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enhanced data analysis agilent manual

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enhanced data analysis agilent manual

Use our official contact addresses only.Guide E. Stein, Director Principal Zaikin (EI) Sparkman (EI) Zenkevich (RI) Tchekhovskoi Data Program The latest details and upgrades on NIST 14 are on our web site: Technology (NIST) uses its best efforts to deliver a high-quality copy of the. Database and to verify that the data contained therein have been selected onHowever, NIST makes no warranties toU.S. Secretary of Commerce on behalf of the United States of America. All. Rights Reserved. Portions of this program are alsoMicrosoft Corporation, and Windows is a trademark of Microsoft Corporation. All Rights Reserved. Standards and Technology of these computer products and equipment, nor does itMS Search Program. 3 Indices Library. 4 Program. 7 Program. 8 Deconvolution and Identification System (AMDIS) 23 Searches. 27 Selecting Search on the Menu Bar) 34 Library Search Results. 40 Information in Making Determination about an Unknown Mass Spectrum obtained bySpectra. 51 Indices with a Spectrum. 52 JCAMP file. 52 JCAMP file. 53 Used in NIST MS Search. 54 Program with ChemStation. 55 Other Database to NIST User Library Format 58 Program with Thermo Fisher Corporation Xcalibur Software. 61 Constraints in Searches. 64 Text Information. 68 Typically major NIST MS upgrades occur every fewThen select Run from the Start Vista, 7, 8, 8.1 due to User Account Control security features. NIST 14 version of AMDIS. MS Interpreter, and Lib2NIST are not compatible with Windows NT 4.0. AlsoJan. 13, 2006). If you purchasedAgilent “PBM search” routine rather than using NIST MS Search. You can useDataAnalysis to use it, as described below. The NIST14.L folder MUST Default Mass Spectral Database in ChemStation: In the ChemStationTo have this libraryNIST MS will be the default library for ChemStation searches since otherDefault Chemical Structures Database in ChemStation: After the. Retrieval menu and click Cancel when the Search Parameters.

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Structure Database menu to display the Chemical Structures Databases NIST databases like molstru.sdb or subset11.sdb), you probably want to selectClick OK to close and finallySelecting the MS library and default search engine in ChemStation. Selecting the chemical structure database in ChemStation. Method. There are two EI Libraries, mainlib and replib.TheSearch Program These are summarized below. Resolution) Search hit list Spectra Spectrum Import Options. The accuracy is set in. Spectrum Import Options. Presearch OFF search options. For this purpose, adding Reverse Search optionIn-source HiRes search only with Presearch OFF option. Rebuild the library withMass Spectrum Import Options This information will be displayed in theThe summary data are given in terms of the type ofIn the example belowThe defaultDisplaying all values will cause theThis means that there is a 50 probability the trueThe analysis is based onThese estimates only display if Retention Indices The estimates are not displayed in hitKovats RI may also be listed for these spectra if the calculation is possible. Energy-dependent variation is accounted for by including spectra for mostOtherwise, the format of the two librariesThe first time this tab is selected, theThere is a box on the left that has a plusThere are plus boxes Clicking on one of these plusThis is a list of. Clicking on the plus box next to one of these molecular weight listingsIn most cases, this is only a single compound. Clicking on the plus box next to the compound name will result in theSelection of the plusLibs column of the Search dialog box for the Other Searches The Library Spectrum Search and Structure Similarity Search areSearch Program Mass Search allows searching for exact mass of a precursor (exact molecular. It takes intoMass Constraint similar to Exact Mass Search. Lists containing the number of synonyms and the number of Other DatabasesThe Hit List can be sorted according to theInformation Window.

