=================================== NIST 12 MS/MS Library =================================== This product is a subset of the NIST Standard Reference Database 1A, NIST/EPA/NIH MASS SPECTRAL LIBRARY It also includes NIST MASS SPECTRAL SEARCH PROGRAM Version 2.0g build June 21, 2012 for use with Microsoft(R) Windows(TM) System requirements This MS Search program is a 32-bit Unicode application and thus requires Windows NT 4.0, 2000, XP, Vista, or Windows 7. To install, run the program Setup.exe and then follow instructions. Note: MS Interpreter is not compatible with Windows NT 4.0. This release contains MS/MS libraries (nist_msms and nist_msms2) with 121,586 spectra of 15,180 ions History of the releases: ======================== Release Number of Number of Year spectra(MS/MS) ions (MS/MS) 2005 5,191 1,920 2008 14,802 5,308 2011 95,409 12,568 2012 121,586 15,180 MS/MS library nist_msms (small molecules, di and tri peptides) ======================== #spectra #compounds #ions collision cell 70,491 4,210 6,530 Ion Trap 9,930 4,806 9,069 Total 80,421 5,999 11,634 MS/MS peptide library nist_msms2 (commercially available peptides) ================================ #spectra #compounds #ions collision cell 38,187 899 2,702 Ion Trap 2,978 917 2,978 Total 41,165 1,000 3,546 MS/MS libraries combined ========================= #spectra #compounds #ions collision cell 108,678 5,109 9,232 Ion Trap 12,908 5,723 12,047 Total 121,586 6,999 15,180 Many other NIST MS/MS Peptide libraries ======================================= are available for download free of charge at http://peptide.nist.gov New features of the program and database ======================================== See also "What's New in MS Search Program" topic in MS Search help. o New MS/MS spectra include metabolites, drugs, peptides (biologically active peptides and all di-peptides and tryptic tri-peptides), surfactants, contaminants, sugars, lipids and more. o A new MS/MS search for small molecules Improved ability to identify compounds with a few dominant peaks - a common situation for Tandem MS. More robust scoring for spectra acquired on imperfectly-tuned instruments. o Import of ‘in-source’ tandem spectra, which do not include a defined m/z of the precursor ion. To import these spectra, select "In-source spectra" in Spectrum Import Options. For more details on in-source spectra, search for “in-source” in the MS Search help. o In-source spectra may be searched in MS/MS library with Normal or MS/MS Presearch OFF search options. For this purpose, adding Reverse Search option may useful. o User-selectable precision for importing spectra. o Exact Mass Search and Constraint allows searching for exact mass of a precursor using its mass or exact m/z of a product ion. It takes into account the presence or absence of an electron, adducts or losses; accepts uncertainty in ppm or millimass units, and allows searching for isotopic or monoisotopic peaks. o Ability to use accurate mass to search exact fragment ion mass values in NIST 11 libraries mainlib, replib, and nist_msms using Exact Mass peak type in the Any Peaks Search. o New MS/MS Instrument Type constraint allows displaying in the hit list only spectra measured on Ion Trap, Q-TOF, Triple quadrupole or Other instrument types. These selections may be combined. o New Mass Spectrum Import Options control the number of decimal places in the input m/z set peak intensity threshold set Prepend/Overwrite/Ask automatic mass spectrum import option o Menu selection "Options" / "Best matching only" displays in the Lib. Search Hit List only the best matching spectrum of a compound. In case of MS/MS search, spectra are considered as belonging to the same compound if they have identical names or CAS Registry numbers. In case of peptide names represented as sequence of aminoacids and a charge, both the name and modificatons are compared. There is also a "Best matching only" button on the Lib. Search window tool bar. o A small portion of spectra have more than one CAS Registry number. Each CAS r.n. may be used in CAS r.n. search o Optionally displayed columns Number of synonyms and Number in other databases and a possibility to sort by them. o Sorting Spec List alphabetically. o Handling and searching up to 127 MS libraries instead of 16. o Max. number of spectra in a library has been increased from 786,420 to 1,048,560. o Search for words in mass spectrum text information window (use context menu displayed on right mouse click.) o Optional exclusion of Homologs from the results of Structure Similarity Search (Library Search Options, Search tab). o Import spectra from mzXML and mzData files in addition to mgf, msp, dta, pkl, JCAMP, etc. o An alternative peak matching method has been added to improve the reliability of the score when searching noisy or high resolution MS/MS spectra o Full compatibility with most recent NIST Peptide MS/MS libraries. o Copy selected lines from Hit List or Spec List into Windows Clipboard as tab-delimited Unicode text; this may be conveniently pasted into Excel. To copy, press Ctrl-K. o Tags for searching in Spectrum Text Info have been added to Tags in Comment Constraint. o When a Tag from the "Comment" field