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Hart-Smith"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Not available"],"submitter_keywords":["Protein correlation profiling","Co-fractionation mass spectrometry","Reference complex profiling","Protein-protein interactions","Protein complexes"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD019513"],"sample_protocol":["Yeast strain, culture conditions and lysis SEC CF-MS data were collected from Saccharomyces cerevisiae strain BY4741 (#YSC1052, Open Biosystems), grown at 30oC in 300 mL YEPD media containing 2% (w/v) glucose, 2% (w/v) bactopeptone and 1% (w/v) yeast extract. Cells were harvested during mid-log phase growth (OD600 of 1.2). Harvested cells were washed with water and resuspended in 10 mL SEC mobile phase (50 mM NaCH3COO, 50 mM KCl, pH 7.2) complemented with cOmplete, EDTA-free Protease Inhibitor Cocktail (Roche) and PhosStop (Roche). To digest yeast cell walls, 600 lytic units of zymolyase (Zymo Research) in 120 uL vendor-supplied resuspension buffer were added and the sample incubated at 30 oC until a stable OD600 of 3.5 was reached. The resulting spheroplasts were subjected to four 30 s rounds of sonication (amplitude 40%, 0.5 s pulse off/on) and centrifuged for 45 min at 14000 rpm at 4 oC. To enrich for protein complexes, lysates were then concentrated to 500 uL using 100 kDa MWCO filters (Sartorius Stedim) by centrifugation for 30 min at 3000 rpm. Size exclusion chromatography Lysates (2 replicate injections of 120 μL each) were loaded onto a 1290 Infinity UHPLC system (Agilent Technologies) and separated by SEC using a 600 × 7.8 mm BioSep4000 column (Phenomenex). The mobile phase (described above) was run at a flow rate of 0.5 mL/min. For each injection 70 fractions were collected at a rate of 2/min from 20 to 55 min, and equivalent fractions from replicate injections were pooled to produce 70 samples of fractionated lysate. Tryptic digestion To each sample of fractionated lysate a solution of 0.467 M dithiothreitol, 2.27 M chloroacetamide and 0.964 mM trypsin was added such that each sample had dithiothreitol and chloroacetamide concentrations of 47 mM and 236 mM respectively, and 3 ug trypsin. Samples were then incubated at 37 °C for 18 h. The resultant proteolytic peptide solutions were evaporated to dryness in a SpeedVac (Savant SPD1010, Thermo Scientific), after which peptides were reconstituted in 1 mL 0.1% (v/v) heptafluorobutyric acid (pH 2.5) and C18 cleanups performed using Sep-pak cartridges (WAT054960) following manufacturer’s instructions. Eluted peptides from each cleanup were evaporated to dryness in a SpeedVac and reconstituted in 20 uL 0.1% (v/v) formic acid. Mass spectrometry Proteolytic peptide samples were subjected to LC-MS/MS analysis on a Q Exactive Plus mass spectrometer (Thermo Scientific, Bremen, Germany) interfaced with an UltiMate 3000 HPLC and autosampler system (Dionex, Amsterdam, The Netherlands). Peptides were separated by nano-LC and eluting peptides ionized using positive ion mode nano-ESI. Survey scans m/z 350–1750 (MS AGC = 1×106) were recorded in the Orbitrap (resolution = 70,000 at m/z 200). The instrument was set to operate in DDA mode, and up to the 12 most abundant ions with charge states of >+2 were sequentially isolated and fragmented via HCD using the following parameters: normalized energy 30, resolution = 17,500, maximum injection time = 125 ms, and MSn AGC = 1×105. Dynamic exclusion was enabled (exclusion duration = 30 s)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":["phosphorylated residue","monomethylated residue"],"data_protocol":["To generate SEC fractionation profiles for individual yeast protein complex subunits, LC-MS/MS raw files were analysed using