The Spectrum Selector node selects the subset of the set of spectra that you want to search. You must use this node with the Spectrum Files node.

When searches are based on MGF, MZDATA, or other external file formats, the extracted spectra might not have information about the activation type, mass analyzer, polarity, and so forth. However, certain processing nodes require some of this information. To enable such searches, you can use the Spectrum Selector node to provide these values.

NOTE

If you specify both a retention time range and a scan range, the application combines them into a single filter criterion; that is, it processes a scan only if it simultaneously falls within the specified retention time range and the specified scan range.

The following table describes the parameters for the Spectrum Selector node.

Spectrum Selector node parameters

Parameters

Description

Precursor Selection

Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans like MS3, MS4, and so forth.

  • (Default) Use MS1 Precursor: Uses the precursor mass in the MS scan.
  • Use MS(n – 1) Precursor: Uses the precursor mass in the parent scan. For example, for MS3, this option would use the MS/MS scan.
  • Use MS(n – 1) with Parent Precursor: Uses the precursor of the direct parent scan and all preceding precursors up to the MS1 scan.

Use Isotope Pattern in Precursor Reevaluation

Determines whether the application considers the isotope pattern in reevaluating precursors.

  • (Default) True: Considers the isotope pattern in reevaluating precursors.
  • False: Does not consider the isotope pattern in reevaluating precursors.

Provide Profile Spectra

Determines whether profile points should be provided. In automatic mode, the node checks whether there is any node in the workflow that requires profile spectra.

Lower RT Limit

Specifies the lower retention-time limit. Retention time is the time in the mass chromatogram when any particular precursor ion is observed. The Lower RT Limit and the Upper RT Limit parameters set limits on the portion of the data that you want to analyze. Because very early and very late portions in the chromatogram typically do not contain the peptide ions of interest, you might want to analyze only that middle portion that contains useful data to save search time.

If the value is 0.0, the application uses the lowest available retention time.

Range: 0–no maximum; default: 0

Upper RT Limit

Specifies the upper retention-time limit.

If the value is 0.0, the application uses the highest available retention time.

Range: 0–no maximum; default: 0

First Scan

Specifies the scan number of the first scan to process. If you set this number to 0, the application uses the first available scan.

Range: 0–no maximum; default: 0

Last Scan

Specifies the scan number of the last scan to process. If you set this number to 0, the application uses the last available scan.

Range: 0–no maximum; default: 0

Ignore Specified Scans

Opens the Edit Parameter Text for Ignore Specified Scans dialog box so that you can enter a single scan or a range of scans to exclude from processing.

To specify a single scan, enter its number in the dialog box.

To specify a range, place a hyphen between the starting scan and the ending scan, for example, 2000–3000.

For multiple entries, place a semicolon (;) between each entry, or place each entry on a separate line.

Lowest Charge State

Filters out spectra with a precursor charge lower than the specified charge.

Range: 0–no maximum; default: 0

Highest Charge State

Filters out spectra with a precursor charge higher than the specified charge. If you set the value to zero, there is no maximum value for the precursor charge.

Range: 0–no maximum; default: 0

Min. Precursor Mass

Specifies the lower mass limit of a singly charged precursor ion to be processed.

Range: 0.0–10 000.0 Da; default: 350 Da

Max. Precursor Mass

Specifies the upper mass limit of a singly charged precursor ion to be processed.

Sequest HT searches rely on indexed FASTA databases. The search engine considers only peptides that fall between 300 and 10000 as PSMs, so setting a value higher than 10000 does not result in the identification of more PSMs.

If you set the value to zero, the value is set to the maximum precursor mass allowed.

Range: 0.0–no maximum; default: 5000 Da

Total Intensity Threshold

Specifies a minimum total intensity value and filters out tandem mass spectra that have a total intensity current (the sum of the intensities of all peaks in a spectrum) below the specified value. You can use this parameter to remove low-intensity data.

Range 0.0–no maximum; default: 0

Minimum Peak Count

Specifies the minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow. Use this parameter to remove spectra that have a small number of peaks, because these typically produce low-quality hits.

Range: 1–no maximum; default: 1

Mass Analyzer

Specifies the type of mass analyzer used to acquire the spectrum. This parameter filters out all but the type you are interested in. It is possible to have data from more than one type of mass analyzer in the same data input, for example, data from a hybrid instrument such as LTQ Orbitrap or LTQ FT.

These are the available analyzers:

  • Ion Trap
  • Fourier Transform (FT) (Fourier transform applies to both FT ICR data and Orbitrap data.)
  • Time of Flight (TOF)
  • Single Quad
  • Triple Quad
  • Sector Field
  • (Default) Any

MS Order

Specifies the level of the mass spectrum to be processed, for example, MS/MS or MS3.

Range: MS1–MS10; default: Is Not MS1

Activation Type

Specifies the fragmentation method used to generate the MS/MS spectra. The following activation types are available:

  • CID (Collision-Induced Dissociation)
  • MPD (Multi-Photon Dissociation)
  • ECD (Electron Capture Dissociation)
  • PQD (Pulsed-Q Collision-Induced Dissociation)
  • ETD (Electron Transfer Dissociation)
  • HCD (High-Energy Collision Dissociation)
  • EThcD (ETD with supplemental HCD)
  • UVPD (Ultraviolet Photodissociation)
  • (Default) Any Activation Type

For descriptions, see Multidimensional separation experiments.

