ProteinPilot Software for performing protein identification using the powerful Paragon™ Algorithm to identify peptides and Pro Group™ Algorithm for reliable reporting of protein, and protein expression analysis for biomarker discovery using isotopic labeling strategies
Deep interrogation of complex proteomes is typically achieved by using orthogonal fractionation to generate reduced complexity samples to analyze and thereby providing increased depth of coverage. Typically, these fractionated samples are analyzed by nanoflow LC, requiring 2-3 hours of LC-MS time for each fraction and therefore days to complete the project. Here, a strategy using microflow LC on the TripleTOF® 6600 System is demonstrated, enabling the identification of over 7100 proteins in just 15 hours of instrument time.
In addition to providing lists of identified proteins and peptides, database search results from ProteinPilot™ Software contain a wealth of additional information that can be analyzed post-acquisition, in the ProteinPilot Report. In this report, there are over 20 detailed dashboards that help characterize the LC-MS results, including sample preparation, chromatographic quality, MS acquisition quality, and many others.
Here, the use of very fast microflow LC gradients was explored for protein identification experiments, using gradients as short as five minutes. Combined with MS/MS acquisition rates as fast as 66 Hz on the TripleTOF® 6600 System, good protein identification results are achieved providing high sample throughput.
TripleTOF® 5600 system with ProteinPilot™ Software provide a seamless solution for investigation of protein changes in a dys-regulated biological pathway, here for investigating IKK inhibition in a breast cancer cell model. Protein expression analysis using iTRAQ® reagents enables sample multiplexing to achieve higher sample throughput with each injection.
The taglet.exe error in ProteinPilot™ software is due to a wide range of issues including incorrect language settings, installation of the software on the incorrect operating system, and the incorrect addition of modifications — to name a few.
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