MaxQuant (version 1.6.2.10). Sequence database searches were performed using Andromeda and the MaxLFQ algorithm was used to quantify proteins across fractions. The following parameters were employed: precursor ion and peptide fragment mass tolerances were ±4.5 ppm and ±20 ppm respectively; carbamidomethyl (C) was included as a fixed modification; oxidation (M) and N-terminal protein acetylation were included as variable modifications; enzyme specificity was trypsin with up to two missed cleavages; only S. cerevisiae sequences in the Swiss-Prot database (February 2017 release, 553,655 sequence entries) were searched; the minimum peptide length was set as 7; the “match between runs” feature was enabled; and MaxLFQ analyses were performed using default parameters with “fast LFQ” enabled. Protein and peptide false discovery rate thresholds were set at 1%. Only fractionation profiles obtained from proteins identified from ≥2 peptides and with non-zero MaxLFQ values in ≥2 fractions were subjected to downstream analysis."],"omics_type":["Proteomics"],"labhead":["Gene Hart-Smith"],"instrument_platform":["Q Exactive"],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia"],"species":["Saccharomyces Cerevisiae (baker's Yeast)"],"publication":["32817346 Pang CNI, Ballouz S, Weissberger D, Thibaut LM, Hamey JJ, Gillis J, Wilkins MR, Hart-Smith G. Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes. Mol Cell Proteomics. 2020 10.1074/mcp.ra120.002154"],"submitter_mail":["gene.hart-smith@mq.edu.au"],"submitter_affiliation":["Macquarie University"],"submitter_country":["Australia"],"pubmed_abstract":["Co-fractionation MS (CF-MS) is a technique with potential to characterize endogenous and unmanipulated protein complexes on an unprecedented scale. However this potential has been offset by a lack of guidelines for best-practice CF-MS data collection and analysis. To obtain such guidelines, this study thoroughly evaluates novel and published Saccharomyces cerevisiae CF-MS data sets using very high proteome coverage libraries of yeast gold standard complexes. A new method for identifying gold standard complexes in CF-MS data, Reference Complex Profiling, and the Extending 'Guilt-by-Association' by Degree (EGAD) R package are used for these evaluations, which are verified with concurrent analyses of published human data. By evaluating data collection designs, which involve fractionation of cell lysates, it is found that near-maximum recall of complexes can be achieved with fewer samples than published studies. Distributing sample collection across orthogonal fractionation methods, rather than a single high resolution data set, leads to particularly efficient recall. By evaluating 17 different similarity scoring metrics, which are central to CF-MS data analysis, it is found that two metrics rarely used in past CF-MS studies - Spearman and Kendall correlations - and the recently introduced Co-apex metric frequently maximize recall, whereas a popular metric-Euclidean distance-delivers poor recall. The common practice of integrating external genomic data into CF-MS data analysis is also evaluated, revealing that this practice may improve the precision and recall of known complexes but is generally unsuitable for predicting novel complexes in model organisms. If studying nonmodel organisms using orthologous genomic data, it is found that particular subsets of fractionation profiles (e.g. the lowest abundance quartile) should be excluded to minimize false discovery. These assessments are summarized in a series of universally applicable guidelines for precise, sensitive and efficient CF-MS studies of known complexes, and effective predictions of novel complexes for orthogonal experimental