Over recent years, ion mobility has commercially emerged as an additional separation dimension for mass spectrometry data and has proven particularly useful to improve sensitivity in proteomics experiments.
SpectroMine offers a vendor-independent proteomics data analysis solution for the most recent ion mobility technologies.
SpectroMine can analyze PASEF data for both label-free and isobaric labeling quantification. It combines deep proteome coverage with impressively fast processing time, taking advantage of our Pulsar search engine’s optimization for PASEF data, .
To benchmark SpectroMine performance, we used data from a published comparison of different DDA analysis tools [Yu, 2020]. In an example dataset with four replicate injections of HeLa samples, SpectroMine outperformed the results reported for other software by 10% or more in peptide identifications.
DDA methods with FAIMS usually come in two main flavors: Single compensation voltage (CV) methods and multi-CV methods. Both of these methods are supported by SpectroMine for ILQ as well as label-free workflows.
In a recent publication [Schweppe, 2020], TMT10plex labeled mouse samples were enriched for phosphopeptides using the SL-TMT workflow [Navarette-Perea, 2018] and analyzed using a FAIMS Pro™ device.
Different multi-CV and no-CV setups were compared in order to test the influence of FAIMS on the number of quantifiable phosphopeptide identifications. We used SpectroMine to reanalyze the data acquired with a Thermo Fusion Lumos instrument (HCD fragmentation) and confirmed the benefit of using multi-CV FAIMS in these experiments.
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