemspider – it’s worth taking some time to read the Press Release on this. This news in its own right is special as the Royal Society of Chemistry (RSC) has for decades promoted Chemistry within the United Kingdom (UK) and out into the global community with an ever expanding worldwide community of members. RSC’s mission is “to be the most effective organization for the advancement of the chemical sciences” and that of Chemspider’s “Intention is to introduce innovative scientific software technologies that can be of value to academia and to chemical, pharmaceutical and biotech companies around the world.” This shared mission of delivering chemistry to the community makes this true partnership of equals in our community and one to be promoted, enhanced and furthered as much as possible. Provide your support by using and contributing to the environment and commenting on topics and blogs of interest to you.

I guess you might say that this acquisition sort of gives Chemspider aka Antony Williams a “Chemical Royal Seal of Approval in Chemistry Search Space” in a metaphorical sense. A justified end goal for the years of thought, passion, patience, endurance and commitment.

For anyone wanting to challenge legality on the use of this statement – please accept that my use of this is not to imply or otherwise indicate that this happened, will happen or expected (of course always something to strive for), in any literal sense. Any reference in my use Yahoo’s video of the Royal Seal of Approval for Google does not indicate any way business or other relationships or interests between any mentioned parties. (Interesting posting of such a video though).

Antony Williams is extremely passionate about the quality and accuracy of structural chemistry and serving chemistry out to the community as a free resource for scientists globally. His investment personally has been immense with long hours invested in structural curation in the world of chemistry for Wikipedia and for Chemspider as a whole. Whereas, many structural environments can be considered as somewhat stale and static environments, Chemspider’s mission to have the community contribute to the quality of its content, by online curation, has given us a living breathing world of chemical space information. Anyone interested in Chemistry really should have this as a bookmark or Favorites web link in their Web Explorers.

On a personal note I applaud both the RSC and Antony Williams for making this happen and for ensuring a commitment to continue to grow our chemical space community. Please keep this going, it is an amazing resource.

Mark Bayliss

(Ph.D., B.Sc., MRSC CChem) for the complete title and affiliations (MRSC CChem – Chartered Member of the Royal Society of Chemistry)

Those of you from Pharma, and chemical synthetic industries; will be familiar with the routine and the process. Synthetic chemists produce some small, medium or large scale; matrix of substances and they want to have answers to the following questions “Have I made what I thought I made, how pure is it, and how much did I actually make?” For decades we have invested time, effort, energy, money and manpower into the act of acquiring data to support these questions. The methodologies and instrumentation have changed over the years, but the ultimate need has been an ever present and an important requirement.

For those not so familiar with these industries and processes, Pharmaceuticals, Agrochemical industries, and most chemistry development companies specialize in the need to produce new chemicals typically targeted to solve some challenge or problem; such as treatment of disease, eradication of weeds or insects and the like. During the development of these new chemicals, lots of testing, including Chromatography and mass spectrometry must be done before the compound is allowed to be commercialized. One small piece of this process right at the very beginning; is to ensure that the chemists made what they thought they had and know how much they made in the process. It is all very well to say I have 1 Kg of a chemical but if it is only 5% pure and the wrong chemical substance, then its value is significantly diminished or nothing. Analytical processes are present to determine such information.

Within many these organizations small, medium and large, we operate within a chain of responsibility, trust and respect, of the results that have been generated in all previous stages of the process. We have too, otherwise our systems would fail to continue being effective. So as part of this chain, I’d like to ask opinions on the need for checking or review of results arising from of our analytical testing of our compound confirmation processes. I’d like to also ask what opinions exist in respect of the importance of accuracy of processing for compound QC screening.

To start with, some indication of my bias might be warranted. As an analytical chemist myself by training, I am concerned about the quality of the results which either I create or I review or have to make conclusions from. So when presented with some series of results, I want to be sure of how these results came to be and what is my level of trust in those results, but at what cost do we do this? By cost I mean time, money and our already challenged teams of the people and scientists who must do this work.

So some questions that I would like to put out there are:

• Does performing physical review of the analytical QC results for compound synthesis make a difference at the level of chemists, laboratory and organizationally?
• Should this be a 100% check or some pseudo random review of some defined % of the samples acquired?
• Does this provide quantifiable value to an organization?

I’ll be following this thread up with a future blog about our experiences from colleagues and how such challenges and needs affects results in real laboratory situations.

Comments welcomed.

Mark Bayliss

I feel very fortunate to have known Joseph Simpkins (CEO of Virscidian) for close to a decade now, meeting him first when he joined Eli Lilly to develop their compound QC informatics solution. Back then the focus, which is still a major part of early drug discovery, was to be able to determine which compounds had been chemically synthesized, which ones hadn’t and how pure the synthesized product was. Sounds simple? Certainly the technologies to acquire the data are easy and routine to use however as each company and group want something different in how they treat their data, what looks on paper to be easy, often turns into something more with extras needs and expectations from different stakeholders?

One of the things that always impressed me with the solutions that Joe created, including Analytical Studio Professional 1.1 that is available from Virscidian Inc., was that they were born from a fundamental need for a company or colleague to solve some time consuming and often repetitive process, both quickly and accurately. His solutions to these problems have been developed typically alongside the person or the activity and thus mimic closely the workflows and functionalities required. The solutions that he created were typically done quickly using a rapid prototyping approach whilst sitting with the chemist, scientist or end user and getting their direct feedback on what developments had been made. Joseph later in his career started Opans LLC, with his friend and colleague Kenneth Lewis back in 2002 and in the year’s in-between has worked tirelessly to produce a commercial software platform for processing LC/MS data for a number of different workflows. I’d like to explore aspects of this in a future blog.  At the end of 2008 Joe spun out from Opans to create Virscidian which now is a commercial company promoting and selling its software solutions and customization services  for the software.

