Sample Components: Difference between revisions
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<span style="display:inline-block; margin-bottom:1em;">[[New Sample Creation#Creating/Cloning Samples|← Back to Creating/Cloning Samples]]</span> | <span style="display:inline-block; margin-bottom:1em;">[[New Sample Creation#Creating/Cloning Samples|← Back to Creating/Cloning Samples]]</span> | ||
{{DISPLAYTITLE: Sample Components/Component Details}} | {{DISPLAYTITLE: Sample Components/Component Details}} | ||
The first table lists possible sample components, while the following tables provide details that can be documented for major component types (e.g., proteins, polymers, biological mixtures). | |||
{| class="wikitable" | {| class="wikitable" | ||
{| class="wikitable" | {| class="wikitable" | ||
|+Sample Component Types | |+Sample Component Types | ||
| Line 10: | Line 13: | ||
|- | |- | ||
| rowspan="4" |Bio Macromolecule | | rowspan="4" |Bio Macromolecule | ||
|Protein | |[[#Protein_Details|Protein]] | ||
| | | | ||
|- | |- | ||
|Nucleic Acid - DNA | |[[#Nucleic_Acid_Details|Nucleic Acid - DNA]] | ||
| | |Deoxyribonucleic acid samples | ||
|- | |- | ||
|Nucleic Acid - RNA | |[[#Nucleic_Acid_Details|Nucleic Acid - RNA]] | ||
| | |Ribonucleic acid samples | ||
|- | |- | ||
|Carbohydrate | |[[#Carbohydrate_Details|Carbohydrate]] | ||
| | |Sugar molecules and polysaccharides | ||
|- | |- | ||
| rowspan="3" |Small molecules | | rowspan="3" |[[#Small_Molecules_Chemical_Formula_details|Small molecules]] | ||
|Metabolite | |Metabolite | ||
| | |Small bioactive molecules involved in metabolism | ||
|- | |- | ||
|Natural Product | |Natural Product | ||
| | |Compounds isolated from natural sources | ||
|- | |- | ||
|Other organic | |Other organic | ||
|Organic compounds not classified elsewhere | |Organic compounds not classified elsewhere | ||
|- | |- | ||
|[[#Small_Molecules_Chemical_Formula_Details|Chemical Formula]] | |||
|Chemical Formula | |Chemical Formula | ||
|Explicit formula-based representation of a compound | |||
|Explicit formula-based representation of a compound | |||
|- | |- | ||
|Polymer | |Polymer | ||
|Polymer | |[[#Polymer_Details|Polymer]] | ||
| | |Synthetic or natural long-chain molecular compounds | ||
|- | |- | ||
| rowspan="2" |Mixtures | | rowspan="2" |Mixtures | ||
|Biological Material | |[[#Biological_Material_Details|Biological Material]] | ||
| | |Mixed biological content such as tissue extracts | ||
|- | |- | ||
|Environmental Sample | |[[#Environmental_Sample_Details|Environmental Sample]] | ||
| | |Samples derived from environmental sources | ||
|- | |- | ||
| rowspan="5" |Components | | rowspan="5" |Components | ||
| Line 95: | Line 98: | ||
|Any sample not classified in the above categories | |Any sample not classified in the above categories | ||
|} | |} | ||
{| class="wikitable" | {| class="wikitable" | ||
|+Protein Details | |+<span id="Protein Details">Protein Details</span> | ||
|'''Name''' | |'''Name''' | ||
|'''Description''' | |'''Description''' | ||
| Line 145: | Line 149: | ||
|} | |} | ||
{| class="wikitable" | {| class="wikitable" | ||
|+Nucleic Acid (DNA, RNA) Details | |+<span id="Nucleic_Acid_Details">Nucleic Acid (DNA, RNA) Details</span> | ||
|'''Name''' | |'''Name''' | ||
|'''Description''' | |'''Description''' | ||
| Line 192: | Line 196: | ||
|} | |} | ||
{| class="wikitable" | {| class="wikitable" | ||
|+Small | |+<span id="Carbohydrate_Details">Carbohydrate Details</span> | ||
|'''Name''' | |||
|'''Description''' | |||
|- | |||
|Molecular Weight | |||
|Molecular weight of the carbohydrate sample | |||
|- | |||
|Purity (%) | |||
|Estimated percentage purity of the sample | |||
|- | |||
|Classification | |||
|Specify type: | |||
* Oligosaccharides | |||
* Polysaccharides | |||
|- | |||
|IUPAC condensed string | |||
|IUPAC condensed notation describing carbohydrate structure | |||
|- | |||
|Tags | |||
|Additional descriptors or identifiers for the carbohydrate | |||
|- | |||
|Modification | |||
