{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/v08/MSV000095213/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Alexander Schmidt"],"instrument_platform":["Orbitrap Exploris 480"],"species":["Staphylococcus Aureus (ncbitaxon:1280)","Homo Sapiens (ncbitaxon:9606)"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=a339c19ace084174a6e254d1d2b34a2e"],"submitter_email":["alex.schmidt@unibas.ch"],"submitter_affiliation":["Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["709"],"ptm_modification":["MS:1002864 - No post-translational-modifications are included in the identified peptides of this dataset"],"data_protocol":[""],"name_synonyms":["FBgn0003149, peptides, Procedures, 0106/05, DmelCG5939, PM/mPM, Methodological, procedures, Procedure, Methodological Study, Peptide, Study, polypeptide, peptide, Polypeptides, Techniques, Para, peptido, l(3)10631, Methodological Studies, prm, mPM, Method, Studies, Peptid, peptidos, l(3)S010605, Polypeptide, techniques, CG5939, methodology., Technique, pm, PM"],"description_synonyms":["FBgn0003149, CDF, Bacterial Disease, human being, Procedures, determination, Peptidomics, Bacterial Protein, Gene, Bacterial Infections, Spectrum Analyses, Foundation, Normalcies, Gene Product, prevention, Human, peptide, Polypeptides, Readability, method, Techniques, Para, POF, peptido, Homo sapiens, Method, sensitive, mPM, method used in an experiment, DmelCG1768, Mass, Gene Products, Studies, HILDA, AGAMOUS-like 61, Low, Analysis, CG5939, prevention and control, Man, Technique, sensitivity, Staphlococcus pyogenes citreus, Mass Spectroscopy, DiA, Normalities, Mass Spectrum Analysis, average, study, me75, Bacterial Infection, Man (Taxonomy), l(2)k07135, reference sample, peptides, Infections, Analyses, Staphilococcus aureus, Tissue, Micrococcus aureus, procedures, DIASP, D17Mit170, DIA, Dia, T1, preventive measures, Study, allergic reaction, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, reaction, Bacterial Gene Proteins, Methodological Studies, 38E.16, Sensitivity, peptidos, Staphylococus aureus, DIA2, Gram Positive Bacteria, Gene Protein, Controlled, Individual Health, Controlling, preventive therapy, cou, DmelCG5939, Modern, Desmoplastic astrocytoma of infancy, Proteins, function, Normalcy, CG1768, Procedure, DRF2, Tl3, Tl2, Spectrum Analysis, Peptide, Spectroscopy, Bacterial Gene Product, polypeptide, ms(2)04138, Desmoplastic infantile astrocytoma, MS, Lr, prm, Protein, MLPLI, chemical analysis, Infection, l(3)S010605, Individual, techniques, Dias, Mass Spectrum Analyses, Bacterial Gene Products, Bacterial, Mass Spectrum, Staphylococcus aureus subsp. anaerobius, Normality, 0106/05, Protein., prophylaxis, Bacterial Diseases, POF2, PM/mPM, F27C12_24, F27C12.24, Spectrometry, Specificity, Bacterial Gene Protein, Methodological, Understanding, Methodological Study, human, Streptococcus aureus, Protein Gene Products, plan specification, Gene Proteins, Health, Micrococcus pyogenes, Staphylococcus pyogenes aureus, l(3)10631, Specificity and Sensitivity, control, Modern Man, DIANA, Bra, Peptid, Polypeptide, assay, humans, pm, PM, methodology"],"additional_accession":[]},"is_claimable":false,"name":"Optimizing SureQuant for Targeted Peptide Quantification: A Technical Comparison with PRM and SWATH-MS Methods","description":"Bacterial infections are a major threat to human health worldwide. A better understanding of the properties and physiology of bacterial pathogens in human tissues is needed to develop urgently needed novel control strategies. Mass spectrometry-based proteomics could yield such data but identifying and quantifying scarce bacterial proteins against a preponderance of human proteins is challenging. Here, we explored the recently introduced SureQuant method for highly sensitive targeted mass spectrometry. Using a major human pathogen, the Gram-positive bacteria Staphylococcus aureus, as an example, we optimized several parameters, including the number of targets and intensity thresholds, for optimal qualitative and quantitative detection. We compared the results with widely used standard techniques (parallel reaction monitoring, PRM) and data-independent acquisition (DIA). We found that SureQuant achieved the same quantitative performance as PRM and allowed accurate and precise quantification of up to 400 targets, surpassing the sensitivity and quantification capabilities of global DIA. We provide optimized MS parameters for sensitive quantification of different peptide panel sizes. This study provides a foundation for the broader application of SureQuant in the analysis of clinical specimens containing trace amounts of bacterial proteins as well as other studies requiring ultrasensitive detection of low-abundant proteins.","dates":{"publication":"Tue Jul 02 08:53:00 BST 2024"},"accession":"MSV000095213","cross_references":{}}