So when Joseph approached me and asked if I’d be interested in joining Virscidian, it was really a very quick decision process that led me to the conclusion that this would be an exciting opportunity and a great match of skills and shared aspirations of both Joseph and myself.

One things that I have personally found very attractive in talking with Joseph has been the company willingness to be open to new possibilities, new directions and to deliver to our customers not just an off-the shelf product that does x, y or z, but a solution that can be adapted to meet the needs and workflows of chemists, scientists in drug discovery companies, synthetic and analytical chemists in other industries such as agrochemical, forensic, sports, food and so on. At this time Virscidan is able offer solutions in the areas of routine Compound QC, Quantitation and Biomarker Validation. This philosophy of delivering to the needs of scientists and analytical chemists forms part of the company motto of aiming to deliver “100% of what you want”.

Posted By Mark Bayliss

Who is Virscidian and where did we come from?  Joseph Simpkins, President of Virscidian, has 15 years of experience in managing engineering and informatics projects in the pharmaceutical, chemical and food industry and was a cofounder of OpAns, LLC.  OpAns is a Contract Research Organization providing services to the pharmaceutical industry and focused on the application of mass spectrometry to a number of issues including quantitative analysis, structure and biomarker validation and determination of physicochemical properties.  At Opans Joseph applied his expertise to the development of software tools to support the needs of the laboratory and was able to produce a platform that excited the customers of OpAns.  With time, the customers were interested not only in the services provided by OpAns but also by the software platform, at that time branded as “Analytical Studio”.

What About Analytical Studio?

The technology was developed over the course of 7 years and during that period several large pharmaceutical companies invested in the software for their laboratories.  In that time, the software architecture underwent three major iterations until it settled on a powerful but flexible plug-in based architecture branded as “The Analytical Studio Framework” (to be discussed in depth in a seperate blog post).  In 2008, the progress of Analytical Studio caught the attention of folks in R&D at Agilent Technologies.  So, by mid-2008, a small limited subset of the software built on the Analytical Studio Framework was licensed by Agilent Technologies (to be discussed in a separate blog post).  The Analytical Studio Framework allows rapid development of full featured work-flow solutions.  Starting with vendor independent raw data reading and viewing.   Then data processing and review with integrated editing of results followed by reporting and publishing and archival of results and raw data.   In essence, it is a high-throughput tool that automates the conversion of raw data to results while allowing the flexibility of vendor independency and is a powerful and flexible viewing tool for some of the major formats adopted in the industry.

With seven years of stress-testing in large pharma labs and a CRO environment,  Analytical Studio has been optimized for performance, throughput and quality of results.   But without loosing the flexibility to adjust the software to be optimized for the customer’s workflow.   Analytical Studio is componentized and can be configured to provide solutions for different environments …this is how we have built solutions for Agilent to have an Analytical Studio Reviewer, why we can rollout a fully enabled version called the Analytical Studio Professional and why we can have an “Express” version for background processing, reporting and have Analytical Studio Repository for the publishing of data.

We will shortly start publishing some movies and presentations about Analytical Studio in its various flavors from highly customized solutions for research projects (parallel HPLC and biological deconvolution) to off-the shelf compound characterization and biomarker validation.

Welcome to the Virscidian Blog. It’s likely that you have not heard of Virscidian before but we believe that will change. Virscidian is a provider of analytical chemistry work-flow solutions to laboratories of all sizes and we already have a track-record of enabling laboratories world-wide to process more efficiently with greater accuracy while integrating with existing IT environments.  What does this mean and what do we stand for?

We built software focused on supporting analytical chemists.  Good software.  Software optimized around processes, throughput and designed with the user in mind based on user requirements and guidance.  This knowledge came from more than 10 years owning, managing and supporting analytical labs.  There are many analytical software packages on the market that have a lot of functionality.  These can be either hardware vendor or third party solutions and they offer a solution to many problems. Unfortunately many of these are complex to use and are not optimal for many of the environments and users they are delivered into.  This is not a surprise as they are trying to service thousands of laboratories with a single package.  We believe there is another way.  We have created a vendor neutral, modular (we call them plug-ins) solution that can be “wired” together to provide a complete targeted solution to address many of the needs of analytical laboratories in the Life Sciences industry specifically.  We already offer off-the-shelf solutions for LC-MS data processing, visualization and reporting but continue to deliver custom solutions for laboratories with specific needs for processing, reporting, integration to databases and much more.  With a platform built on tried and tested Microsoft platforms, and with a commitment to the .NET architecture, our software is efficient, scalable and affordable.  That’s our business – we deliver the complete solution to meet your needs.

We will introduce you to our science, our technologies and our “secret sauce” over the next few months. Welcome to Virscidian…come back and hear about what we’re up to…checkout these two posters as teasers.

Elimination of the LC/MS Data Analysis Workflow Bottlenecks Using Analytical Studio

Enabling High-Throughput MRM Based Biomarker Validation Studies Through a Vendor Neutral Application