validation."],"pubmed_title":["Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes."],"pubmed_authors":["Pang Chi Nam Ignatius CNI, Ballouz Sara S, Weissberger Daniel D, Thibaut Loïc M LM, Hamey Joshua J JJ, Gillis Jesse J, Wilkins Marc R MR, Hart-Smith Gene G"],"sample_synonyms":["sodium salt, ammonium formate, 13C-labeled, cadmium salt, PLXN5, muriate of potash, ion, Laboratory, YPD, Glukose, Ethylenediaminetetraacetic acid, growth and development, magnesium formate, zinc salt, (ethylenedinitrilo)tetraacetic acid, Long Term, SeP, 5730420M11Rik, Polypeptides, protein polypeptide chains, CEH, cobalt(II) formate dihydrate, Cultural, Dextrose, B1, SEC, 1, 2, NEPII, 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system, Mass Spectrum, Separation, 10^[-9], CC1, H4edta, DmelCG2916, Tripcellim, sample population, chromic formate, Anhydrous Dextrose, Holland, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, Ion, calcium salt, Peptid, edetic acid, assay, AA407739, growth, Baker Yeast, Glc"],"pubmed_title_synonyms":["Mass Spectrum Analysis, Saccharomyces oviformis, Mass Spectrum, Yeast, criteria, Analyses, Saccharomyces cerevisiae 'var. diastaticus', Protein., protein complex, Spectrometry, Brewer's, baker's yeast, Baker, proteins, protein, Spectrum Analyses, guidelines, Saccharomyces uvarum var. melibiosus, protein-containing complex, Spectrum Analysis, Saccharomyces italicus, S. cerevisiae, Spectroscopy, Baker's Yeasts, protein polypeptide chains, S cerevisiae, Candida robusta, native protein, natural protein, polypeptide chain, Saccharomyces capensis, Saccharomyces diastaticus, Mass, Baker's, Mycoderma cerevisiae, Analysis, Baker's Yeast, brewer's yeast, protein aggregate, Brewer's Yeast, Mass Spectrum Analyses, Mass Spectroscopy, Baker Yeast"],"data_synonyms":["liquid chromatography tandem mass spectroscopy, Bru, IPP2A2, Raw, determination, False, FBN, Gene, baker's yeast, protein, precursor, protein-containing complex, Saccharomyces italicus, PHAPII, LC-MS-MS, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, ClvPrd, peptido, polypeptide chain, template-activating factor I, ECTOL1, LC-MSMS, SEC, Gene Products, Del(8)44H, protein aggregate, WMS, T6K12_14, Svc, SET, proportion, F, LCMSMS, peptides, TAF-I, protein amino acid acetylation, Selb, phosphatase 2A inhibitor I2PP2A, sec, ipp2a2, beta-Trypsin, chemical analysis., 2pp2a, proteins, Saccharomyces uvarum var. melibiosus, CG10574, S. cerevisiae, OCTD, DmelCG4299, set, IGAAD, Candida robusta, 2PP2A, 10^[-6], DmelCG10574, Saccharomyces capensis, taf-ibeta, ppm, dSET, dSet, peptidos, Mycoderma cerevisiae, brewer's yeast, GPHYSD2, SGS, ratio, LC-MS2, phapii, Saccharomyces cerevisiae 'var. diastaticus', protein complex, Proteins, LC-MS/MS, igaad, StF-IT-1, macromolecule complex, Peptide, ACMICD, polypeptide, LC/MS/MS, secret agent, native protein, natural protein, Saccharomyces diastaticus, I-2PP2A, Algorithm, Protein, Dm I-2, I2PP2A, sequence, MFS1, Data Base, WMS2, T6K12.14, parent ion, Saccharomyces oviformis, Yeast, macromolecular complex, Col4a-1, HLA-DR-associated protein II, DI-2, I-2Dm, protein containing complex, proportionality, Tripcellim, rate, MASS, CG4299, inhibitor of granzyme A-activated DNase, beta Trypsin, primary structure of sequence macromolecule, Protein Gene Products, I-2PP1, Gene Proteins, Trypure, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, precursor ion, liquid chromatography-tandem mass spectroscopy, SSKS, quotient, liquid chromatography tandem mass spectrometry, Peptid, TAF-Ibeta, Polypeptide, assay, variable, AA407739, i2pp2a, protein-protein complex"],"description_synonyms":["scale tissue, dmBest1, d230, criteria, APEN, human being, degree (angle), genomic profiling data, Procedures, APX, determination, experimental, H-PAST, False, peltate