Optimizing Performance

Optimizing Performance

  • Sorting

  • Filters

Using the Skyline / Panorama AutoQC tools for continuous monitoring your TripleTOF system performance

Using the Skyline / Panorama AutoQC tools for continuous monitoring your TripleTOF system performance

The Skyline team has developed a nice pipeline for evaluation of LC-MS/MS performance over time for MS systems in the research lab environment.  To help you use this solution, we have set up two Skyline Documents that you can use for continuous system monitoring....

Using the Skyline / Panorama AutoQC tools for continuous monitoring your TripleTOF system performance

Files for running the SWATH acquisition performance kit – ion library, performance trackers

The FASTA file required for use with the SWATH acquisition performance kit installs with ProteinPilot software or is available within OneOmics suite. Download this SWATH acquisition ion library for use with the SWATH acquisition performance kit Human2D_SOP_PepCalMix_...

Troubleshooting low flow LC – LC-MS peak area is lower than expected

Troubleshooting low flow LC – Loss of early eluting peptides during trap-elute workflow

Symptom: Early eluting peptides are missing (based on monitoring PepCalMix LC-MS test or observing a change in the shape of the proteome TIC). Test: Use PepCalMix LC-MS test to monitor binding of early eluting peptides. There are a number of very hydrophilic peptides...

High level method optimization considerations for Echo MS system

High level method optimization considerations for Echo MS system

While an in-depth discussion of method development and optimization for the Echo® MS system is beyond the scope of a community post, here are some points to consider as part of the process: The maximum recommended ion spray voltage for prolonged electrode life is 5000...

Keep your system running at optimal performance with the SWATH acquisition performance kit

Keep your system running at optimal performance with the SWATH acquisition performance kit

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 correctly? How do you know if you are getting the best data possible? And if you are a seasoned proteomics researcher, how do you know if your system is still running at peak performance from one study to the next?