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 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. |
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 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.