{"database":"PeptideAtlas","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_RAW.tar"],"Other":["ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_Search_Results_242_201104181133.properties","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_mzXML_201104181133.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_242_sequest.params","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_prot_242_201104181133.properties","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_Search_Results_242_201104181133.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_README","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_prot_242_201104181133.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_mzXML_201104181133.properties","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Halobacterium/PAe000244/PAe000244_242_search.params.tar.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Y. A. Goo, E. C. Yi, N. S. Baliga, W. A. Tao, M. Pan, R. Aebersold, D. R. Goodlett, L. Hood and W. V. Ng"],"disease":[""],"software":["TPP"],"full_dataset_link":["'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=271'"],"synonyms":[""],"submitter_email":["","nbaliga@systemsbiology.org"],"repository":["PeptideAtlas"],"sample_protocol":[""],"data_protocol":[""],"omics_type":["Proteomics"],"pubmed":[""],"instrument_platform":["Unknown"],"project_tag":[""],"species":["Halobacterium Nrc-1 (halobacterium)"],"publication":[""],"pubmed_abstract":["For many research questions in modern molecular and systems biology, information about absolute protein quantities is imperative. This information includes, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes, or quantitative comparisons of different proteins within one sample or across samples. To date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers of samples. Here we describe and demonstrate the utility of a targeting MS technique for the estimation of absolute protein abundance in unlabeled and nonfractionated cell lysates. The method is based on selected reaction monitoring (SRM) mass spectrometry and the \"best flyer\" hypothesis, which assumes that the specific MS signal intensity of the most intense tryptic peptides per protein is approximately constant throughout a whole proteome. SRM-targeted best flyer peptides were selected for each protein from the peptide precursor ion signal intensities from directed MS data. The most intense transitions per peptide were selected from full MS/MS scans of crude synthetic analogs. We used Monte Carlo cross-validation to systematically investigate the accuracy of the technique as a function of the number of measured best flyer peptides and the number of SRM transitions per peptide. We found that a linear model based on the two most intense transitions of the three best flying peptides per proteins (TopPep3/TopTra2) generated optimal results with a cross-correlated mean fold error of 1.8 and a squared Pearson coefficient R(2) of 0.88. Applying the optimized model to lysates of the microbe Leptospira interrogans, we detected significant protein abundance changes of 39 target proteins upon antibiotic treatment, which correlate well with literature values. The described method is generally applicable and exploits the inherent performance advantages of SRM, such as high sensitivity, selectivity, reproducibility, and dynamic range, and estimates absolute protein concentrations of selected proteins at minimized costs."],"pubmed_title":["Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry."],"pubmed_authors":["Ludwig Christina C, Claassen Manfred M, Schmidt Alexander A, Aebersold Ruedi R"],"pubmed_title_synonyms":["Mass Spectrum Analysis, Mass Spectrum, MRM, Analyses, protein complex, Proteins, Spectrometry, Gene, protein, Spectrum Analyses, protein-containing complex, Spectrum Analysis, Protein Gene Products, Multiple Reaction Monitoring, Spectroscopy, Gene Proteins, MS, native protein, Protein, Gene Products, Mass, Mass., Analysis, protein aggregate, Mass Spectrum Analyses, Mass Spectroscopy"],"description_synonyms":["Integral Membrane Proteins, Cell Membrane, Cell Membrane Protein, gastric outflow obstruction, gastric outlet obstruction, Surface, pyloric stenosis (disease)., Proteins, Membrane-Associated, Surface Proteins, Cell