is displayed separately, its display in the "Comment" field is suppressed. Some noteworthy features of the program and database are: ========================================================= o MS/MS browsing window and MS/MS library o New type of mass spectrum search: MS/MS Identity search for searching for MS/MS spectra in MS/MS libraries. The updated Lib2NIST converter is a tool for creating MS/MS libraries. To create a MS/MS library, run Lib2NIST and check "MS/MS spectra only" option. The latest version of Lib2NIST may be downloaded from http://chemdata.nist.gov/mass-spc/ms-search/Library_conversion_tool.html For the MS/MS search to work, the MS/MS spectra must contain precursor m/z values. The previously named Similarity "MS\MS" search has been renamed to Similarity "MS/MS in EI" mass spectral library search. o Structure searching - the program will find all chemical structures similar to the structure of the search spectrum. The searching can be done using structural data from the NIST MS database, from the user database or from a structure drawn in most chemical drawing packages. A structure may be exported to chemical drawing software. The Structure similarity search algorithm has been changed: now it Includes homologue recognition that generates a match factor of 1000 for homologs. Homologs may be excluded from the hit list. You will need to rebuild structure search databases in user libraries (as you usually need to do after editing a user library containing structures.) o Searching in the Contributor/Comment spectral records and extracting tagged fields into the displayed spectrum text information. o Drag and Drop - Data can be dragged and dropped between windows. Point mouse to the name of the compound in the spectrum plot window, press and hold the left mouse button, drag the spectrum and drop it into Spec List or Compare Window. o User Library Structures - This feature has been present for some time, but many are unaware of it. o Compare Views - There are a number of different ways for you to visually compare two spectra. o Direct interaction with a number of chemical drawing packages - the clipboard can be used with some of them, most can be used by use of intermediate files. o The NIST MS Search program takes advantages of many normal Windows conventions. Look at the context sensitive options on the right mouse button click and on buttons at the top of the window. Look also for "Keyboard shortcut keys" in the index to the Help or search Help for "short cut keys" o Thermodynamics-based MS Interpreter program version 2.0. A spectrum with a structure may be sent to MS Interpreter by right-clicking the windows with a mass spectrum and structure and selecting Send To MS Interpreter. A spectrum and/or structure may be pasted or dragged and dropped into the Mass Spectrum or Structure panes of MS Interpreter. Release notes ================= o Vista and Windows 7 specific (1) To restore connections between NIST MS software and other applications designed for or adapted to Vista or 7, select the "Connect NIST MS software" shortcut created by the setup. You may be asked to enter the administrative credentials. The program, nistlink_admin.exe, is executed momentarily and updates contents of the win.ini file located in Windows folder. This is needed because NIST MS software running in unelevated (that is, without a full administrative privileges) mode cannot make any changes to win.ini. Alternatively, one may run as Administrator and then shutdown the MS Search and AMDIS. This will also update the contents of win.ini. (2) For use with legacy instrument data systems under Windows Vista or 7 (as described in the MS Search v.2.0 Manual, section "Use with Instrument Data Systems") it may be necessary to change the NISTMS section of the user's virtualized copy of win.ini file. Under Windows Vista or 7, each user may have two copies of win.ini: the global win.ini located in Windows folder and the user's virtualized copy created by legacy applications. The setup modifies only the global win.ini; it doesn't modify the user's virtualized copy. If the user's virtualized copy of win.ini exists the legacy applications read from it instead of the global win.ini located in Windows folder. An attempt by a legacy application running in unelevated mode to modify win.ini actually creates or updates the user's virtualized copy of win.ini. To apply the necessary changes to your virtualized copy of the win.ini file, run (open) the nistlink_user.exe application. The nistlink_user.exe application is located in the MS Search program directory, "c:\nist11\mssearch" by default. If you installed only AMDIS then nistlink_user.exe is in the AMDIS program directory, "c:\nist11\amdis32" by default. Look for the user's virtualized copy of win.ini in the folder %localappdata%\VirtualStore\Windows or, typically, c:\Users\Username.Userdomain\AppData\Local\VirtualStore\Windows To apply changes to the global win.ini, one needs to run the nistlink_admin.exe application, which requires administrative credentials. o 64-bit-specific (3) Isotopes Calculator cannot be run under 64-bit Windows. Therefore, its shortcut is not installed under 64-bit Windows.