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Loss the contact closure signal

Loss the contact closure signal

our 7600 couple with nanoLC Ultimate 3000 via contact closure. it has run without any loss connection during the batch. Just yesterday, the last injection keep equilibrating system until the LC finished the gradient run. We closed the software and power off LC and MS then started again but it did not help. The Dionex engineer also checked their LC and triggerring cable found both are ok.

Loss the contact closure signal

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

Loss the contact closure signal

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?

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

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...

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....

How do I check the quality of the Auto Retention Time Calibration used in my Extractor processing?

How do I check the quality of the Auto Retention Time Calibration used in my Extractor processing?

When using the Auto-Calibration option in Extractor, a set of retention time calibration peptides will be determined automatically from the library and used for RT calibration. To determine how the fit looks for the calibration on each datafile, follow these steps....

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