Lipidomics Quantification of lipids in complex biological samples is challenging and often requires a detailed knowledge of lipids and lipid analysis methods. The inherent complexity of the lipidome means that identifying and quantifying different lipid classes and...
Life Science Research
Life science research is the study of living organisms, including human beings, animals and plants, covering subjects in biology, biotechnology, bioinformatics, target discovery and the Omics. Chat with your peers about how to get the most out of your proteomics, metabolomics and lipidomics studies.
ProteinPilot phosphopeptide library and DIA-NN
I have prepared a spectral library for a phosphopeptide enriched sample and I am generating my SWATH samples from similarly enriched samples. The problem is that when I use DIA-NN for the retention time alignment and quant, it doesn’t recognise the terminology of the spectral library annotated by ProteinPilot. DIA-NN recognises Unimod:21 for phosphorylation, but PP uses phospho(Tyr) etc. Other than changing the data dictionary to get around the mismatch, anyone have any suggestions for how I might resolve this? Thank you, Roz
Current proteomics software compatibility for ZenoTOF 7600 system
Below is a summary of various other software packages that are useful for processing proteomics data from the ZenoTOF 7600 system. Note this list is not comprehensive and only covers the tools we have lightly tested to date. Acquisition Type Software Files needed...
Easy switching of sources and LC flow regimes on the ZenoTOF 7600 system
This series of videos outlines how a user can easily switch sources and operate the system in different LC flow regimes.
Creating a library from a FASTA file for library-free data analysis
While generating proteomic spectral libraries today is relatively easy, sometimes a library is needed and there is not time or need to generate a deep library using the traditional data-dependent acquisition approach. Here, a strategy will be outlined to generate a...
Processing ZenoTOF 7600 system data with DIA-NN software
DIA-NN software is a powerful software tool for processing data-independent acquisition (DIA) proteomics datasets. It uses neural networks and other algorithms to identify and quantify peptides and proteins from DIA data and is specifically optimized for fast...
Setting up custom on-column nanoflow calibration for the ZenoTOF 7600 system using PepCalMix
For nanoflow workflows using the ZenoTOF 7600 system and the standard nanoflow interface, on-column calibration is required and can be incorporated automatically into the SCIEX OS software acquisition batch. Here, step-by-step instructions are provided to set up a...
Using Scheduled Ionization to reduce system ion load for proteomics data acquisition
When analyzing highly complex samples from biological matrices, there can be significant amounts of material that elute in the wash cycle of the LC run, depending on the up-front sample preparation used. The Scheduled Ionization mode, available in both SCIEX OS...