hair, apex, Brewer's, baker's yeast, dTAFII250, protein, Spectrum Analyses, guidelines, protein-containing complex, anon-WO0118547.380, EfW1, DmelCG6264, Saccharomyces italicus, dmTAF[[II]]230, protein polypeptide chains, method, Techniques, sampling, polypeptide chain, dmTAF1, Method, Taf230, sensitive, method used in an experiment, Mass, Studies, ARB, Analysis, PAST, protein aggregate, Data Collection Method, REF1, Technique, sensitivity, APEX, Mass Spectroscopy, TAF250, Mass Spectrum Analysis, study, Taf200, F, methods, dTAF[[II]]250, TFIID TAF250, Analyses, Data Collection, cel, Dual Data, cell, VMD2, experimental section, plant peltate hair, Taf1p, proteins, Baker, procedures, BMD, Saccharomyces uvarum var. melibiosus, man, Apex, S. cerevisiae, Study, genomic profiling, allergic reaction, dTAF250, S cerevisiae, Candida robusta, Methodological Studies, Saccharomyces capensis, Baker's, scale (sensu Metazoa), Mycoderma cerevisiae, HPAST1, hypersensitivity reaction, brewer's yeast, TAF, RP50, data, dTAF[[II]]230, TAF[[II]]250, Data Collection Methods, CG6264, Data Set, Saccharomyces cerevisiae 'var. diastaticus', protein complex, TAF200, total expressed protein, l(3)84Ab, BG:DS00004.13, TAFII-250, Procedure, TAF250/230, Spectrum Analysis, Cell, dTAF230, Spectroscopy, Baker's Yeasts, TAFII250, native protein, natural protein, Saccharomyces diastaticus, p230, Protein, chemical analysis, TAF[[II]]250/230, TFIID, techniques, scales, Collection, TU15B, Library, HAP1, Mass Spectrum Analyses, specimen collection, Methods, dBest1, Saccharomyces oviformis, Taf[[II]]250, Mass Spectrum, Yeast, hypersensitivity, Dbest, hypersensitive, TAF[[II]]230, scale, best, Collection Methods, dbest1, Spectrometry, common, TAF[II]250, arc degree, Methodological, PAST1, CG17603, TAF[[II]], Methodological Study, human, plan specification, sample collection, Ref-1, APE1, DmelCG17603, Taf250, Data, SR3-5, data collection, hypersensitivity reaction disease, REF-1, Dual Data Collection, assay, APE, Baker's Yeast, experimental procedures., Collection Method, BEST, Proteomes, Brewer's Yeast, Data Analyses, Baker Yeast, TAF230, methodology, TAF1"],"pubmed_abstract_synonyms":["scale tissue, dmBest1, d230, criteria, APEN, human being, degree (angle), genomic profiling data, Procedures, APX, determination, experimental, H-PAST, dSmurf1, peltate hair, apex, Brewer's, baker's yeast, dTAFII250, protein, guidelines, protein-containing complex, anon-WO0118547.380, EfW1, DmelCG6264, Saccharomyces italicus, dmTAF[[II]]230, protein polypeptide chains, method, Techniques, DSmurf, sampling, polypeptide chain, dmTAF1, Method, Taf230, sensitive, Associations, method used in an experiment, Studies, ARB, Analysis, PAST, protein aggregate, Data Collection Method, REF1, Guilts, Technique, sensitivity, APEX, TAF250, study, Taf200, methods, dTAF[[II]]250, TFIID TAF250, Data Collection, Analyses, cel, Dual Data, cell, VMD2, experimental section, plant peltate hair, Taf1p, proteins, Baker, procedures, BMD, Saccharomyces uvarum var. melibiosus, man, Apex, S. cerevisiae, Study, genomic profiling, allergic reaction, dTAF250, S cerevisiae, d-smurf, Candida robusta, Methodological Studies, Saccharomyces capensis, Smurf, Baker's, scale (sensu Metazoa), Mycoderma cerevisiae, HPAST1, hypersensitivity reaction, brewer's yeast, TAF, CG4943, D-smurf, RP50, data, dTAF[[II]]230, TAF[[II]]250, Data Collection Methods, CG6264, Data Set, Saccharomyces cerevisiae 'var. diastaticus', protein complex, TAF200, total expressed protein, l(3)84Ab, BG:DS00004.13, Lack, TAFII-250, Procedure, Dsmurf, TAF250/230, Cell, dTAF230, dSmurf, Baker's Yeasts, TAFII250, native protein, natural protein, Saccharomyces diastaticus, p230, Smurf ubiquitin ligase, Protein, chemical