Root element of the instance document. Any bibliographic references associated with the file. The date on which the file was produced. The version of the schema this instance document refers to, in the format x.y.z. Changes to z should not affect prevent instance documents from validating. Summary information about the analysis in terms of the type of analysis, any global scores or metrics and global thresholds used. The list of controlled vocabularies used in the file. All the raw files, identification files and databases used in the quantitation A database used for searching mass spectra. Examples include a set of amino acid sequence entries, or annotated spectra libraries. The database name may be given as a cvParam if it maps exactly to one of the release databases listed in the CV, otherwise a userParam should be used. Any additional parameters describing the database. The version of the database. The date and time the database was released to the public; omit this attribute when the date and time are unknown or not applicable (e.g. custom databases). The total number of entries in the database. A file from which this MzQuantML instance was created, including potentially MzQuantML files for earlier stages in a workflow. The list of experimental conditions used to group results. A source controlled vocabulary from which cvParams will be obtained. The full name of the CV. The version of the CV. The URI of the source CV. The unique identifier of this cv within the document to be referenced by cvParam elements. The definition of ratios of study variables or assays, referenced elsewhere in the document. The list of all groups of proteins with conflicting evidence for which quantitation values are being reported along with quantitative values about those protein groups. If quantitation is done on individual proteins only, ProteinGroupsList should not be included. Global values corresponding to the ProteinGroup such as the total intensity of the protein group in all assays, Anova etc. Quant layer for reporting data values about protein groups related to different assays i.e. the column index must refer to Assays defined in the file. Quant layer for reporting data values about protein groups related to different study variables i.e. the column index must refer to StudyVariables defined in the file. Quant layer for reporting data values about protein groups related to different ratios i.e. the column index must refer to Ratio elements defined in the file. CV terms for the entire list. The unique identifier for the object within the file. The list of all individual proteins (i.e. ungrouped) for which quantitation values are being reported. If quantitation is done on protein groups, the constituent proteins should be listed here with no QuantLayers. Global values corresponding to the Protein such as the total intensity of the protein in all assays, Anova etc. Quant layer for reporting data values about proteins related to different assays i.e. the column index must refer to Assays defined in the file. Quant layer for reporting data values about proteins related to different study variables i.e. the column index must refer to StudyVariables defined in the file. Quant layer for reporting data values about proteins related to different ratios i.e. the column index must refer to Ratio elements defined in the file. CV terms for the entire list. The unique identifier for the object within the file. A grouping of quantified proteins based on ambiguous assignment of peptide evidence to protein identification. The semantics of elements within the group, such as a leading protein or those sharing equal evidence can be reported using cvParams. Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the ProteinAmbiguityGroup. The proteins contributing to this protein group on which quantitative values are based. Additional parameters or values about this protein group. The unique identifier for the object within the file. Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the ProteinAmbiguityGroup. The peptides on which the quantitative protein values in the QuantLayer(s) are based. Note this should not be used to report all peptides that can support the protein identification, only quantitation. Additional parameters or values about this protein. The unique identifier for the object within the file. The accession of the protein in the source database. In most use cases it is expected that accession will be unique within the ProteinList, although in rare cases there may be different entries for the same protein for example if quantifying different PTMs on the same protein. A reference to an external identification file defined in the document, plus a unique identifier for the object in that file, such as an ID of a SpectrumIdentificationItem, ProteinDetectionHypothesis or ProteinAmbiguityGroup in mzIdentML. Reference to the unique identifier of this object in the referenced external file. Reference to the IdentificationFile object in this file. A reference to an object identified in the SearchDatabase object defined in this file. Reference to the unique identifier of this object in the referenced external file. Reference to the SearchDatabase object in this file from which this identification was made. The list of all peptides objects for which quantitation values are reported. Global values