Surface, Cell Surface Protein, Cell Membrane Proteins, Membrane-Associated Proteins, Membrane, Integral, Cell, pyloric stenosis, Integral Membrane Protein, GOO, Membrane-Associated Protein, Protein, Membrane Proteins, Surface Protein, Membrane Associated Proteins, Membrane Protein, Cell Surface Proteins, Integral Membrane, Membrane Associated Protein"],"name_synonyms":["APUM4, pumilio 4."],"pubmed_abstract_synonyms":["dmBest1, artificial sequence, Activity, Laboratory, antimicrobials, Ass-1, Compounds, antimicrobial agents, protein, Measure, DmelCG6264, Cost-Minimization, dmTAF[[II]]230, peptide, Polypeptides, Techniques, microbicides, peptido, Costs and Cost Analyses., Method, Anti Mycobacterial Agent, AA408052, ARB, fold, Analysis, Research Activity, protein aggregate, Bacteriocide, Cost Comparison, Laboratory Research, BEST1_HUMAN, Leptospira icteroides, Priorities, Mass Spectrum Analysis, antimicrobial, treatment, Log-Linear Models, Antimycobacterial Agents, TFIID TAF250, peptides, Biology, Analyses, cel, Antibiotika, Cost-Minimization Analyses, Anti Bacterial Compound, Comparison, Anti-Bacterial Compounds, ASS, allergic reaction, Cost Analysis, Methodological Studies, sample, disease management, Therapies, Antimycobacterial Agent, Research Priority, Comparisons, Affordabilities, antibiotic, Therapy, dTAF[[II]]230, anatomical protrusion, CG6264, TAF200, Linear Model, Research Priorities, Procedure, TAFII-250, Antibacterial Agent, TAF250/230, SPDSY, Spectrum Analysis, Multiple Reaction Monitoring, Spectroscopy, Literatures, TAFII250, microbicide, Anti Bacterial Agent, TU15B, Bacteriocides, Anti-Mycobacterial Agent, Antimycobacterial, dBest1, Research and Development, parent ion, Antibacterial, MS/MS, dbest1, Spectrometry, Methodological, CG17603, Methodological Study, TAF[[II]], Treatments, Activities, Antibacterial Agents, SYNTHETIC CONSTRUCT sequences, precursor ion, Agents, Taf250, Specificity and Sensitivity, spine, SR3-5, Linear, artificial, Polypeptide, Linear Regression, Proteomes, TAF230, Spirochaeta nodosa, Cost Analyses, protein levels, d230, Procedures, antibiotique, SRML1, BEST1, number, Gene, dTAFII250, Spirochaeta icterohaemorrhagiae, Cost Comparisons, Spectrum Analyses, precursor, protein-containing complex, anon-WO0118547.380, EfW1, presence, protrusion, Agent, method, Cost Minimization Analysis, dmTAF1, Taf230, sensitive, method used in an experiment, Gene Products, Studies, Mass, Antibiotic, Bacteriocidal, synthetic genetic interaction (sensu inequality), Log-Linear, Models, Technique, sensitivity, Mass Spectroscopy, antibiotics, TAF250, Taf200, dTAF[[II]]250, MRM, Research, cell, Cost Measures, VMD2, MS2, Affordability, Anti Bacterial Compounds, synthetic genetic interaction defined by inequality, Measures, Taf1p, BMD, Anti-Mycobacterial, Study, dTAF250, Anti-Bacterial, Anti-Mycobacterial Agents, Sensitivity, peptidos, Antibiotics, Development and Research, TAF, Model, SPS1, RP50, Antibiotikum, vitelliform macular dystrophy 2 (Best disease, TAF[[II]]250, protein complex, Proteins, PAPT, Regressions, Log Linear Models, total expressed protein, l(3)84Ab, artificial gene, BG:DS00004.13, function, synthetic DNA, Cell, Peptide, dTAF230, Anti Mycobacterial Agents, polypeptide, count in organism, Linear Regressions, Priority, MS, native protein, p230, Systems, Protein, Research Activities, TAF[[II]]250/230, synthetic, TFIID, Bacteriocidal Agents, Mass Spectrum Analyses, bestrophin), tandem MS, Taf[[II]]250, Mass Spectrum, Costs, Dbest, Log-Linear Model, Anti Bacterial Agents, TAF[[II]]230, best, Cost, Specificity, Cost-Minimization Analysis, TAF[II]250, Pricing, Spirochaeta biflexa, synthetic constructs, sample population, Bacteriocidal Agent, Protein Gene Products, plan specification, Anti-Bacterial Agent, Gene Proteins, DmelCG17603, Spirochaeta interrogans, Regression, Therapeutic, Compound, Spirochaeta icterogenes, cardinality, Peptid, Treatment, Anti-Bacterial Compound, Cost Measure, BEST, hypothesis, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"pum4","description":"enrichment for specialized purple membrane proteins; Goo et al., unpublished data.","dates":{"publication":"2011-12-31","export":"2016-03-29"},"accession":"PAe000244","cross_references":{"pubmed":["22101334"],"taxonomy":["64091"]}}