analysis, TAF[[II]]250/230, TFIID, techniques, scales, Collection, TU15B, Library, HAP1, specimen collection, Methods, dBest1, Saccharomyces oviformis, Taf[[II]]250, Yeast, hypersensitivity, Dbest, hypersensitive, TAF[[II]]230, scale, DmelCG4943, best, Collection Methods, dbest1, common, TAF[II]250, arc degree, Methodological, PAST1, CG17603, TAF[[II]], Methodological Study, human, plan specification, sample collection, Ref-1, APE1, DmelCG17603, Taf250, Data, SR3-5, data collection, hypersensitivity reaction disease, REF-1, Dual Data Collection, assay, APE, Baker's Yeast, experimental procedures., Collection Method, BEST, Brewer's Yeast, Proteomes, Data Analyses, Baker Yeast, TAF230, methodology, TAF1"],"name_synonyms":["Mass Spectrum Analysis, Saccharomyces oviformis, Mass Spectrum, Yeast, criteria, Analyses, Saccharomyces cerevisiae 'var. diastaticus', Protein., protein complex, Spectrometry, Brewer's, baker's yeast, Baker, proteins, protein, Spectrum Analyses, guidelines, Saccharomyces uvarum var. melibiosus, protein-containing complex, Spectrum Analysis, Saccharomyces italicus, S. cerevisiae, Spectroscopy, Baker's Yeasts, protein polypeptide chains, S cerevisiae, Candida robusta, native protein, natural protein, polypeptide chain, Saccharomyces capensis, Saccharomyces diastaticus, Mass, Baker's, Mycoderma cerevisiae, Analysis, Baker's Yeast, brewer's yeast, protein aggregate, Brewer's Yeast, Mass Spectrum Analyses, Mass Spectroscopy, Baker Yeast"],"additional_accession":[]},"is_claimable":false,"name":"Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes","description":"Co-fractionation mass spectrometry (CF-MS) is a technique with potential to characterise endogenous and unmanipulated protein complexes on an unprecedented scale. However this potential has been offset by a lack of guidelines for best-practice CF-MS data collection and analysis. To obtain such guidelines, this study exploits very high proteome coverage libraries of gold standard Saccharomyces cerevisiae complexes to thoroughly evaluate novel and published yeast CF-MS datasets. A new method for identifying gold standard complexes in CF-MS data, Reference Complex Profiling, and the Extending ‘Guilt-by-Association’ by Degree (EGAD) R package are used for these evaluations, which are reinforced with concurrent analyses of published human data. By evaluating data collection designs, which involve fractionation of cell lysates, it is found that near-maximum recall of complexes can be achieved with fewer samples than published studies. Distributing sample collection across orthogonal fractionation methods, rather than a single high resolution dataset, leads to particularly efficient recall. By evaluating 17 different similarity scoring metrics, which are central to CF-MS data analysis, it is found that two metrics rarely used in past CF-MS studies – Spearman and Kendall correlations – and the recently introduced Co-apex metric frequently maximise recall, while a popular metric – Euclidean distance – delivers poor recall. The common practice of integrating external genomic data into CF-MS data analysis is also evaluated, revealing that this practice may improve the precision and recall of known complexes but is generally unsuitable for predicting novel complexes in model organisms. If studying non-model organisms using orthologous genomic data, it is found that particular subsets of fractionation profiles (e.g. the lowest abundance quartile) should be excluded to minimise false discovery. Together these guidelines identify avenues for precise, sensitive and efficient CF-MS studies of known complexes, and effective predictions of novel complexes for orthogonal experimental 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