{"doi":"10.3390/molecules27082411","title":"Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research","abstract":"<jats:p>Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.</jats:p>","journal":"Molecules","year":2022,"id":20972,"datarank":2.0715793812725205,"base_score":4.919980925828125,"endowment":4.919980925828125,"self_citation_contribution":0.7379971388742189,"citation_network_contribution":1.3335822423983017,"self_endowment_contribution":0.7379971388742189,"citer_contribution":1.3335822423983017,"corpus_percentile":null,"corpus_rank":null,"citation_count":136,"citer_count":132,"citers_with_citation_signal":82,"citers_with_endowment":82,"datacite_reuse_total":2,"is_dataset":false,"is_dataset_confidence":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":136786,"name":"Madhuri Jayathirtha","orcid":null,"position":1,"is_corresponding":false},{"id":136787,"name":"Emma Baxter","orcid":null,"position":2,"is_corresponding":false},{"id":136788,"name":"Mary Donnelly","orcid":"0000-0002-9266-1580","position":3,"is_corresponding":false},{"id":136789,"name":"Brindusa Alina Petre","orcid":"0000-0002-0208-6560","position":4,"is_corresponding":false},{"id":136790,"name":"Costel C. Darie","orcid":"0000-0001-6402-2311","position":5,"is_corresponding":false},{"id":136784,"name":"Anca-Narcisa Neagu","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":4.919980925828125,"endowment":4.919980925828125,"datacite_reuse_total":2,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35458608","pmcid":"PMC9031286","openalex_id":"https://openalex.org/W4224255595","authors":[],"funders":[{"funder_name":"National Institute of Health","grant_id":"R15CA260126","title":null},{"funder_name":"National Institutes of Health","grant_id":"3R15CA260126-01A1S1","title":"PA-21-071 for Pathea Bruno to CA260126-01 Identifying a proteomic signature for breast cancer detection in breast milk and serum"},{"funder_name":"National Institutes of Health","grant_id":"3R15CA260126-01A1S2","title":"PA-23-189 for Kaya Johnson to CA260126-01: Identifying a proteomic signature for breast cancer detection in breast milk and serum"}],"total_grants":3,"fwci":13.3902,"citation_percentile":0.9962111,"influential_citations":1,"citation_trend":[{"year":2022,"count":6},{"year":2023,"count":17},{"year":2024,"count":42},{"year":2025,"count":56},{"year":2026,"count":15}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/1420-3049/27/8/2411/pdf?version=1649648639","host_type":"journal"},{"url":"https://www.mdpi.com/1420-3049/27/8/2411/pdf?version=1649648639","host_type":"GOLD"},{"url":"https://www.mdpi.com/1420-3049/27/8/2411/pdf?version=1649648639","host_type":"publisher"},{"url":"https://www.mdpi.com/1420-3049/27/8/2411/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/molecules27082411","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35458608","host_type":"repository"},{"url":"https://doaj.org/article/69119c22bc8c4ee1b531bd2829a0bab3","host_type":"repository"},{"url":"https://dx.doi.org/10.3390/molecules27082411","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9031286","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9031286","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9031286?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.3390/molecules27082411","host_type":""}],"fields_of_study":["Mass Spectrometry Techniques and Applications","Advanced Proteomics Techniques and Applications","Metabolomics and Mass Spectrometry Studies","Medicine","Biology","Chemistry","0301 basic medicine","0303 health sciences","03 medical and health sciences","Amino Acid Sequence","Biomedical Research","Peptide Mapping","Peptides","Proteins","Spectrometry, Mass, Electrospray Ionization","Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","Tandem Mass Spectrometry"],"mesh_terms":["Amino Acid Sequence","Peptide Mapping","Peptides","Proteins","Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","Spectrometry, Mass, Electrospray Ionization","Biomedical Research","Tandem Mass Spectrometry"],"keywords":["Bottom-up proteomics","Top-down proteomics","Protein mass spectrometry","Chemistry","Mass spectrometry","Tandem mass tag","Tandem mass spectrometry","Proteomics","Sample preparation in mass spectrometry","Isobaric labeling","Electrospray ionization","Chromatography","Peptide mass fingerprinting","Capillary electrophoresis–mass spectrometry","Peptide","Fragmentation (computing)","Quantitative proteomics","Biochemistry","Biology","Biomarkers","Biomedical Research","Tandem Mass Spectrometry (Ms/ms)","Spectrometry, Mass, Electrospray Ionization","Organic chemistry","Proteins","Review","Peptide Mapping","QD241-441","Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","Amino Acid Sequence","Peptides"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.22611487.v1","title":"Additional file 1 of Analysis and comparison of tear protein profiles in dogs using different tear collection methods","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.22611487","title":"Additional file 1 of Analysis and comparison of tear protein profiles in dogs using different tear collection methods","publisher":"figshare","resource_type":"JournalArticle"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-06T13:52:17.180604Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}