corresponding to the Peptide such as the total intensity of peptide in all assays, Anova in a quantitative peptidome experiment etc. Quant layer for reporting data values about peptides related to different assays i.e. the column index must refer to Assays defined in the file. Quant layer for reporting data values about peptides related to different study variables i.e. the column index must refer to StudyVariables defined in the file. Quant layer for reporting data values about peptides related to different ratios i.e. the column index must refer to Ratio elements defined in the file. CV terms for the entire list. The unique identifier for the object within the file. Multiple peptide lists are allowed for reporting the evidence trail to create a final peptide list, but the final result e.g. to be loaded into a database, should be flagged with finalResult=true List of small molecules and associated data values. Global values corresponding to the small moleculee such as the total intensity of peptide in all assays, Anova in a quantitative peptidome experiment etc. Quant layer for reporting data values about small molecules related to different assays i.e. the column index must refer to Assays defined in the file. Quant layer for reporting data values about small molecules related to different study variables i.e. the column index must refer to StudyVariables defined in the file. Quant layer for reporting data values about small molecules related to different ratios i.e. the column index must refer to Ratio elements defined in the file. CV terms for the entire list. The unique identifier for the object within the file. An element representing a peptide in different assay that may or may not have been identified. If it has been identified, the sequence and modification(s) should be reported. Within the parent list, it is allowed for there to be multiple instances of the same peptide sequence, for example capturing different charge states or different modifications, if they are differentially quantified. If peptides with different modifications or charge states are aggregated, they should be represented by a single PeptideConsensus element. The amino acid sequence of the (poly)peptide. If a substitution modification has been found, the original sequence should be reported. The peptide sequence is mandatory unless this is a PeptideConsensus that has not been assigned to a peptide sequence. Reference for the identification evidence for peptides from the referenced external file and unique identifier e.g. a link to an mzIdentML file and ID for the SpectrumIdentificationItem. The features that have been matched together within one raw file (label-based) and/or across multiple raw files (label-based or label free). References to the assays to which the features referenced above have been assigned. This element is REQUIRED for label-based examples and the size of the list MUST always match the size and order of the Feature_refs list. Additional parameters or values about this peptide. The unique identifier for the object within the file. The charge of this instance of Peptide. If more than one value is provided, it is assumed that this Peptide element is summarising multiple charge states of the Peptide. An element to represent a unique identifier of a small molecule for which quantitative values are reported. External database references for the small molecule identification Optional references to features on which peptide values in the QuantLayer were based. Additional parameters or values about this small molecule. The unique identifier for the object within the file. A molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. A cvParam must be provided with the identification of the modification sourced from a suitable CV e.g. UNIMOD. If the modification is not present in the CV (and this will be checked by the semantic validator within a given tolerance window), there is an _unknown modification_CVerm that must be used instead. A neutral loss should be defined as an additional CVParam within Modification. If the Peptide element is intended to represent a summary of both modified and unmodified instances of the peptide, then the Feature_refs qualifier must be used on Peptide. CV terms capturing the modification, sourced from an appropriate controlled vocabulary. If the Peptide entity is intended as a summary of both modified and unmodified instances of the peptide, then the Feature_refs element MUST be completed to document those peptides only that are modified. If this element is excluded, it is assumed that all features have the modification. Location of the modification within the peptide - position in peptide sequence, counted from the N-terminus residue, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1. Specification of the residue (amino acid) on which the modification occurs. If multiple values are given, it is assumed that the exact residue modified is unknown i.e. the modification is to ONE of the residues listed. Multiple residues would usually only be specified for PMF data. Atomic mass delta considering the natural distribution of isotopes in Daltons. Atomic mass delta when assuming only the most common isotope of elements in Daltons. A small molecule modification specification, given by cvParams. CV terms capturing the modification, sourced from an appropriate controlled