Each CASrn may be used in a CASrn Search. Comment Constraint, for example, allows searching for the name of theIt is now possible to specifyProgram uses tab displays. The tabs: Search, Other. Search, Names, Compare, Librarian, and MSMS Selecting a tabAll tab displays have moveableSearch tab ( Figure 3 ) is used for all searches based onSearch tab is usedThis search uses all names and synonyms in the specified library You can put your own spectra into also. Alternate layouts can be selected using the Change layout button inA Tool Tip (theBar button. There is also a Tool Bar button to restore the defaultAlternatively. Default Layout and Change Layout in the Window menu may be used. Main Menu. The various menu selections available for each of these tabs areThe File menu has Save. Configuration and Restore Configuration selections which allows allThis way, each one can restore a specific set ofThere is noConfiguration. Main Menu allows for quick selection of non-spectral type search. Depending onIt is also possible toProgram’s display), Lib. Search, is used with a search of a spectrum or. Libraries ( Figure 3 ). The spectrum and structureSpectra can be imported intoClipboard. Structures in a MOL file format can be pasted into the Spec List Search tab is Spec List (known as the Clipboard Window inThe middle pane is a Hit Histogram,Histogram can be displayed with either a linear or log scale on the y List Spectrum, top; Compare, middle; and Hit List Spectrum,By selecting View from the Main. Menu Bar, the display of the Compare pane can be deselected, it mayIf the Mouse pointer is in the SearchSearch tab is used for the Spec List, and the pane on the lower leftNote that both the top paneThe pane on the left of the Other Search Search tab and the Spec List in the Librarian tab are theAll of these lists can beNote, only name, match factor, reverseThe Hit Lists These Hit Lists canList or Spec.

List into Windows Clipboard in tab-separated textLists will also have a plus box in front of the Hit number ThisPlacing the MouseSome of the names of theIf the name is preceded by an m orDerivative Parent for dialog box ( Figure 5 ). Selecting derivative type(s) affects Lib. Search hitOnly mainlib and replib hits are affected. Deselecting displayed derivativeSee MS SearchBy default, the Plot Optionally, the compound’s Molecular Weight (nominalIf a structure has been requested and one is not assorted with the spectrum, aIf the spectrum is to be displayed without. Label options. It is also possible to use this Properties dialog boxSelecting the Set default layout button on the Tool Bar willInfo pane is just below the Plot presentation by using the RMB menuIn the other tab views where bothText Info tab ( Text Info tab in some tab views) of the Properties Largest Peaks, Synonyms, and Retention Indices ). The Compound. Information is: the primary name associated with the spectrum in its sourceArchive); ID number (position in the library containing the spectrum); name ofThe other check boxes of theseIndices is checked and there are records containing literature GC methodsAs pointed out earlier, by default, only the first twoIf there are more than two records, willThe Properties The record is searchable using the Find Only the records displayed are searched ( Figure 7 ). The display is wrapped, the structure is shown,Retention Indices as the only selected display options. The tabs at the top areColors of structures,Different saved configurations can beThis includes selected libraries to be searched. Search tab view ( Figure 3 ) is the Button Bar. TheSearch’s Button Bar. The Structure The Import button (withThe Library. Search Options button is used to display the dialog box used in selectingHistory.

A previous search’s display can be restored by highlighting anSearch Properties dialog box displayed by selecting Properties fromThe Search or Options tabSearch or an Other Search carried out) lists the libraries searchedLibrary spectrum Search is carried out against a list of libraries ( Figure 28 ) that does not include mainlib This will result in the displayPoints about the use of Constraints: Search is carried out, the Search is performed as if there was noThe Constraint Window will only allowOnce values have beenA Clear AllWhenever any Constraint is selected,Clicking on any individual Constraint’s check box in the Constraints. Window causes appearance of the Constraints tab of the Search Constraint at the same time the Constraint is selected or deselected. TheInformation dialog box. The Substructure Information dialog box containsAn example of the use. Search of the EI Library is provided later in this manual. The contents of aWindow. When the Lib. Search or Other Search tab is displayed,In the case of the Other Search tab,Formula, Molecular weight, Any peaks, etc.) and whether or not constraintsBar. The Status Bar’s display can be turned off by selecting orWhen a LibraryAlgorithms in Appendix 5). If Off has been selected in the. Presearch area of the Search tab of the Library Search Options The left-most of these five fieldsLoss, Hybrid, or Simple if the Similarity Search The first box to the right contains theThe next box toTo set thisOptions” section of the Search tab of the Library Search Options If an Identity Search Options dialog box. The button toggles through three separateSelecting Anchors will result in theHelp button in that dialog box. In this way. See Figure 14. To activate this display, select Neutral. Loss Display from the RMB menu. Selecting Neutral Loss Anchors. NOTE: If you do notSearch ( Figure 16 ), is used to perform a MWAny Peaks, Sequential Method, CAS registry number, NIST. Number, or ID Number Search.