|Users can document modification '''type''' and provide '''description'''. Supported types include: | |||
* Glycopeptides | |||
* Glycolipids | |||
* Glycosides | |||
|} | |||
{| class="wikitable" | |||
|+<span id="Small_Molecules_Chemical_Formula_Details">Small Molecules/Chemical Formula Details</span> | |||
|'''Name''' | |'''Name''' | ||
|'''Description''' | |'''Description''' | ||
| Line 229: | Line 262: | ||
|} | |} | ||
{| class="wikitable" | {| class="wikitable" | ||
|+Polymer Details | |+<span id="Polymer_Details">Polymer Details</span> | ||
|'''Name''' | |'''Name''' | ||
|'''Description''' | |'''Description''' | ||
| Line 243: | Line 276: | ||
|- | |- | ||
|Branching | |Branching | ||
| | |Specify whether the polymer is linear or branched | ||
|- | |- | ||
|Source | |Source | ||
| | |Indicate whether the polymer is synthetic or biological. If biological, an option is available to enter the biological source. | ||
|- | |- | ||
|Weight Average Molecular Weight | |Weight Average Molecular Weight | ||
| Line 257: | Line 290: | ||
| | | | ||
|- | |- | ||
| | |Polymer repeat sequence | ||
|User | |User can provide following details: | ||
Number of Subunits | |||
Degree of substitution | * Number of Subunits | ||
Length of repeated sequence | * Degree of substitution | ||
Sequence order | * Length of repeated sequence | ||
Total number of repeats | * Sequence order | ||
* Total number of repeats | |||
|- | |||
|Description | |||
|Additional notes or information about the polymer | |||
|- | |||
|Polymer subunit | |||
|User has an option to add one or more polymer subunits. Following details can be provided: | |||
* Abbreviation | |||
* Full Name | |||
* Chemical Formula | |||
* Subunit molecular weight (Da) | |||
|} | |||
{| class="wikitable" | |||
|+<span id="Biological_Material_Details">Biological Material Details</span> | |||
|Source Organism | |||
|Organism from which the material is derived (e.g., Human, Mouse, ''E. coli''). User-defined values are also allowed. | |||
|- | |||
|Biological sample type | |||
|Type of biological material. Options include: | |||
* Serum | |||
* Urine | |||
* Whole Blood | |||
* Cell Extract | |||
* Tissue | |||
|- | |||
|Sample Category | |||
|Defines the role of the sample in the study. Options include: | |||
* Study Sample | |||
* Buffer Bank, | |||
* Extraction Bank | |||
* Internal QC | |||
* External QC | |||
|- | |||
|Local Sample ID | |||
|Identifier assigned to the sample within a multi-sample experiment | |||
|- | |||
|Extraction | |||
|Indicates whether the sample was extracted. If yes, methods include: | |||
* Methanol:water 80:20% | |||
* 100% Methanol | |||
* 100% water | |||
* 100% isopropanol | |||
* 100% DMSO | |||
* Chloroform:methanol (2:1) | |||
* Other | |||
* None | |||
|- | |||
|Description | |||
|Additional notes or information about the biological material | |||
|} | |||
{| class="wikitable" | |||
|+<span id="Environmental_Sample_Details">Environmental Sample Details</span> | |||
|'''Name''' | |||
|'''Description''' | |||
|- | |||
|Source Location | |||
|Physical origin of the sample (e.g., river, soil) | |||
|- | |||
|Source Class/Material | |||
|Type of material collected | |||
|- | |||
|Geo Location | |||
|Geographic coordinates or descriptive location | |||
|- | |||
|Sample Category | |||
|Defines the role of the sample in the study | |||
|- | |||
|Local Sample ID | |||
|Identifier assigned to the sample within a multi-sample experiment | |||
|- | |||
|Extraction | |||
|Indicates whether the sample was extracted. If yes, user can specify the extraction method | |||
|- | |- | ||
|Description | |Description | ||
|Additional information about the | |Additional notes or information about the environmental sample | ||
|} | |} | ||
Latest revision as of 18:42, 21 August 2025
← Back to Sample Columns ← Back to Creating/Cloning Samples
The first table lists possible sample components, while the following tables provide details that can be documented for major component types (e.g., proteins, polymers, biological mixtures).
