I am Using Sciex Qtrap 4500 for quantification of nitrosamines (NDMA&NDBA). I am facing issue with higher baseline intensity. When developed the method in APCI the basline was at about 5e4. but now even after cleaning the source (i.e. Changed capillary to new, Curtain plate & Corona needle cleaning, given blank injection overnight ), my base line decreased from 1e6 to 4 e5, but settled at 4 e5 from past 24 hours. can you suggest me how decrease my baseline intensity further to below 1e5. My standard peaks are like noise now.
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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.
General question on SCIEX 7500
Library database file types imported into LibraryView™
As is stated in official guidance, many different types of compound and library databases can be imported into LibraryView™ software, such as Excel file (*.xls) and Third Party Library Package (*.tplp). Can somebody tell me what's the format like "tplp", which is so...
Protein Pilot Cysteine Modification
New features in OneOmics suite
I just wanted to thank the readers here, both the OneOmics suite users who’ve shared their time and watched OneOmics grow, and for all the talented developers and scientists who’ve made OneOmics suite what it is today.
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
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?
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...