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1 | mass spectrometry table describes how the assay was performed - from extraction to data generation | |||||||||||||||||||||||||||||||||||||||||||
2 | OSD Number: | |||||||||||||||||||||||||||||||||||||||||||
3 | Sample Name | ProtocolREF | Extract Name | Protein Digestion | ProtocolREF | Labeling | Label | Reporter Ion Mass | ProtocolREF | mass spectrometry instrument | Fractionation instrument | Liquid Handler | chromatography device | ionization type | ionization energy applied (numberic value) | units ionization energy applied | fragmentation method | Mass to charge analyzer | analyzer | mass spectrometry acquisition method (http://purl.obolibrary.org/obo/MS_1003213) | Enrichment Type | Alkylating reagent | Alkylating reagent modification | Unimod Accession | Injection Volume | Injection Mass | MS Assay Name | Raw Spectral Data File | Schedule File | Normalization File | ProtocolREF | Derived Reference Search Database | Derived Spectral Data File | Peptide Assignment File | Protein Assignment File | Post Translational Modification Assignment File | ||||||||
4 | Sample names in the sample table and assay table should match exactly | extraction | Short hand processed sample? | Method used to digest proteins into peptides before MS analysis (e.g. Trypsin, lysc). Possible NCIT ontology ('protein digestion' https://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C70845) | labeling | Was labeling used? TRUE/FALSE | Indicates a chemical or biological marker, such as a radioactive isotope or a fluorescent dye which is bound to a material in order to make it detectable by some assay technology (e.g. P33, biotin, GFP, TMT 6-plex, iTRAQ 4-plex, SILAC). | Reporter ion mass, m/z ratio (e.g. iTRAQ 114, 116, 118; TMT 126, 127, 128, 129, 130, 131; etc.). If we call this parameter a 'ratio' we ought to be reporting a ratio so I would like to propose a change here (even if this is a well understood norm in proteomics). Would 'reporter ion intensity' (http://purl.obolibrary.org/obo/MS_1001847, defined as: Intensity of MS2 reporter ion (e.g. iTraq).) work here? Or 'reporter ion mass'? | mass spectrometry | the name of the mass spectrometer, use PSI-MS cv (e.g. LTQ-Orbitrap Velos Pro MS, Q Exactive HF-X Hybrid MS, TripleTOF 6600+ MS, SYNAPT G2-Si HDMS) | Off line fractionation instrument, e.g. capilary electrophresis; chromatography (low pH reverse phase LC) | If a liquid handler is used input the name of the machine, if samples were prepared manually, enter "MANUAL" | Technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure, e.g. chromatography method. Would 'chromatography device' be more appropriate here? It looks like the expected inputs are the names or models of instruments ("chromatography device: A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated." http://purl.obolibrary.org/obo/OBI_0000048) | the type of ionization used by the mass spectrometer; LC e.g. Electrospray Ionization (ESI), Atmospheric Pressure Chemical Ionization (APCI), Atmospheric Pressure Photoionization (APPI); GC e.g. Electron Ionization (EI), Chemical Ionization (CI) http://purl.obolibrary.org/obo/MS_1000008 | keV | Fragmentation method used for dissociation or fragmentation of peptides (e.g. CI, photo dissociation, electron dissociation, HCD, infered dissociation, chemical (aka free-radical) dissociation). http://purl.bioontology.org/ontology/SNOMEDCT/246399006 | the detector used by the mass spectrometer, e.g. ion trap Is there a relatively small list of possible values here? Anywhere where we can implement a controlled list we try to do that. If the group would be able to provide a list of all or most possible values for this parameter that would be very helpful | the analyzer used by the mass spectrometer, e.g. Linear ion tap, TOF/TOF, Quad-tof Is there a relatively small list of possible values here? Anywhere where we can implement a controlled list we try to do that. If the group would be able to provide a list of all or most possible values for this parameter that would be very helpful | Data Independent / Dependent Acquisition (e.g. DIA, DDA, PRM, Singe Reaction Monitoring (SRM), hybrid, All Ion Fragmentation (AIF), TMS2, Intelligent Data Acquisition (IDA)) I am sure these are all common acronyms in the field but curators hate undefined acronyms. I would prefer to use the full terms, ex. data-independent acquisition, http://purl.obolibrary.org/obo/MS_1003215) if the community is amenable | Type of enrichment used, if applicable (e.g. phospho enrichment, glyco enrichment, acetylation enrichment, ubiquitin enrichment, methyl/di-methyl enrichment, TMT enrichment (used to clean up poorly labeled datasets), etc.) | Alkylating reagent used to prevent the reformation of disulfide bridges by modifying free thiol groups on cysteine residues (e.g. IAA, IAA-COOH, CAA, NEM, 4-VP, ECM, acrylamide) | Heavy or light | Unimod Accession number used. If other chemical modifications were performed, add them e.g. TMT, heavy peroxide, heavy oxygen, beta elimination. Do the subclasses of 'sample label' work for a controlled list here? https://ontobee.org/ontology/MS?iri=http://purl.obolibrary.org/obo/MS_1002602 | Amount of sample added to the mass spec, in uL | Amount of sample added to the mass spec, in ug | Assay Name (e.g. proteomics, metabolomics, lipidomics) | Name of the raw spectral data file generated by an assay. | File contining the timing each sample was assayed (useful to identify batch effects), e.g. *.sld (scheduling list data frame), *.hy, *.csv | Spectral file containing the total mass (useful to determine contamination types and amount), used for normalization/correction, e.g. *.nda, *.tiff, *.csv, *.tsv, etc. | data transformation | *fasta file (could be referred to as any of the following in a publication: a reference assemble, open reading frame, reference proteome or reference genome, or reference assemblies, or peptide file, or protein file) | Name of the derived data file generated from spectral data by an assay. | Name of the peptide assignment file gathered for this assay. | Name of the protein assignment file gathered for this assay. | Name of the post translational modification file gathered for this assay. | |||||||||
5 | Mouse_1_spaceflight_liver | Please describe the extraction protocol here. Be sure to include the following: - Extraction buffer (Soluble / Non soluble proteins?) Why is there a question mark here? - Reconstitution buffer (e.g. 0.5% TFA) | M1_FLT_liver | Trypsin | Please describe the labeling protocol here. | TRUE | iTRAQ 8-plex | 113 | Please describe the mass spectrometry protocol here. Include the following info: - Amount used for fractionation (e.g. 100g) - Fractionation method (e.g. high pH reverse phase chromatography) - Number of fractions used for MS - How many MS levels (e.g. MS 1 [OT], 2, 3, 4, 5, etc., or just OT, OT, etc. and then number would be the number of levels) - Analyzer (type of trap used, e.g. OT) - Ion source used (e.g. EZspray, Hesi, etc.) - Quant level (MS level used for quantification) - Fraction redissolve buffer (15 L 5% acetonitrile, 0.1% formic acid) - Trap column used (e.g. C18, PepMap100, 300 mID x 5mm, 5m particle size) - Flow rate (e.g. 5 L/min for 3.5min with 2% acetonitrile, 0.1% formic acid) - These should be in uL or nL - Peptide separation column used (C18, nanoAcquite CSH130, 25cm x 75 m, 1.7m) - Flow rate (0.26 L/min) - These should be in uL or nL - Separation gradient (mobile phase A, 0.1% formic acid; mobile phase B, 0.1% formic acid in 80:20 acetonitrile:water), - add enrichment method (e.g. biological or chemical) - add depletion method (e.g. bead fractionation) - specify the types of resin/beads used at each step | LTQ-Orbitrap Velos Pro MS | Waters H Class | U3000 RSLCnano HPLC | electrospray | Collision induced dissociation (CI) | Time of Flight (TOF) | FTICR | DIA | glyco-enrichment | CAA | heavy | 4 | proteomics | *.sld | Please describe the data transformation protocol here. | ||||||||||||||||||||
6 | Mouse_2_spaceflight_liver | M2_FLT_liver | Trypsin | TRUE | iTRAQ 8-plex | 114 | LTQ-Orbitrap Velos Pro MS | U3000 RSLCnano HPLC | electrospray | Photo dissociation | orbitrap (type of FTICR) | DIA | glyco-enrichment | CAA | heavy | 4 | proteomics | *.sld | ||||||||||||||||||||||||||
7 | Mouse_3_ground_control_liver | M3_GC_liver | Trypsin | TRUE | iTRAQ 8-plex | 115 | LTQ-Orbitrap Velos Pro MS | U3000 RSLCnano HPLC | electrospray | Electron dissociation | orbital trap | DIA | glyco-enrichment | CAA | heavy | 4 | proteomics | *.sld | ||||||||||||||||||||||||||
8 | F1 | F1 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) What is this unit supposed to me? If we expect numeric values to be reported here I can split this column and include a distinct units column | higher-energy collisional dissociation (HCD) | -TOF/Q-TOF - Orbitrap - triple quad - Ion trap -ICR | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_F1_raw.zip | ||||||||||||||||||||||||||||||||||
9 | F2 | F2 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_F2_raw.zip | |||||||||||||||||||||||||||||||||||
10 | F3 | F3 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_F3_raw.zip | |||||||||||||||||||||||||||||||||||
11 | F4 | F4 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_F4_raw.zip | |||||||||||||||||||||||||||||||||||
12 | F5 | F5 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_F5_raw.zip | |||||||||||||||||||||||||||||||||||
13 | F6 | F6 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_F6_raw.zip | |||||||||||||||||||||||||||||||||||
14 | GC1 | GC1 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_GC1_raw.zip | |||||||||||||||||||||||||||||||||||
15 | GC2 | GC2 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_GC2_raw.zip | |||||||||||||||||||||||||||||||||||
16 | GC3 | GC3 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_GC3_raw.zip | |||||||||||||||||||||||||||||||||||
17 | GC4 | GC4 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_GC4_raw.zip | |||||||||||||||||||||||||||||||||||
18 | GC5 | GC5 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_GC5_raw.zip | |||||||||||||||||||||||||||||||||||
19 | GC6 | GC6 | Orbitrap Fusion Tribrid | nanoAcquity UPLC system (Waters) | electrospray (2.15‚ÄâkV) | higher-energy collisional dissociation (HCD) | Fourier Transform mass spectrometry (FTMS) analyzer | proteomics | GLDS-639_proteomics_Mao_062218_GC6_raw.zip | |||||||||||||||||||||||||||||||||||
20 | proteomics | |||||||||||||||||||||||||||||||||||||||||||
21 | proteomics | |||||||||||||||||||||||||||||||||||||||||||
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