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ProteinPilot phosphopeptide library and DIA-NN

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

ProteinPilot phosphopeptide library and DIA-NN

Sequential processing of multiple data-files in ProteinPilot

I would like to use ProteinPilot 5.0.2 to process data-sets containing 16 wiff files acquired from fractionated peptides on a 6600 TripleTOF. A Precision T7910 workstation struggles to process four files in parallel and I would like to be able to queue sequential processing of individual files overnight. I currently use the ‘LC ‘ tab to load and process individual data-files but this leads to parallel processing. Is it possible to generate 16 .group files sequentially?

Telling the PFAS story with pine needles

Telling the PFAS story with pine needles

As an ever-expanding group of chemicals, per- and polyfluoroalkyl substances (PFAS) require novel techniques to monitor their current and historical presence in the environment. Concerns over exposure to PFAS chemicals continue to grow, with some having known toxic characteristics and the potential effects of others remaining unknown.1 In addition, while PFAS are one of the most persistent synthetic chemicals to date, most of them hardly degrade in the environment.2 So, how long do traces of PFAS last in our environment? Two tools used to help answer this question are active samplers and passive samplers.

Setting up custom on-column nanoflow calibration for the ZenoTOF 7600 system using PepCalMix

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...