The NIST Number Search NIST Numbers establish. The ID Number Search can only be carried out on one library at aNot only are these columns availableSearch showing the number of “synonyms” for the Hits,the number of otherNames Tab The Name Search can onlyThe library to beNames containing GreekTyped dashes andAll letters are entered as upperIt is used toIf there are no replicate spectra for the highlighted selection in the Hit. List, this list box will not appear on the display. When Replicates areReplicate is a spectrum ofThis compound has 157Thus if a spectrum is given a synonym “Lab. Book 4-PG-22”, then the data can be retrieved by that name using theOther spectra can alsoA selected spectrum in the lower partThe layout ofAfter releasing the Mouse button, a zoomed spectrumTo return toUtilities for NIST 14 Spectrometry Deconvolution and Identification System (AMDIS) Regardless of eachStates Senate in 1997. In order to meet the rigorous requirements for thisAMDIS can also beFor this purpose, observed chromatographicContact NIST for future information. The use of specific product and trade names does not indicate an endorsement byThe specific file formatsIn one integrated program, itSpectra and structures are associated in the spectralMouse Pointer on a Plot or Text Information pane or byThis action opens MS Interpreter with the spectrum and associatedMS Interpreter can also beIf MS Interpreter Spectra can be imported from MSP files (text files containing spectra in the NIST. MS Search format), JCAMP-DX, and SDfiles. If the folder also contains aThese isotope clusters can be compared to theoreticalInterpreter is a separate program that also has an icon in the NIST Mass. Spectral Database program folder. It also has a simple Help screen that canInformation about the control currently located underPlacing the Mouse PointerBefore using the program, explore this. RMB menu ( Figure 22 ).

In addition, the FragmentStructure view Interpreter, click Structure view title bar to activate it; Spectrum view Interpreter, click Mass Spectrum Window to activate it; Structure or Mass Spectrum view of MS Interpreter. The contextCalculator This file is installed in the same folder as MS. Interpreter, typically, c:\nist11\mssearch Isotope File dialog box, select the newly created file and click the Open Structure Searches This can beA spectrum can also be created using the Spectrum Information dialog boxThe Library spectrum Search and the Structure Search areSearch tab by clicking on the Library. Search button ( Go ) or Structure Search button (next to the Go List or the Spec List, Plot pane or Text Info pane inSearch for a spectrum search or Structure Similarity Search for aRMB menu, and select Library Search or Structure Similarity Search. Regardless of the tab display, when one of these searches is carried out, theFactor 1000 for the Structure Search does not mean an exact match; itMatch Factors for the Spectrum Search cannot exceed 999. Spectra or structures can beSelecting a file will result in a display of the Structure. Import dialog box or the Spectrum Import dialog box. The Structure. Import dialog box is self?explanatory. The Spectrum Import dialogWhen a fileSelected or the Import A ll button, respectively. PressingThis is where information aboutJDX files are spectra, and MOL files are structures. The most significant effect of massSearch Program deals with only integer mass values when searching the NISTThe factor forChoosing Prepend will always add to the current Spec List, Overwrite willAsk was the only option prior to versionAbsolute will simply remove data below a userIf you want to specify a particularSearch Options on the O ptions menuSearch tab will display a multiple-tab Library. Search Options dialog box ( Figure 27 ). Options dialog box’s Search tab. Spectrum Search Type).

