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The Quantification Tab provides a view on quantitative data. It displays all identified proteins and peptides, along with their quantitative values. Additionally, it provides visualization for comparing protein quantity and spectrum.

From top to bottom, you can see three main areas of information:

You can get more information about the principles behind these quantitative data from: Quantification Principles

If you want to focus on just one section of the data, you can use the little arrows on the split bar to hide and show component.

Protein Quantification

To better illustrate the protein quantification information, a short summary is shown on top of the protein table. It shows the Method of quantification technique, such as: ITRAQ.

You can set the control sample by clicking on the Set Control Sample button on top of the protein quantification table. Every time a new control sample is set, the columns which relates to quantification ratios will change both the headers and their contents. This action is also synchronised to the peptide quantification table and the protein comparison histogram.

Click on Decoy Filter to set a filter to show or hide decoy protein identifications

More information on Decoy Filter

You can click on Show/Hide Icon to show or hide columns, and the table below gives a short description for every column in the protein table, most of them are hidden by default, you can show them by clicking on the icon at the top-right corner of the table:

The number of columns for showing quantification data depend on the input data, for instance, for an ITRAQ 4-plex experiment using 114 as the control sample, three ratio can be shown: 115/114, 116/114 and 117/114.

The column which contains a list of checkbox allows you to select the proteins of your interest to compare them in the protein quantification comparison histogram.

Column Description
Row Number Displays the row number
Submitted Protein Accession This is the original protein accession in the file/PRIDE experiment.
Mapped Protein Accession As submitted protein accessions are sometimes in none-standard formats PRIDE Inspector will try to convert it to a more common format.
Protein Name Protein name downloaded using the mapped protein accession
Status Status of the protein accession, the accession could be active, unknown, deleted, merged, demerged, changed.
Coverage Protein sequence coverage calculated using protein sequence downloaded and its peptide identifications.
pI Theoretical isoelectric point calculated using protein sequence.
Score PRIDE protein b1Score
Threshold PRIDE protein threshold
#Peptides Number of peptides identifying this protein.
#Distinct Peptides Number of distinct peptides identifying this protein.
#PTMs The total number of post translational modifications identified in the protein.
Identification ID unique protein identification id.
More column to show all the additional params in an extra dialog.
A bar chart is drawn for each quantification value, this is to better illustrate the results. For values are less than 1, a red bar is shown, for values are greater than 1, a blue bar is shown. The size of the bar represents the change of the quantity.

Peptide

This table shows a list of peptides used to identify the selected protein, it also shows to the quantitative results detected for these peptides.

You can click on Show/Hide Icon to show or hide columns, and the table below gives a short description for every column in the peptide table, like the protein table, most of these columns will be hidden by default, you can show them by clicking at the table control icon on the top-right corner of the table.

Clicking a row in the peptide quantification table selects a peptide, if the spectrum used to identify this peptide is available, it will be shown in the Spectrum Browser below.

Column Description
Row Number Displays the row number
Peptide Sequence The complete peptide sequence is shown with modified amino acids highlighted in red. If you mouse over the peptide sequence, a tooltip with PTM details will be displayed.
Fit In Sequence whether the peptide sequence fits the protein sequence, it could be unknown when the protein sequence is no available, or fit if the peptide sequence can be found at the given start and stop position of the protein sequence, or fuzzy fit if the peptide position no longer fit, but the peptide sequence can still be found in the protein sequence.
Submitted Protein Accession The peptide's protein accession from the original data file/PRIDE experiment.
Mapped Protein Accession As the submitted protein accessions can sometimes be in none-standard format PRIDE Inspector will try to convert it to a more common format.
Precursor Charge Precursor ion charge
Delta m/z The difference between the observed and theoretical m/z.
Precursor m/z Precursor ion m/z value.
#PTMs Number of post translational modifications on this peptide.
PTM List A distinct list of PTM accessions with their count
#Ions Number of fragment ions assigned to this peptide identification.
Peptide Score Peptide b1Score given by the search engine, the number of columns depends on the search engine used. For instance, mascot b1Score will be displayed if Mascot search engine is used. Both X correlation and Delta Cn will be displayed for SEQUEST search engine.
Length Peptide length
Start The start position of the peptide within protein sequence.
Stop The stop position of the peptide within protein sequence.
pI Theoretical isoelectric point
Spectrum Spectrum ID
Identification ID Unique protein identification ID
Peptide ID Peptide ID for a given protein identification
More Show additional params for the peptide

Sample Table

Sample Table shows a summary of all the samples used in this experiment, each row reprents a sub sample, it includes reagent name, species, tissue, GO term and a sample description.

Protein Quantification Comparison Histogram

This histogram shows the quantitative values of the selected proteins from the protein table, the values are grouped by the reagent ratios. Due to screen size limitation, maximum ten proteins are allowed.

Every time a new control sample is set, this hisgram will be updated automatically as well.

You can right click on the histogram to save the histogram, supported formats are: pdf, svg, png, jpeg and gif. You can also print the histogram by right click.

Spectrum Browser

The Spectrum Browser shows the spectrum identifying the selected peptide.
For more details, please refer to: Spectrum Browser.

See Also

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