Min. Collision Energy

Filters out the spectra of ions fragmented with low collision energy from the spectra of ions fragmented with high collision energy. This parameter filters out values below the specified value.

Range: 0–100; default: 0

Max. Collision Energy

Filters out the spectra of ions fragmented with high collision energy from the spectra of ions fragmented with low collision energy. This option filters out values above the specified value.

Range: 0–1000; default: 1000

Scan Type

Specifies the scan type of the spectrum. These are the available scan types:

  • (Default) Full: Scans the full mass range to acquire the data. The mass spectrometer detects a wide range of mass fragments. Used for typical data-dependent scanning.
  • Selected Ion Monitoring (SIM): Scans a very small mass range to acquire the data. The mass spectrometer detects only certain mass precursors.
  • Selected Reaction Monitoring (SRM): The mass spectrometer detects specific product ions from specific parent ions.

Polarity Mode

Specifies the polarity of the spectrum:

  • Positive: The detector monitors positive ions.
  • Negative: The detector monitors negative ions.
  • (Default) Any: The detector monitors either positive or negative ions.

MS1 Mass Range

This filter applies only to MS1 spectra. Those matching the specified mass range pass the filter.

FAIMS CV

When the FAIMS CV value is unspecified (empty), the analysis ignores CV values and all spectra pass the filter. When you specify a CV value, the analysis processes only the input files that include spectra for this CV value.

IMPORTANT The compound detection node requires MS1 spectra from every input file in an analysis, but it can process spectra for only one CV value per input file. To prevent an analysis with compound detection from failing, do the following:

  • When the input files include CV switching, specify the CV value to process and make sure that every file in the Files for Analysis list includes spectra for this CV value.
  • When the input files include only one CV value per file but not the same CV value for every file, do not specify a CV value.

S/N Threshold (FT-only)

Specifies a signal-to-noise value below which peaks are removed. The S/N threshold has an effect on FT data only. Data acquired with other mass analyzers are not affected.

Range 0.0–no maximum; default: 1.5

Unrecognized Charge Replacements

Specifies the charge states of the ions to be included in the search, if they are not in the scan header. If the charge state of the precursor cannot be determined, the spectrum is replicated for each of the specified precursor charges. Select from these settings:

  • (Default) Automatic: Automatically assigns the +2 and +3 charge states to any spectrum whose precursor charge state is not defined.
  • Select All: Assigns charges states +1 through +8 to any spectra whose precursor charge states are not defined.
  • 1–8: Assigns a charge state that you select from +1 to +8, inclusive, to any spectrum whose precursor charge state is not defined.

If you select Automatic, the application applies a simple check for a +1 spectrum; otherwise, it generates a +2 and a +3 spectrum.

Unrecognized Mass Analyzer Replacements

Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header. Select from these settings:

  • (Default) Ion Trap (ITMS)
  • Fourier Transform (FTMS)
  • Time of Flight (TOFMS)
  • Single Quad (SQMS)
  • Triple Quad (TQMS)
  • Sector Field (SectorMS)

Unrecognized MS Order Replacements

Specifies the MS order to use in case the application cannot retrieve it from the input.

Range: MS1–MS10; default: MS2

Unrecognized Activation Type Replacements

Specifies the activation type to use in case the application cannot retrieve it from the input. Select one of these activation types:

  • (Default) CID (Collision Induced Dissociation)
  • MPD (Multi Photon Dissociation)
  • ECD (Electron Capture Dissociation)
  • PQD: Pulsed Q Collision Induced Dissociation)
  • ETD (Electron Transfer Dissociation)
  • HCD (High Energy Collision Dissociation)
  • EThcD (ETD with supplemental HCD)
  • UVPD (Ultraviolet Photodissociation)

Unrecognized Polarity Replacements

Specifies the polarity to use in case the application cannot retrieve it from the input.

  • (Default) Positive: Specifies a positive polarity.
  • Negative: Specifies a negative polarity.

Unrecognized MS Resolution@200 Replacements

Specifies the resolution to use at mass 200 for MS scans in case you cannot retrieve this information from the input.

Range: 0–no maximum; default: 60 000

Unrecognized MSn Resolution@200 Replacements

Specifies the resolution to use at mass 200 for MS/MS scans in case you cannot retrieve this information from the input.

Range: 0–no maximum; default: 30 000

Precursor Clipping Range Before

Specifies the lower limit below the isolation window of the mass range from which to extract peaks for the Precursor Isotope Pattern view, in Da. This view shows the m/z range of the corresponding master scan from which the fragmented precursor ion was extracted. For more information, see Use the Precursor Isotope Pattern view.

The Precursor Clipping Range After specifies the upper limit of the m/z range.

Range: 2.5–100.0 Da; default: 2.5 Da

Precursor Clipping Range After

Specifies the upper limit above the isolation window of the mass range from which to extract peaks for the Precursor Isotope Pattern view, in Da. This view shows the m/z range of the corresponding master scan from which the fragmented precursor ion was extracted. For more information, see Use the Precursor Isotope Pattern view.

The Precursor Clipping Range Before specifies the lower limit of the m/z range.

Range: 5.5–100.0 Da; default: 5.5 Da