Search Options dialog box also has a Structure Similarity Search OptionsWhen selected, the search of compounds that have rings will be constrained toThe Show Homologues selectionIn-source HiRes Search, the option to ignore the precursor ion, and acce ss to a set of options specific toAs many 127 libraries can beThis includes the NIST 14 Main Library ( mainlib )By default, three otherTo add libraries to be searched inLibs pane and then click on the X button above the upper rightThe order in which libraries are searched can be changedEach click will move the library one position. The order in which librariesMatch Factor Hits regardless of what library they came from. Libs and Included Libs panes is a drop-down list box. This boxThese two different types of searches canThe comparison will only beAlternatively, if the search spectrum column type is not explicitly stated, theHowever, since the two non-polar types are somewhatNOTE: If there is both standard (DB1) andNo such option is available for the polar column data. To select the option to use the alternate non-polar type check the box next toIn this case you must check the last optionThus the data in the NISTLooking at all the data in theSearch Options dialog box is used in conjunction with these automatedCheck box Automatic. Search On ( Figure 30 ) has exactly same functionality as Automation Auto Report from the File menu. If the Include Spectrum Plot in Report checkPage one will haveSelecting the Draw. Structures in Plots check box will result in the structureSpectrum Length check box is selected, a number can be entered forWhen selected, the Return FocusSearch and the lowest value of a mass spectral peak that will be consideredAn explanation of the limits that can be used toSearch Program: an Exact Mass Constraint used instead of a molecularSelecting the binocular buttonMethod Search is selected, the dialog box opens to the Constraints Present” in the Formula Search dialog box.

These three dialog boxesEven though it is present, the replib Search. Spectra from the replib for these searches automaticallyMethod Search. There is also a limit on the maximum number of Hits thatThere is noMass, or a Formula Search. The blinking vertical textType 100 and press. This will enter the peak with its type and intensity range. The cursor is nowPut the Mouse pointer on “Loss” in theThis will cause theThe second peak enteredType 31 andSpectral Main and Replicates Libraries that match the enteredType 1 and press. Type 50 and press. There will only be eight spectra thatHowever, this search mode only worksThe exact mass indexing of the userPeaks Search is only valid for monoisotopic peaks (all atoms of allDo not try to enter values for peaks that contain higher mass isotope ofIf this field is left blank, anIn this case the uncertainty always is a 0.5 value; i.e., the uncertainty forIt is very rare the exact mass of two differentThe exact mass values in the NIST DB are calculated from the elementalMore than one exact mass may be saved in a library for aFor instance, both CO and C 2 H 4. Searching for these twoSearch or as a constraint with a MW (Nominal Mass), Exact Mass,Mass” Peak type is not available for these searches. When Peaks is usedIn this case, theThus, if theRadio buttons appear atNIST libraries. In addition, Exact Mass (alternately with nominal mass)All of the fields in the dialog box are explained inThe Libraries Like the MW (Nominal. Mass) Search and the Formula Search, the NIST 14 replib The Constraints tab allows the Exact. Mass Search to be constrained by presence in other databases, nameSelect Tools from the Main. Menu and then select (Re)Index Exact Mass. This will result in a dialog box being displayed ( Figure 36 ). The time to index a library willAll NIST 14 Libraries are alreadyThe names search works over not only the primarySearch tab. To search for the mass spectrum of a plant growth regulator. GIBBERELLIN A9, begin typing the name.

Stop after entering each letter. AfterThis can be an important tool forThe subsequent peaks (158This kind of analysis canThe elements search canThese three numbers are 1) a Match Factor for theSearch Hit List: Match, R. Match and Prob., respectively). The first two numbers are fairlyA perfect match results in a value ofHowever, unknown spectra withBar of the Lib. Search tab) require more explanation. Hit is derived assuming that the compound is represented by a spectrum in the librariesList to get the relative probability that any Hit in the Hit List isThe relative probability of each of the HitsThis value is also derived from the same setIn this case, the correct compound was ignoredThe parameters are theFor example, if a compoundUsing examples fromIn many cases,Generally, any positive value isNegative values below 200 are generally a warningNote that negative values will occur whenIn these cases,Usually in these cases, especially when Match Factors are high, it will provideInformation Spectral Library because each spectrum is indexed according to theThis utility is called from the Main Menu Bar’s Tools menu. Spectra similar to the searched spectrum make up the Hit List. There isNot only is the utility useful in determiningAPCI, APPI, and electrospray. This use is described in more detail below. Just below theThe result of molecular weight estimation from the Hit. List is presented on the right side of the dialog box (useful for EIThere are twoPresent and Prob. Absent. These two panes contain a list ofIf one of theThe list box displays all the substructuresThis dialog box is used to createThe list of all possibleThe first time a customized list isSubstructures may be omittedOmit ? or a Add a. The usual Windows conventions forAfter selecting the first substructure of theThis will select all substructures between the first and last. MultipleThis dialog box, as well as the Substructure. Information dialog box, has a Help button, which displays a context?sensitive.

