Sample Components: Difference between revisions

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<span style="display:inline-block; margin-bottom:1em;">[[Sample Columns#Sample Table|← Back to Sample Columns]]</span>
<span style="display:inline-block; margin-bottom:1em;">[[Sample Columns#Sample Table|← Back to Sample Columns]]</span>
<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}}
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
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|-
|-
| 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
|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
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|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'''
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|-
|-
|Modification
|Modification
|Enter protein modification, its type, location in the AA sequence and description.
|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.
There is a list of suggested modification types but user can enter their custom type
Suggested modification types:
Suggested types include"
 
# Linkage - Disulfide
# Linkage - Disulfide
# Post-translation Modification  
# Post-translation Modification  
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#* N-Trx (Thioredoxin)
#* N-Trx (Thioredoxin)
#* C-Trx
#* C-Trx
|}
{| class="wikitable"
|+<span id="Nucleic_Acid_Details">Nucleic Acid (DNA, RNA) Details</span>
|'''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:
# Linkage
# Post-translation Modification
#* Phosphorylation
#* Acetylation
#* Glycosylation
#* Lipidation
#* Nitrosylation
#* Ubiquitination
# Non-standard NA
# Paramagnetic Tags
# Purification Tags
#* N-His6
#* C-His6
#* N-Strep
#* C-Strep
#* N-GST
#* C-GST
#* N-Trx (Thioredoxin)
#* C-Trx
|}
{| class="wikitable"
|+<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'''
|'''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:
* Small molecule
* Polycrystalline
* Amorphous
* Zeolite
* Single Crystal
* Heterostructure
* Glass
|-
|Class Description
|Detailed description of the material class
|}
{| class="wikitable"
|+<span id="Polymer_Details">Polymer Details</span>
|'''Name'''
|'''Description'''
|-
|Tacticity
|Define tacticity type:
* Atactic
* Eutactic
* Isotactic
* Syntactic
* Indeterminate
|-
|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:
* Number of Subunits
* Degree of substitution
* Length of repeated sequence
* 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
|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).

Sample Component Types
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
Protein Details
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:

  1. Linkage - Disulfide
  2. Post-translation Modification
    • Phosphorylation
    • Acetylation
    • Glycosylation
    • Lipidation
    • Nitrosylation
    • Ubiquitination
  3. Non-standard AA
  4. Paramagnetic Tags
  5. Purification Tags
    • N-His6
    • C-His6
    • N-Strep
    • C-Strep
    • N-GST
    • C-GST
    • N-Trx (Thioredoxin)
    • C-Trx
Nucleic Acid (DNA, RNA) Details
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:

  1. Linkage
  2. Post-translation Modification
    • Phosphorylation
    • Acetylation
    • Glycosylation
    • Lipidation
    • Nitrosylation
    • Ubiquitination
  3. Non-standard NA
  4. Paramagnetic Tags
  5. Purification Tags
    • N-His6
    • C-His6
    • N-Strep
    • C-Strep
    • N-GST
    • C-GST
    • N-Trx (Thioredoxin)
    • C-Trx
Carbohydrate Details
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
Small Molecules/Chemical Formula Details
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:
  • Small molecule
  • Polycrystalline
  • Amorphous
  • Zeolite
  • Single Crystal
  • Heterostructure
  • Glass
Class Description Detailed description of the material class
Polymer Details
Name Description
Tacticity Define tacticity type:
  • Atactic
  • Eutactic
  • Isotactic
  • Syntactic
  • Indeterminate
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:
  • Number of Subunits
  • Degree of substitution
  • Length of repeated sequence
  • 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)
Biological Material Details
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
Environmental Sample Details
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
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