vocabulary. Atomic mass delta considering the natural distribution of isotopes in Daltons. Atomic mass delta when assuming only the most common isotope of elements in Daltons. A collection of data relating to the objects within the parent list type (e.g. PeptideConsensus, Protein or ProteinGroup) Type of data in the quant layer e.g. cvParam = "Intensity|RawAbundance|NormalisedAbundance|PeptideCount|ConfidenceScore|Anova|MaxFoldChange|...." Space separated unique identifiers for each column of data, must refer to an object in the file i.e. StudyVariable, Assay or Ratio, depending on the context where the QuantLayer resides. The unique identifier for the object within the file. A QuantLayer in which different data types are allowed in each column. Definition of the data types in each column The unique identifier for the object within the file. The definition of all the columns of data about the features Type of data in the column e.g. cvParam = "Intensity|RawAbundance|NormalisedAbundance" The column position within the data matrix - incrementing positive integers starting from zero. TODO - add a data type to enforce positive integers A matrix of data stored in rows and columns, as defined in the parent QuantLayer. One row of data in a data matrix. Reference to the data type represented in this row e.g. Feature, Peptide, Protein. TODO - we should add a constraint that this should be unique within the data matrix A logical grouping of assays into conditions or user-defined study variables such as wild-type versus disease or time points in a time course. The type of StudyVariable e.g. Phenotypic, biological replicate, technical replicate, time points etc. and references to all the assays that are part of this study variable Reference to the assay that is part of this study variable The unique identifier for the object within the file. A human readable name for the study variable. The list of assays represented by the file, where each assay captures the concept of one experimental run - this can be one or more raw files. Describes a single experimental run (e.g. with the channel mapping in iTRAQ), which could constitute multiple raw files e.g. if pre-separation steps have occurred. The unique identifier for the object within the file. The raw file or group of raw files that constitute this assay. One or more identification files used within this assay. Additional cvParams about the Assay. The unique identifier for the object within the file. Human readable name for the assay. The raw file or collection of raw files that together form one unit of analysis. This is mandatory unless raw files were not used for quantitation e.g. spectral counting. Multiple raw files should only be provided within a group if they have been used for sample pre-fractionation which are later summed together. Additional parameters about the raw files specified or the grouping process. Unique identifier for the group of raw files that constitute one analysis unit. A raw mass spectrometry output file that has been analysed e.g. in mzML format. The same raw file can be referenced in multiple assays, for example if it contains multiple samples differentially labelled or tagged. Note, the name raw file does not necessarily imply that the file has not been processed, since in some quant methods, processed peak list formats such as MGF or dta can be used, which could be referenced here. Additional parameters about the raw file. All identification files associated with this quantitation analysis to be referenced elsewhere. A single identification file associated with this analysis. A specification of labels or tags used to define the assay within the raw file, such as heavy labelling or iTRAQ tag mass. If the label cannot be described by a modification (e.g. from UNIMOD), a cvParam can be used to describe the type of label or tag applied in this assay The setup of a ratio of study variables or assays that is referenced elsewhere in the file. Information should be provided about how ratios are calculated if they differ from simple division of numerator by denominator Reference to a StudyVariable or an Assay Reference to a StudyVariable or an Assay The unique identifier for the object within the file. Optional name for the ratio. All the features identified on a single raw file or raw file group. All the data values about features in one raw file or raw file group, such as feature raw intensity, feature RT window size etc. Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different assays i.e. the column index must refer to Assays defined in the file. Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different study variables i.e. the column index must refer to StudyVariables defined in the file. Quant layer for reporting data values about MS2 features (e.g. iTRAQ) related to different ratios i.e. the column index must refer to Ratio elements defined in the file. CV terms for the FeatureList, such as the MassTrace encoding scheme. Refernece to the raw file or group of raw files from which this feature list was generated. The unique identifier for the object within the file. A region on an MS1 mass spectrum, defined by the RT, MZ and optionally a mass trace. Quantitative values about features can be added in the associated QuantLayers. The coordinates defining the feature in RT and MZ space, given as boundary points or a series of rectangles, as encoded by the MassTraceEncoding cvParam on the FeatureList. Additional parameters or values about this feature. unique identifier for the feature. The centre point of the feature on the retention time axis in minutes. The centre point of the feature on the mass over charge axis in daltons over charge. The assumed charge of the feature, used to calculate the M/Z value. The modification searched for, sourced from e.g. UniMod and the mass delta The name of the modification imported from a relevant CV The mass delta of the searched modification in Daltons The residue(s) searched with the specified modification List and descriptions of data processing applied to this data. Description of the way in which a particular software package was used to analyse data and for example produce different quant layers or lists in the file. References to raw file groups, FeatureList, PeptideConsensusList, ProteinList or ProteinGroupList or QuantLayers that were inputs to the data processing step. References to raw file groups, FeatureList, PeptideConsensusList, ProteinList or ProteinGroupList or QuantLayers that were the outputs of the data processing step. The unique identifier for the object within the file. This attribute must reference the 'id' of the appropriate SoftwareType. Description of one step within the data processing pipeline. Parameters used in the processing method. This attributes allows a series of consecutive steps to be placed in the correct order. List and descriptions of software used to acquire and/or process the data in this file. A software package used in the analysis. Additional parameters about the software or version. The unique identifier for the object within the file. The software version. Helper complexType to include one cvParam as a sub-element A single entry from an ontology or a controlled vocabulary. A reference to the cv element from which this term originates. The accession or ID number of this CV term in the source CV. Abstract entity allowing either cvParam or userParam to be referenced in other schemas. The name of the parameter. The user-entered value of the parameter. An accession number identifying the unit within the OBO foundry Unit CV. The name of the unit. If a unit term is referenced, this attribute must refer to the CV 'id' attribute defined in the cvList in this file. A single user-defined parameter. The datatype of the parameter, where appropriate (e.g.: xsd:float). Helper type to allow multiple cvParams or userParams to be given for an element. Helper type to allow either a cvParam or a userParam to be provided for an element. A choice of either a cvParam or userParam. Data external to the XML instance document. The location of the data file is given in the location attribute. A URI to access documentation and tools to interpret the external format of the ExternalData instance. For example, XML Schema or static libraries (APIs) to access binary formats. The location of the data file. The format of the ExternalData file, for example "tiff" for image files. cvParam capturing file formats The provider of the document in terms of the Contact and the software the produced the document instance. The Contact that provided the document instance. The Software that produced the document instance. A person's name and contact details. Any additional information such as the address, contact email etc. should be supplied using CV parameters or user parameters. The organization a person belongs to. The Person's last/family name. The Person's first name. The Person's middle initial. A reference to the organization this contact belongs to. Organizations are entities like companies, universities, government agencies. Any additional information such as the address, email etc. should be supplied either as CV parameters or as user parameters. The containing organization (the university or business which a lab belongs to, etc.) A reference to the organization this contact belongs to. A contact is either a person or an organization. Attributes of this contact such as address, email, telephone etc. The role that a Contact plays in an organization or with respect to the associating class. A Contact may have several Roles within scope, and as such, associations to ContactRole allow the use of a Contact in a certain manner. Examples might include a provider, or a data analyst. When a ContactRole is used, it specifies which Contact the role is associated with. The roles (lab equipment sales, contractor, etc.) the Contact fills. CV term for contact roles, such as software provider. Represents bibliographic references. The names of the authors of the reference. The name of the journal, book etc. The publisher of the publication. The editor(s) of the reference. The year of publication. The volume name or number. The issue name or number. The page numbers. The title of the BibliographicReference. The DOI of the referenced publication. The complete set of Contacts (people and organisations) for this file. Other classes in the model can be specified as sub-classes, inheriting from Identifiable. Identifiable gives classes a unique identifier within the scope and a name that need not be unique. An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use. The potentially ambiguous common identifier, such as a human-readable name for the instance.