AB Sciex is doing business as SCIEX. © 2010-2018 AB Sciex. The trademarks mentioned herein are the property of the AB Sciex Pte. Ltd. or their respective owners. AB SCIEX™ is being used under license. Beckman Coulter® is being used under license. Product(s) may not be available in all countries. For information on availability, please contact your local representative. For research use only. Not for use in diagnostic procedures.

Software

Join the software discussions for in-depth answers to your questions. Dive deep into understanding the innovative algorithms and features that are core to our innovative SCIEX software solutions.

  • Search

  • Sorting

  • Filters

ProteinPilot phosphopeptide library and DIA-NN

ProteinPilot phosphopeptide library and DIA-NN

by | May 25, 2022 | , , , , ,

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

by | May 12, 2022 | , , , ,

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?

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

by | Apr 29, 2022 | , , , , ,

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

Using Scheduled Ionization to reduce system ion load for proteomics data acquisition

by | Apr 29, 2022 | , , , , , , , ,

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...