ProteinPilot software 4.0 and higher releases include a new method for calculating protein confidences that improves reliability at the end of protein lists. Figure 1 shows a simulated example that demonstrates how more accurate protein confidence is computed. Figure...
There are 2 key protein scores that are computed in ProteinPilot™ Software: Total ProtScore and Unused ProtScore. Total ProtScore is simply a sum of all the peptide evidence related to a given protein, while Unused ProtScore reflects the amount of total, unique...
In highly complex proteomics data, some percentage of MS/MS spectra is chimeric due to the transmission of more than 1 precursor through the MS isolation step, even with a 1 Da window like the one used on TripleTOF systems. The ProteinPilot software 5.0 release...
During a ProteinPilot software search, the Pro Group algorithm assembles all the peptides into their appropriate proteins. Before the protein ratios are computed, the peptides are automatically annotated according to specific properties that make them more or less...
This short video provides an overview of the Paragon algorithm, a novel search engine that enables a researcher to search and identify a broad range of proteins and post-translational modifications in a single search, without increasing false positives and not...
To perform automatic mass recalibration, ProteinPilot software first conducts a rapid search using mass tolerances that are wider than expected for the instrument in use. The mass tolerance used in this initial search is defined in the MSTOLERANCE VALUE and...
ProteinPilot software is the only database search engine that provides a user interface which is "easy on top, powerful underneath!" Learn how the parameter translation layer turns knowledge of chemistry and mass spectrometry into their complex informatic...
Watch this video as Christie Hunter explains the Pro Group algorithm and how it works in ProteinPilot software. Let us know if you have any questions by commenting below. RUO-MKT-11-1780-A
Walk into any modern pharmaceutical company these days, and you’ll likely find at least one if not many, SCIEX LC-MS/MS instruments. Assays for the detection and quantitation of small molecule drugs, metabolites, biotherapeutics, biomarkers, and many other analytes...
Reproducibility is one of the key tenets of the scientific method. But in a recent survey published in Nature, more than 70% of researchers were not able to reproduce another scientist's experiments, and more than half could not reproduce their own experiments1. While...
With its introduction at the HUPO World Congress in 2010 in Sydney Australia by Ruedi Aebersold, SWATH® Acquisition instantly intrigued scientists around the world. Here was a new technique with the potential to revolutionize the way proteomics studies were...
Standards, protocols, and templates for generating your best quantitative proteomics data If you are just starting out as a proteomics researcher using mass spectrometry, the workflow can seem particularly daunting. How do you know if your system is set up...