Software Introductions at ASMS 2017 Focus on Workflow and Automated Analysis

The introduction of powerful, but user-friendly, software designed to help ease workflow and help automate data analysis at ASMS’s annual meeting highlighted the importance of workflow solutions beyond instrumentation and consumables. Held June 4-8 in Indianapolis, the meeting included sessions in which users detailed the important advances, particularly in protein profiling, targeted software solutions are enabling in their labs.

According to a survey of 700 lab managers—commissioned by Agilent and carried out by Frost and Sullivan—half of lab managers listed data management as one of their top five challenges. “[W]hen you combine this with the fact that almost half of the lab managers also said they are under significant pressure to process more samples every week, that just means there’s even more data. This pressure on data management as a pain point is only getting bigger,” says Monty Benefiel, vice president and general manager of Agilent’s Mass Spectrometry Division. During the meeting, Agilent announced an update to their BioConfirm software for biopharma applications, which includes five different options for the workflow. It allows the user to confirm the presence or absence of the protein they are trying to isolate without requiring MS expertise. New functionalities include the ability to quantitate glycoforms and identify released glycans.

Bruker introduced some new hardware at the show, but the star was software and how it is advancing life science and translational research, as well pharmaceutical and applied markets.

SCiLS Cloud and SCiLs Lab, for use with Bruker’s rapifleX high-throughput MALDI-TOF/TOF system and MALDI-Magnetic Resonance Mass Spectrometry (MRMS) extreme resolution system for drug and metabolite tissue imaging, offer web-based tools to ease workflows. Data and analysis results can be shared, viewed, and manipulated with a web browser. SCiLS Lab provides user-friendly data handling, visualization and computational analysis for Bruker MALDI imaging datasets. “If you’re looking at thousands of tissue samples, you need software that is going to stay with you as you try to make sense of the data,” says Rohan Thakur, Executive Vice President at Bruker Daltonics. The University of Maastricht’s MultiModal Molecular Imaging Institute is using SCiLSLab to apply mass spectrometry as a diagnostic and prognostic tool for personalized medicine in oncology, neurology, and cardiovascular medicine.

MALDI imaging is increasingly being used in pharmaceutical drug development, tissue-resolved biomarker research, and translational pathology research as a complement to immunohistochemistry. Richard Drake, Ph.D., Professor and Director of the Medical University South Carolina Proteomics Center, discussed how his laboratory is applying N-glycan MALDI-MS tissue imaging to visualize the tumor microenvironment.  While cancer metathesis is linked to degradation of glycans, the process is understudied because glycans are so complicated. “You need big instruments and big software solutions to start all this out,” Dr. Drake says. “It’s a complicated scenario, the way these glycans interact with the cell surface. They’re attached to different proteins, they’re attached to lipids, they’re attached to themselves, other things bind to them. And when cancer is forming, all that changes.” The SCiLs Lab software has been “priceless” in sorting this out, he adds.

Bruker also introduced MetaboScape 3.0, which includes a new algorithm that automatically extracts all relevant information in sample cohorts in a region-complete manner.  ProteoformProfiling 1.0 analyzes intact proteins, something that has been “neglected for far too long because it was essentially not doable,” says Frank H. Laukien, Ph.D., Bruker’s President and CEO. Traditional bottom-up proteomics analysis of digested proteins “scrambles” key biological information, he adds.

Waters introduced the latest version of Progenesis® QI for proteomics software, which enables scientists to generate more accurate results in less time. This version is designed to keep Progenesis QI for proteomics compatible with current MS approaches, while also increasing flexibility and usability. “Proteomics and biopharmaceutical applications are constantly changing,” said Steve Smith, Vice President of Informatics at Waters. ”This latest iteration of Progenesis QI for proteomics software has the added integration, connectivity and functionality required to keep pace with the new ways that these scientists are looking for insights in their data sets.” Among other new features, a spectral library search option keeps researchers from spending time identifying peptides and proteins that have already been verified, while SONAR, a recently introduced data-independent acquisition (DIA) mode for Waters High Resolution Mass Spectrometry (HRMS) instruments, provides additional specificity and clarity to DIA experiments.