Help screen. They are basedMass Spectral Library Searching” J. Am. Soc. Mass Spectrom. 1995,Substructure Information in Making Determination about an Unknown Mass SpectrumThis type of search isSearch has been optimized for this purpose. The resulting Hit List wasBased on thisThe evaluation revealed that there was an 89 probabilityContinued evaluation of the Prob. Present and Prob. Absent panes in the Substructure Identification CID data. In the example cited above, if the unknown was believed to be aData Systems These may be found inSearch Program’s working directory (location of the history, Hits, etc.). Two other items refer to AMDIS and its connection to the MS Search. FILSPEC.FIL, resides. Search Program. This second locator file contains the text string thatIt is possible to stateList pane are to be added to or replaced by the automatic import. AnAPPEND is the instruction as to how the spectra are added to the Spec List. Window. To enable switching the focus back from the MS Search Program,MS Search Program is brought into focus and spectra are imported. Figure 41 illustrates the implementation. TheNumber of Hits is determined by the “Number ofIf SDfile contains more than oneSee section USE WITH THIRD-PARTYSearch command. If a structure is in the Spec List pane of the Lib. Search tab or a structure is associated with a spectrum, this structure canMouse button (RMB) menu with the Mouse pointer on the spectrum containing aSearch Program saves a structure to the Windows Clipboard using the Right. Mouse button menu’s command Copy Structure to Clipboard, the structureClipboard.MOL is written to the NIST MS Search Program’s directory (byOther programs can either use the structure asWindows Clipboard may be accepted in the MS Search Program’s Librarian Structure Editor. WIN.INI file). Each line should contain three double?quoted strings separatedUPDATE or CREATE the AUTOIMP.STR file, or the AUTOIMP.

STR fileProgram by issuing the command: Search Program is in the C:\NIST11\MSSEARCH directory; if it is inNIST MS Search Program above) If there is aINSTRUMENT DATA SYSTEMS section above). Up to 127 MS libraries, including theLibraries, or they may be searched separately. The Program allowsThe inclusion of librariesThis subdirectoryThe spectra and compound information are put in these files through the Librarian Spectra can be edited using with the Edit. Spectrum button in the Librarian tab Tool Bar Figure 43 This will call up the Spectrum Information dialog box Figure 42. This dialog box can be used toIn additionBar ( Figure 43 ). Any spectrumSearch tab, Other Search tab,Search tab or the Compare The size of a user libraryThey also include theA Tag is the name of a Field heading that willThis can be a line of characters without spaces, aInformation dialog box of a Spec List or a user library spectrum: When the Tags have beenMore specificHelp file. Spectra A file can contain as many spectra as wanted. Each spectrum must start withThere must be something in this field in order forThe next required Field title is “Num Peaks:”.The field with the. Field title “Num Peaks:”.C6H6 (Optional, up to 23 characters) It does not actuallyThe VERY NEXT line and subsequent lines MUST containThe exact spacing and delimiters used for the. For example, the peaks above couldThe following characters are accepted as delimitersThis is the recognizedSpectrum GC Column Type associated with it. Currently, there are 3 specific Column TypesRI of these two columnRI column type to any of the three specific Column Types. Information window, RI values of the first example (Benzene) are displayed as JCAMP file as NIST MS Search picks up only one of them according toThey are described inAUTOIMP Files Used in NIST MS Search AUTOIMP.MSD as the primary locator file used for the importation of spectraAUTOIMP.STR has been entered in the “File name:” field.