| Type | Subtype | Comments |
|---|---|---|
| Bio Macromolecule | Protein | |
| Nucleic Acid - DNA | Deoxyribonucleic acid samples | |
| Nucleic Acid - RNA | Ribonucleic acid samples | |
| Carbohydrate | Sugar molecules and polysaccharides | |
| Small molecules | Metabolite | Small bioactive molecules involved in metabolism |
| Natural Product | Compounds isolated from natural sources | |
| Other organic | Organic compounds not classified elsewhere | |
| Chemical Formula | Chemical Formula | Explicit formula-based representation of a compound |
| Polymer | Polymer | Synthetic or natural long-chain molecular compounds |
| Mixtures | Biological Material | Mixed biological content such as tissue extracts |
| Environmental Sample | Samples derived from environmental sources | |
| Components | Solvent System | |
| Buffer | ||
| Salt | ||
| Internal Standard | ||
| Indirect Referencing Standard | ||
| Additives | Detergent | |
| Lipid | ||
| Micelle | ||
| Bicelle | ||
| Nano-disk | ||
| Stretched or Compressed Gell | ||
| Excipient | ||
| Polarizing Agent | ||
| Paramagnetic compound | ||
| Other | Other | Any sample not classified in the above categories |
| Name | Description |
| Molecular Weight | Molecular weight of the protein |
| Purity (%) | Estimated percentage purity of the sample (e.g., from SDS-PAGE or gel filtration) |
| Uniport ID | Accession ID linking the protein to the UniProt database. |
| Number of subunits | How many subunits |
| AA Sequence | Exact sequence of construct in the NMR tube (including any uncleaved tags or additional amino acids) |
| Protein conformational state | Specify if the protein is globular, membrane, fibril or disordered |
| Monomer/Homo-Oligomer | Indicate if the protein exists as a monomer or homo-oligomer; if oligomeric, specify whether it is symmetric or asymmetric. |
| Modification | Users can document modifications type, location in the amino acid sequence, and an optional description. While a list of common modification types is provided, custom types may also be entered.
Suggested modification types:
|
| Name | Description |
| Molecular Weight | Molecular weight of the nucleic acid |
| Purity (%) | Estimated percentage purity of the sample (e.g., from SDS-PAGE) |
| GenBank ID | |
| NA Sequence 5’-3’ | Nucleic Acid Sequence (Note: Fasta format entry) |
| Non-Standard | If the sequence has non-standard bases, provide a description |
| Covalent Linkage | If the sequence has covalent linkage, define its type and location |
| Modification | Users can document modifications type, location in the sequence, and an optional description. While a list of common modification types is provided, custom types may also be entered.
Suggested modification types:
|
| Name | Description |
| Molecular Weight | Molecular weight of the carbohydrate sample |
| Purity (%) | Estimated percentage purity of the sample |
| Classification | Specify type:
|
| IUPAC condensed string | IUPAC condensed notation describing carbohydrate structure |
| Tags | Additional descriptors or identifiers for the carbohydrate |
| Modification | Users can document modification type and provide description. Supported types include:
|
| Name | Description |
| Molecular Weight | Molecular weight of the chemical substance |
| Purity (%) | Estimated percentage purity of the sample |
| PUBChem ID | Identifier from the PubChem database of chemical molecules (Compound ID number) |
| CAS ID | Unique identification number assigned by the Chemical Abstracts Service (CAS) |
| Chemical Formula | Enter chemical formula |
| InChI | Standardized InChI identifier |
| Class | Class of Material:
|
| Class Description | Detailed description of the material class |
| Name | Description |
| Tacticity | Define tacticity type:
|
| Branching | Specify whether the polymer is linear or branched |
| Source | Indicate whether the polymer is synthetic or biological. If biological, an option is available to enter the biological source. |
| Weight Average Molecular Weight | In kDa |
| Number Average Molecular Weight | In kDa |
| Dispersity | |
| Polymer repeat sequence | User can provide following details:
|
| Description | Additional notes or information about the polymer |
| Polymer subunit | User has an option to add one or more polymer subunits. Following details can be provided:
|
| Source Organism | Organism from which the material is derived (e.g., Human, Mouse, E. coli). User-defined values are also allowed. |
| Biological sample type | Type of biological material. Options include:
|
| Sample Category | Defines the role of the sample in the study. Options include:
|
| Local Sample ID | Identifier assigned to the sample within a multi-sample experiment |
| Extraction | Indicates whether the sample was extracted. If yes, methods include:
|
| Description | Additional notes or information about the biological material |
| Name | Description |
| Source Location | Physical origin of the sample (e.g., river, soil) |
| Source Class/Material | Type of material collected |
| Geo Location | Geographic coordinates or descriptive location |
| Sample Category | Defines the role of the sample in the study |
| Local Sample ID | Identifier assigned to the sample within a multi-sample experiment |
| Extraction | Indicates whether the sample was extracted. If yes, user can specify the extraction method |
| Description | Additional notes or information about the environmental sample |