Editing Sequence analysis (section)

== Analyzing protein sequences ==

Proteome sequence analysis studies the complete set of proteins expressed by an organism or a cell under specific conditions. It describes protein structure, function, post-translational modifications, and interactions within biological systems. It often starts with raw [[mass spectrometry]] (MS) data from proteomics experiments, typically in mzML, mzXML, or RAW file formats.<ref name=sequence_analysis/>

Beyond preprocessing raw MS data to remove noise, normalize intensities, and detect peaks and converting proprietary file formats (e.g., RAW) to open-source formats (mzML, mzXML) for compatibility with downstream analysis tools, other analytical steps include [[peptide]] identification, peptide quantification, protein inference and quantification, generating quality control report, and normalization, imputation and significance testing. The choice and order of analytical steps depend on the MS method used, which can either be data dependent acquisition (DDA) or independent acquisition (DIA).<ref name=sequence_analysis/><ref>{{cite web |title=Quantitative mass spectrometry workflow |url=https://nf-co.re/quantms/1.2.0 |website=nf-core}}</ref>