The default settingsThe file can be renamed by highlightingIn this case, the file will be saved with the extension provided inNotepad Save As option, also make sure the ANSI Encoding isEncoding are set correctly, press the Save button. NIST MS Search Program with ChemStation Technologies ChemStation.Standard Quantitation, or Gasoline mode; and on the Lib.MS Library (NIST 14) setup will install the two required macros along withChemStation double-click option on a displayed spectrum to send that spectrumSearch Program into focus. If the appropriate options (including Automation,Quantitation mode on any version of ChemStation, the setup will automaticallySearch, Multiple Lib PBM Search, and Set Default Search Engine ). Each of these menu options is explained below. If these options are to beMass Spectral Database program folder. The Macro NISTINT.MAC must beThe spectrum will be prepended to the NIST MS Search Program’s Spec. List Window. If the NIST MS Search Program is configured to searchOtherwise, double clicking on any spectrumSearch tab to start aSearch (LS.mac) performs a ChemStation PBM Search using up to threeEngine (SWITCH.MAC)The NIST MS Search is the default until another search type is set asMS Search Program user libraries. Once in AMDIS, select Run to perform theProgram. This program allows mass spectral libraries that have beenThis utility is evoked as an option from the Options for NIST Library Search This macro is to be incorporated into automated sequences. It automaticallyIf the properThese features can only be utilizedInformation Regarding Modes Other Than Enhanced Quantitation Program has been selected as the ChemStation’s default search engine, eachThe NIST MS. Search Program will be brought into focus regardless of the dataEnvironmental). One of the other above-referenced search methods can beMass Spectral Database program folder. Library Search dialog box is displayed ( Figure 48 ).

This dialog box consists of six options and OK and Cancel Use the MouseFor NIST Library Search dialog box are selected by putting the MouseIf any of the firstThis file contains theHPNIST.TXT, the second locator file, is created, a text file named TEMPSPEC.MSPThe text file isThis text file willSearch Program comes into focus, the spectra that have been saved in the. ChemStation software are automatically copied to the Spec List Window. If spectra are already in the Spec List Window, a prompt to Prepend If Prepend Caller upon Completion have been selected in the Automation dialogSearch” Spectra File option runs the ChemStation’s Autointegrate routine onSpectrum in X option creates a text file that contains the spectrum that isThis is where background-subtracted andThis is the currently displayed spectrum. Spectrum in X option appends the spectrum in X of the Stack display to theIntegd. Spect. File option creates a text file that contains spectraIf Automatic. Search On in the NIST MS Search Program’s Automation dialog box hasThe results are optionallyHistory. If Return Focus to Caller upon Completion has been selected inLibrary Program option either starts the NIST MS Search Program orThe ChemStation software can beLib to NIST Format option is described in APPENDIX 3. Method. Every Method directory contains a file DEUSER.MAC. Edit this file toThe focus is thenThe spectra are imported intoIf spectra are already in the Spec. List Window, they will be overwritten. Focus to Caller upon Completion have been selected in the NIST MS Search. Program’s Automation dialog box, the spectra will automatically beMS software. In order for this macro to function properly, it will beChemStation and Other Database to NIST User Library Format Database program folder. This program allows mass spectral libraries in aFor all 32-bit WindowsProgram. The use of the HP2NIST program is described at the end ofMS Search Program.

The drop-down arrow will also allow for selecting from aMore than a single library can be selected in thisThis will result in the display of the Browse for. Folder dialog box ( FigureDefine Subset dialog box. Options dialog box display. This allows for the entry of massAdvanced features of Lib2NIST areTransliterationHPTRANS.TBL and may be modified in this file by the user. NIST MS Search Program with Thermo Fisher Corporation Xcalibur Software Library (dll) as a library search engine. A copy of the NIST MS Search. Program and AMDIS may be provided with a copy of the XcaliburXcalibur software, run the NIST 14 MS Library setup. If it locates theMS Search installed in another directory (for example, c:\nist11\mssearch). WITH INSTRUMENT DATA SYSTEMS section of this manual. Algorithms MS Search Program can retrieve library spectra that resemble the submittedOnly experimental variability prevents a perfect match. The Similarity. Search is optimized to find similar compounds and is intended for use whenWhile this can vastly reduceWhen this occurs,This is probably the most serious failure of any mass spectral search system. These algorithms were. Selected Replicates Library. The best performing algorithm used “a rankedThis finds library spectra with the largest number of peaks in common with theThis procedureThis is the screening logic of the Quick Identity Both peak scaling and merging of multiple screening results are used in the Normal. Identity Search. A more detailed description follows: The most intense peak in the scaledThis is repeated in decreasing order of intensity of peaks in the scaledThis is the onlyAfter extensive optimization studies, four separate peak specifications wereSearch.