Re: Masslynx User Guide
Elpidio Heart
This user guide provides details and procedures that explain how to use the graphic user interface (GUI) of the Waters MassLynx Laboratory Information Management System (LIMS) interface. 715008798 replaces 715005112.
The MassLynx LIMS Interface help system provides instructions on the use of the MassLynx LIMS Interface application. This Help system and the MassLynx LIMS Interface application are intended for professionally trained and qualified laboratory personnel wh...
This disk imaging procedure documents the application of a Windows 10 Enterprise Long Term Servicing Channel (LTSC) 2021 customized image in English for an Optiplex 7000 Micro computer. This is for MassLynx software for the ACQUITYTM QDaTM Detector and RA...
This user guide explains how the Waters ICF Support Layer 3.7 is used to access Gas Chromatography (GC) and the CTC PAL3 autosampler instruments using Waters applications, such as Empower Chromatography Data System (CDS) and MassLynx software.It also ex...
The attached reference guide covers the Informatics Workstation for MassLynx P-520 Windows 7. It includes preparing the system, establishing BIOS settings and preparing for re-imaging, re-imaging the disk, initializing and configuring system settings, Win...
IonLynx software is a component of MassLynx software and is a constituent of the RenataDX Screening System. IonLynx is intended to process mass spectrometry data based on user-specified parameters to identify and quantify organic compounds contained in hu...
NIST Peptide Library Browser (NIST MS Search) is a 32-bit Windows application for browsing and searching mass spectral libraries. A small peptide MS/MS library, BSA, is included. You can also download other peptide libraries.
This program may import centroided mass spectra from mgf, msp, dta, pkl, mzXML, and mzData files and search them in MS/MS or MS libraries. NIST MS Search displays the imported and library spectra and provides various ways for visual comparison of the searched, found and imported spectra. The imported and library mass spectra may be exported in plain text format, msp.
NIST MS Search may be configured to import and search mass spectra directly from another application (e.g. AMDIS, Xcalibur, MassLynx, ChemStation, etc.) The search results may be saved in a text file. See user's guide for details.
Note: The peptide software does not contain the NIST/EPA/NIH Mass Spectral Library for interpretation of EI mass spectra. However, NIST Peptide Library Browser (NIST MS Search) is fully compatible with NIST EI and small molecules MS/MS libraries.
The installed software includes bovine serum albumin (BSA) peptide MS/MS library.To obtain other peptide libraries, please visit a compressed library folder from a link ending with nist.tar.gz, expand into the folder where the BSA library folder has been installed, and restart the NIST MS Search to connect it to the newly installed library.
NIST Peptide Library Browser (NIST MS Search) and BSA Library Installer, NIST_PEP.exe, may be redistributed without restriction. The user may make and distribute unlimited copies of the Installer. You may not alter or modify the Installer program or create a new Installer for the NIST Peptide Library Browser (NIST MS Search) and BSA Library.Peptide mass spectral libraries are freely available; however, the libraries may not be redistributed without permission.The National Institute of Standards and Technology (NIST) uses its best efforts to deliver high-quality reference data and software products. However, NIST makes no warranties to that effect; and NIST shall not be liable for any damage that may result from the use of the above mentioned products.Certain commercial equipment, instruments, or materials are identified in this document. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products identified are necessarily the best available for the purpose.
I was wondering if the new version of Skyline (v.4.2) allows to export SRM methods to MassLynx version 4.2. Last year I was unable to do so and I received a response that Waters was working on making it possible. As a solution to the problem I have been exporting the method to a computer not connected to the equipment (Xevo TQ-XS) and to an older version of MassLynx (v.4.1). Do you know if it is possible now to export directly to MassLynx 4.2?
This turned out to be a compatibility issue between a DLL in MassLynx and the method export DLL Waters gives us to write their methods, which they were able to fix for their case with an updated DLL in MassLynx.
"We looked into this earlier today and it appears that it can be case specific. The customer should probably contact her/his local support team to get an updated software version or a copy of the required library but we should probably review this on a case by case basis. I have cc-ed one of our GSS colleagues so that they are aware this as well and can provide assistance."
The following MassLynx 4.2 versions are supported. Please note that these are tandem/triple quadrupole instrument releases. If the instrument type is not listed, please contact the local service support organization for advise.
During installation, also specify the instrument and the TargetLynx application manager. The former is required to create a method template and the latter to populate the newly created method with the SRM/MRM transitions.
Please be aware that even with the above MassLynx4.2 SCNs, if MassLynx Security is installed method export from Skyline may fail, all be it with a different error message. Do not install MassLynx Security option if you intend to export methods from Skyline.
Dear,
We have a Xevo-TQXS in the laboratory, and usually we like to export the method in a computer that is not connected to the instrument (just for our convenience).
We have been using two computers for that in which we installed MassLynx older version (v.4.1). We would like to use other computers or even laptops to export the MRM method but we understand it is necessary to install MassLynx software in the same computer in which Skyline is also installed for the method to be exported correctly? Is that true and necessary?Do I always have to install the MassLynx software together with Skyline to export the method? Thank you very much. Best, Daniela
The PC being used to export an MRM method must have both a supported version of MassLynx and a copy of the TargetLynx application manager installed, as well as Skyline. Supported MassLynx versions are listed in this article on support.waters.com
_Inf/MassLynx/WKB92770_With_which_MassLynx_42_SCNs_can_Skyline_be_used_to_successfully_export_MRM_methods
Note that only MassLynx 4.2 software change notes (SCNs) support this, not MassLynx 4.1 that you say you're using. Please contact your local Waters service organisation via iRequest for assistance with workarounds that may allow Skyline to export MRM methods using MassLynx 4.1
Dear Neil,
Thank you for your reply. We have called our Waters MS specialist to install MassLynx 4.2 (SCN982) for us, and we followed your recommendation regarding installation in the case the computer is not connect to the instrument . Unfortunantly, we are unable to export the method. Now we are getting a different error (attached). Could you help us understand what may be going on. Thank you very much. Best, Daniela
I wonder if the users reporting the issues here were able to solve the problem. We recently got the latest version of Masslynx and were no longer able to export methods. I was getting the error about the library file not been able to be found. After looking into Skyline support, I was able to find that targetlynx is also needed. Yesterday, masslynx along with targetlynx was reinstalled, but now I am getting the error "ERROR: Method not found: 'Boolean CompoundDatabaseClassLibrary.CompoundDatabase.InsertNewIonDetails(Int32, Int32, TransMode, Int32, Int32, Int32, Int32, Int32, Int32)'."
The error message you're seeing is a known issue with some MassLynx SCNs. If you click on the link in my reply to Danielacgranato it takes you to a waters support article explaining which SCNs work, and which don't. If your SCN is one of those listed in that article as not working with Skyline please raise an iRequest via the Waters website mentioning the above support article. It may be possible to provide you with a solution to enable other MassLynx 4.2 SCNs to work with Skyline.
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