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* [MS-Align\+|MS-Align+ algorithm for finding protein-spectrum matches] \- finds protein-spectrum matches.
* [Multiplex Denovo Sequencing|Multiplex Denovo Sequencing] \- simultaneous Denovo sequencing of spectral networks of peptidic natural products.
* [Multistage Denovo Sequencing|Multiplex Sequencing|Multstage Denovo Sequencing] \- sequencing non-linear peptides using multistage mass spectra.
* [Cycloquest|Cycloquest] \- database search for non-linear ribosomal peptides.
* [MSDPR|MSDPR] \- computing statistical significance of peptide spectrum matches