Smart MSMS

From Spectroglyph, LLC

Smart MSMS

Our Smart MS2 software suite is used to efficiently control hybrid ion trap FTMS instruments manufactured by Thermo Fisher Scientific. The objective is to provide reliable identifications of peptides and proteins from highly complex biochemical mixtures. In real time, the software fully controls instrumental settings and data acquisition parameters. To enable highly efficient identification strategy, our algorithm selects chromatographic profiles of potential precursor candidates and initiates their collisional activation at the maximum of precursor signals in chromatographic domain. Fragment ion signal from consecutive LC runs aligned relative to each other to ensure minimum overlap in identifications from one run to another.

The software is amenable to user-defined modifications for advanced data activation strategies, and can be used as a platform for development of novel proteomic approaches with hybrid FTMS instruments.

Figure 1: Two Hela cell digest LC runs using Smart MS2 approach.

Using our proprietary alignment algorithms, unique precursor candidates are selected from one run to the next with <10% overlap. This ensures deeper analysis of proteome per unit time.

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Figure 2: Overlap in unique peptide identifications using Smart MS2
with Exclusion and Alignment Peptide Lists.

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Figure 3: Identification results using HeLa cell digest
experiments with Smart MS2 approach.

Contact Us

Due to proven performance enhancing capabilities, the Smart MSMS Software Suite has already received interest from individual customers. Interested customers and distributors can contact us for a quotation by writing to

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