|A KNIME Pipeline for the Analysis of GC-MS Data in Metabolomics|
Sonia Liggi1, Maria Laura Santoru1, Cristina Piras1, Antonio Murgia2, Pierluigi Caboni2, Luigi Atzori1
A KNIME pipeline was developed to perform pre-processing of GC-MS data in an automated way and applied to a Inflammatory bowel diseases case study
|PredRet: Prediction of Retention Time by Direct Mapping between Multiple Chromatographic Systems|
Jan Stanstrup, Steffen Neumann, Urška Vrhovšek
Retention time (RT) information is under-utilized in LC-MS based metabolomics and sharing of RTs between systems is not currently possible. PredRet is a new system that allows highly accurate mapping and prediction of RTs between LC systems.
|Profiling of metabolomic changes induced by testosterone esters in pig plasma and urine|
Kamil Stastny, Martin Faldyna, Milan Franek
In this study, metabolic fingerprinting to discriminate between pigs treated with 17ß-testosteron esters and control animals has been investigated. Multivariate statistical analysis showed significant metabolic differences between test and control groups on day 28 after aplication of the testosterone hormonal preparation.
|Sample Stabilization and Purification Devices for Superior Forensic DNA Storage, Purification and Profiling|
Geoffrey Routh,& Bassam El-Fahmawi
The tools used for evidentiary sample collection are often challenged in criminal cases. Maintaining the integrity of evidentiary samples continues to be a major challenge - especially when samples stay in transit during transportation where sample integrity is highly compromised. Thus, there is a crucial need for a cost-effective, efficient DNA collection and storage system that maintain sample integrity from collection until processing, while providing a means to ensure proper chain of custody
|A Simple Plate Based Assay Using pH Sensor Dye to Screen for Internalizing Antibody|
Nidhi Nath, Becky Godat, Cesear Corona, Chad Zimprich, Mark McDougall, Poncho Meisenheimer, Marjeta Urh
Receptor mediated internalization is a key mechanism of action (MOA) for antibody drug conjugates (ADCs). However, current methods of studying antibody internalization have several limitations including: 1) A multistep process not suitable for screening; 2) Low signal-to-background ratios; 3) Not suitable for kinetic measurements. We have developed a method that mitigates problems associated with traditional internalization assays.
|An IgG Cleaving Protease from S equi with Improved Activity Against Mouse IgGs|
Chris Hosfield, Philip Compton, Luca Fornelli, Paul Thomas, Neil L. Kelleher, Michael Rosenblatt & Marjeta Urh
Here we have expressed and purified a modified recombinant IdeZ, and show that it has significantly improved activity against mouse IgG2a and IgG3 subclasses when compared to IdeS. We also demonstrate the use of IdeZ in LC-MS workflows for human and mouse IgG characterization.
|Minimizing Carry-over for High Throughput Analysis|
Christian Berchtold1, Reto Bolliger2, Guenter Boehm2, Götz Schlotterbeck1
Minimal carry-over is a prerequisite for high throughput analysis. However, minimized carry-over and cycle time are competing and a careful optimization is mandatory. In this study the influence of wash conditions on carry-over of various compounds was investigated. A strategy to minimize carry-over was developed. The influences of different wash tasks were investigated. Finally the contribution of different system components such as injector valve or column was studied.
|A Comparison of ITEX Dynamic Headspace–GC/MS to other Enrichment Techniques for Analysis of Flavoring Compounds|
Douglas Doster1; Roger Pearson1; Sean Eppel1; Ken Rice1; Tom Flug2; Brian Peat2; Guenter Boehm2
Enrichment techniques are commonly used for the analysis of flavoring compounds in different matrices with GC/MS. Analysis of flavoring compounds is done by purge & trap, SPME or headspace, depending on requirements for sensitivity. The In-Tube Ex¬traction (ITEX) Dynamic Headspace uses a micro trap filled with an adsorbent material to efficiently extract the compounds. Here we evaluate if the ITEX can be used to effectively analyze for these compounds and reduce the analyst’s time involved.
|Automated in-gel digestion on a commercial autosampler directly coupled to nanoLC-MS/MS|
Achermann François, Bolliger Reto, Buchs Natasha, Doiron Nicholas, Lagache Braga Sophie, Heller Manfred, Boehm Guenter
SDS-PAGE separates protein samples from LC-MS incompatible contaminations, and is frequently used to fractionate proteins of entire proteomes. One disadvantage is that gel lanes have to be cut into many slices, followed by in-gel digestion of proteins and extraction of peptides. The number of these gel slices goes into the hundreds, rendering this process very repetitive and prone to mistakes and errors during sample handling. Automation reduces such risks and improves reproducibility.