Job Summary

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The Summary Tab

Selecting one spectrum will update the details tab. Double-click on one item to automatically open the details tab with the corresponding spectrum. You can export this table as an Excel or text file (see Exports)

Job Detail

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On top of this page, you can select the spectrum for witch you want to display the identification results. (this selection will automatically update the selection of the summary tab). The theoretical peptides of each protein candidate can be sorted by mass or by position on the sequence.

The Detail Tab

The results are composed of three parts:

1. The Header gives general information on the request
2. The Summary displays a summary of the best proteins candidates
3. The details are displayed for each protein candidate

Result Header

Spectrum
Short description of the spectrum: number of peaks, mass range and intensity range.

Release
Release of the different databases used in this identification.

Proteins

1. In range: Number of sequences in the selected database(s) and taxon(s), in the defined mass range, pI range, keywords, etc... Several sequences can be merged in a single Swiss-Prot or TrEMBL entry, whereas sequence variants for one protein entry are counted as separated sequences.
2. After digestion: Number of proteins with at least the number of hits after digestion and before the alignment process. This means: Number of proteins with enough theoretical peptides matching an experimental peak in the error space defined by the user to limit the comparison (e.g. 0.2 Da and 200 ppm) and before alignment (e.g. 25 ppm for internal error).
3. First analysis: The first analysis is run with a low precision for a quick scan of the set of proteins selected according to the previous filters (database, taxon, mass and pI ranges, number of hits, error tolerance). This first run will discared very unlikely proteins.
4. After alignment: Number of proteins with at least the number of hits aligned (low resolution).
5. Second analysis: The second analysis is run on the best X proteins of the first analysis (X is the number of proteins to displayed, at least 30). If the number of proteins after the first analysis is less than 30, only these proteins goes into the second analysis.
6. After alignment: Number of proteins with at least the number of hits aligned (high resolution).
7. Displayed: Number of proteins displayed defined by the user or less if there are not enough proteins to display. Note! Because of the higher resolution, some proteins can be discarded after the second analysis. Then the protein number displayed may be less than the max number of proteins defined by the user.

Peptides

1. Generated: Number of theoretical peptides generated.
2. Matching a peak: Number of these peptides matching a peak of the spectrum (e.g. ± 0.2 Da and ± 200 ppm).
3. Average per proteins: Average of peptides generated per proteins.

Random

1. Generated: Number of random sequences generated. It is the same number as the number of sequences in range in the database. The random sequences are generated using the same properties as the sequences used for the request: lenght, amino acid composition...
2. Best score: Score of the best random protein. It is used to display a threshold on the scores, In red = a protein with a score lower than this random score, in green = a protein with a score greater than this random score.

Identification Summary

Rank
Rank of the proteins by decreasing score.

Score
Aldente score of the protein. The background color indicates in red or green if the score is lower or greater than the best random score; this threshold should help to eliminate wrong identifications, taking into acount the possibility to produce a better score randomly for these proteins.

You can uncheck in the submision form "Statistics on random sequences", this will remove the calculation on random sequences and will speed up the request.

The number of random sequences generated are the same as the number of proteins "in range" in the database. The significancy of a result, based on the best random score, will differ with the size of the searching database. It makes sense that a given score can be significant while searching in a very small database and can be insignificant searching in a larger one.

Hits
Number of hits realigned and used in the score.

AC
Swiss-Prot / TrEMBL Accession number.

ID
Swiss-Prot / TrEMBL Entry name. Suffix "C_1" means Chain 1 from original entry. Suffix "_V1" means Varsplice 1 from original entry.

DE
Swiss-Prot / TrEMBL Description line.

Mw
Protein mass. The theoretical calculation is done also for chains, varsplices, fragments...

pI
Protein isoelectric point. The theoretical calculation is done also for chains, varsplices, fragments...

Cov
Coverage: Number of amino acids present in at least one peptide over the number of amino acids of the protein.

TaxID
Exact taxID where the protein has been found. (See Newt)

TaxID
Exact taxID where the protein has been found. (See Newt)

Detail of a Protein Candidate

Shift
Shift of the line used to recalibrate the spectrum (Dalton).

Slope
Slope of the line used to recalibrate the spectrum (ppm).

First column (Ambiguities)

1. (*) Peptide marked by a black asterisk: the peptide has a mass that is very similar to another one in the protein (within the tolerance) and the alignment has selected this one.
2. (*) Peptide marked by a red asterisk: This peptide has a mass that is very similar to another one in the protein (within the tolerance) but the alignment cannot discriminate between them. Discrimination has been done on the score.

Exp
Experimental mass = One peak from your peak list.

Theo
Theoretical mass = the calculated mass of a peptide issued from a theoretical digestion.

Intensity

1. First column: Intensity value from your sample.
2. %: Percentage intensity, the highest peak will show 100%.
3. Rank: Intensity rank of the peaks, the most intense peak will have value 1.

Delta

1. Da: Exp - Theo displayed in Daltons.
2. ppm: Exp - Theo displayed in ppm.

Dev
Distance of the hit to the alignment displayed in ppm.

MC
Missed Cleavage

Modifs
For each modification a column is added with the modification label. 1/2 means 1 locus is modified for 2 potential locus on the peptide.

Position
Starting and ending positions of the peptide in the protein sequence.

Sequence
Peptide sequence

Job Parameters

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The Param Tab

This window displays the parameters used to submit this job. The same parameters are used to identify all the peak lists of a given job. When resubmitting this job, these parameters will be proposed as default values.

Job Comment

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The Comment Tab

Use this text area to store all the information relative to this job; for example, the sample preparation, your comments on the output, etc...

Exports

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A job summary can be exported to an Excel or text file. Each spectrum result (the detail tab) can be exported to an HTML file.

Export Summary

Click on the menu Jobs / Export summary or right click on the desired job in the job list and select "Export summary" in the sub menu. You can export the summary tab in an Excel or text file.