Peptide Spectrum Match Identification Details view parameters - Proteome Discoverer Software - Peptide Spectrum Match Identification Details view parameters - Proteome Discoverer Software

Peptide Spectrum Match Identification Details view parameters - Proteome Discoverer Software - Peptide Spectrum Match Identification Details view parameters - Proteome Discoverer Software - Proteome Discoverer Software

Proteome Discoverer 3.1 User Guide

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User Guide

Software version

3.1

The following table lists the parameters on the pages of the Peptide Spectrum Match Identification Details view.

Peptide Spectrum Match Identification Details view parameters
Command or option	Description
Options pane
	Loads the last saved default fragment match settings for the selected mass analyzer/activation type combination.
	Saves the current fragment match settings as the default fragment match settings for the selected mass analyzer/activation type combination.
	Loads the original factory fragment match settings for all mass analyzer/activation type combinations.
Display Options area
Charge Detail Level	Selects the appropriate charge state to display. The values are as follows: (Default) All: Displays all fragment ions, regardless of charge. +1: Displays singly charged fragment ions. +2: Displays doubly charged fragment ions. +3: Displays triply charged fragment ions. +4 …: Displays additional charged fragment ions if available.
Annotation Threshold	Specifies a peak intensity limit. The application does not annotate peaks below this limit. This limit prevents the addition of too many labels to a spectrum, especially if the low-intensity peaks are possibly noise peaks. (Default) % of Base Peak: Specifies an intensity threshold as a percentage of the base peak in the spectrum. The base peak is the largest peak in a spectrum. Absolute: Specifies an absolute intensity threshold.
Show Legend	Determines whether a legend consisting of colored lines that denote the displayed ion series appears at the bottom of each spectrum image.
Show Reference Spectrum	Determines whether to display the reference spectrum from the reference spectrum library.
Ref. Spectrum Source	Selects the reference spectrum source. The prediction is local or over the cloud. From Identifying Node Spectrum Library Inferys_2.1_fragmentation Inferys_3.0_fragmentation CHIMERYS (if activated)
Use Search Settings	Annotates the spectra using the match tolerances and ion series that you chose for the search node.
Match Tolerances area
Mass Analyzer	Specifies which mass analyzer is used to obtain the spectrum.
Mass Tolerance	Specifies the mass tolerance. The application annotates the spectrum with ions that it assigns within this mass tolerance. You can use daltons or millimass units.
Fragments area
Activation Type	Specifies what type of activation produced the fragments.
Ion Series area	Selects which series of fragment ions the application displays in the ion table and in the extracted data plot. By default, the spectrum displays the most relevant ion types for each activation type. See Displaying fragment ions for a list of the ions series that you can display. By default, the ion series are displayed in the following colors: Red: a, b, c–1, c, c+1 fragment ions Blue: x, y, z, z+1, z+2 fragment ions Magenta: immonium ions Green: precursor ions Yellow background: phosphorylation losses
Neutral Losses area	Determines whether to display water or ammonia neutral losses in the ion table and in the extracted data plot. The application adds a column for each type of neutral loss ion that you select on the Neutral Losses page. For example, if you select the b and y ions in the Ion Series area and then choose the –NH3 checkbox, the application adds both a b–NH3 column and a y–NH3 column to the table on the Neutral Losses page. It also adds these ions to the extracted data plot. The application only calculates water neutral loss fragments if side chains contain the potential neutral loss groups of aspartic acid, glutamic acid, serine, or threonine. It only calculates ammonia neutral loss fragments if side chains contain the potential neutral loss groups of lysine, asparagine, glutamine, or arginine.
Other area	Annotates the spectra with immonium ions or precursor ions.
Peptide Summary pane
Description of spectra in a scroll box	Displays the following spectra information: Amino acid sequence of the peptide PTMs, if any Charge state of the precursor ion Mass-to-charge ratio (m/z) of the precursor ion, in daltons MH+ (the protonated monoisotopic mass), in daltons Retention time of the precursor ion, in minutes Below this information appears the following: Search node used XCorr (Sequest HT) or Ions Score (Mascot) value, which scores the number of fragment ions that are common to two different peptides with the same precursor mass and calculates the cross-correlation score for all candidate peptides queried from the database. Probability of a match (for Sequest HT) Number of matched fragments found out of the total number of different potential fragments in the sample Fragment match tolerance, in daltons
Fragment Matches pane
Value Type list	Specifies which unit is used to display the fragment ion masses in the ion table: (Default) Theo. Mass [Da]: Displays the fragment ion masses in daltons. Delta Mass [mmu]: Displays the fragment ion masses in millimass units. Delta Mass [ppm]: Displays the fragment ion masses in parts per million. Intensity [counts]: Displays the intensity of the precursor ion.
Ion table	Ion Series page: Displays the calculated fragment ion masses for the best-fit sequence for each specified activation type. Entries in the table are colored if they match peaks in the spectrum within the match tolerance. The application displays the a, b, and c fragment ions from the N terminal to the C terminal. It displays x, y, and z fragment ions from the C terminal to the N terminal. It lists the peptide sequence in the Seq. column in the middle of the table. On the far left and far right of the table are sequential numbers that the application automatically assigns to the fragment ions in the order that the amino acids appear in the fragment from either the N terminus or the C terminus until each amino acid is numbered in the peptide. Neutral Losses page: Displays the calculated fragment ion masses for ions that have lost a water or ammonia neutral fragment. The application colors entries in the table if they match peaks in the spectrum within the match tolerance. Phosphorylation Loss Series page: Displays the calculated fragment ion masses for ions that have lost a H₃PO₄ fragment. The application colors entries in the table if they match peaks in the spectrum within the match tolerance. Multiple Neutral Losses page: Displays the calculated fragment ion masses for ions that have lost multiple neutral fragments (H₂O, NH₃, or H₃PO₄). The application colors entries in the table if they match peaks in the spectrum within the match tolerance. Precursor Ions page: Displays the calculated fragment ion masses for precursor ions. The application colors entries in the table if they match peaks in the spectrum within the match tolerance.
Fragment Spectrum pane
Extracted data plot	Shows the annotated spectrum with all the fragments that matched an expected fragment from in-silico digestion. The header of the plot displays the following: - Name and location of the raw data file - Numbers of any grouped spectra - Retention time of the precursor ion - Type of mass spectrometer used - Fragmentation method used - Charge state of the precursor ion - Mass-to-charge ratio of the precursor ion - MH+ (the protonated monoisotopic mass) - Match tolerance The axes of the plot are as follows: Intensity [counts] (y axis): Displays the intensity of the fragment ions, in counts. m/z (x axis): Displays the mass-to-charge ratio of the precursor ion.