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+ | ====== NIST MSQC Pipeline ====== | ||
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+ | <WRAP center round important 60%> | ||
+ | **Attention**: | ||
+ | </ | ||
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+ | |||
+ | ===== Software for Monitoring LC-MS Performance ===== | ||
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+ | This program was written to systematically evaluate analytical performance of a common discovery-based proteomics platform by monitoring selected output from a liquid chromatography -mass spectrometry (LC-MS/MS) system. The software was developed to help researchers identify sources of variations due to analytical problems. The idea behind the software is that if analytical variations can be minimized using defined mixtures and metrics, variations due to biological differences in complex samples can be more confidently identified. | ||
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+ | NIST MSQC expects that the MS/MS spectra are produced from analysis of a tryptic digest of a protein mixture. However, future releases will allow any set of MS/MS data files, such as those from analysis of metabolites or other small molecules and can be identified by a spectral library search, to be used. Typically, data files might come from routine analysis of a QC standard over time but may be from different instruments in the same or different laboratories. Analysis is carried out by calculating and comparing a defined set of data metrics from one or more set of MS data files. The use of this program does not require any new data acquisition; | ||
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+ | This software contains many component software applications which are controlled by a single Perl program. The software is intended to be run as a " | ||
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+ | **Important Note on Data Formats**: Use of this version is limited to analysis of data acquired on Thermo Scientific ion traps (e.g., LTQ, LTQ-Orbitrap, | ||
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+ | ===== Additional Requirements ===== | ||
+ | |||
+ | * Program runs under Microsoft© Windows™ operation system (XP or later versions) | ||
+ | * XCalibur™ (preferably the same version used on the data acquisition computer) or [[http:// | ||
+ | * Perl (freely available from (freely available from [[http:// | ||
+ | |||
+ | ===== Download and Installation Instruction ===== | ||
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+ | <WRAP center round important 60%> | ||
+ | **Attention**: | ||
+ | </ | ||
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+ | * 1. Download the NIST MSQC Pipeline software appropriate for your Windows operation system. If you are in doubt, select 32-bit version. | ||
+ | <WRAP center 70%> | ||
+ | | [[https:// | ||
+ | </ | ||
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+ | * 2. Extract the NIST MSQC Pipeline zip archive in a working directory on your hard drive (e.g., C: | ||
+ | |||
+ | * 3. One or more search library/ | ||
+ | |||
+ | ===== Operating Instructions ===== | ||
+ | |||
+ | <WRAP group> | ||
+ | <WRAP half column> | ||
+ | {{: | ||
+ | <wrap lo> | ||
+ | </ | ||
+ | |||
+ | <WRAP half column> | ||
+ | The main window of the program is divided into three tabs: | ||
+ | * [[# | ||
+ | * [[# | ||
+ | * [[# | ||
+ | |||
+ | More detailed description for each tab is followed. | ||
+ | |||
+ | </ | ||
+ | </ | ||
+ | |||
+ | ==== Settings ==== | ||
+ | |||
+ | * **Input directories**: | ||
+ | * **Output directory selection**: | ||
+ | * **Report file name**: The name of the report file is automatically generated by the program using the format // | ||
+ | * **Instrument types**: It is used to specify the instrument model used to generate the data. If ORBI or FT is specified, precursor tolerance will be reduced and monoisotopic precursor masses will be used. Additionally, | ||
+ | * **Search engines**: The three options are MSPepSearch, | ||
+ | * **Sort**: The option is used to order the runs as columns in the final output file. If names of files give a better ordering (" | ||
+ | * **Mode**: In the Full running mode additional peptide and protein-level analysis will be performed. NOTE: Information generated in the output by specifying this option is experimental and no documentation is available. | ||
+ | * **Optional Settings** | ||
+ | * **Fasta File**: | ||
+ | * **Overwrite all**: If checked, all processing on RAW files will be repeated and any output files will be overwritten. Useful if converter has been updated, for example. | ||
+ | * **Overwrite searches**: If checked, searches will re-run and older output files (TSV or pepXML) will be overwritten. Peak list converter (i.e., ReAdW4Mascot2) will not re-run. | ||
+ | * **No peptide**: If checked, only a spectral library search engine is allowed and FASTA option is ignored. Useful if searching a library of metabolite MS/MS spectra. | ||
+ | * **ProMS**: If checked, results from ProMS, a NIST - developed MS1 data analysis program, will be used instead of values calculated by ReAdW4Mascot2. ProMS requires MS1 profile spectra mzXML format, so these (large) files will additionally be generated during data conversions. ProMS' | ||
+ | * **Create log file**: If checked, output from the pipeline will be sent to a log file. These files can be viewed in the " | ||
+ | * **Verbose**: | ||
+ | * **Ini tag**: Name of tag in scripts\ms.ini file, (e.g, test}. This option allows manual editing of a section of the ms.ini file. This may be used to re-run an analysis after changing the ordering of files or by grouping them as series. To group a set of runs by series, insert SERIES between FILE links. In order to use this option, edit the value between the braces in ms.ini and save the file. NOTE: Editing this file incorrectly may cause problems; use caution when editing the file. Additionally, | ||
+ | |||
+ | ==== Run Progress ==== | ||
+ | |||
+ | <WRAP group> | ||
+ | <WRAP half column> | ||
+ | {{: | ||
+ | <wrap lo> | ||
+ | </ | ||
+ | |||
+ | <WRAP half column> | ||
+ | |||
+ | * While processing the data NIST MSQC Pipeline will display output information in the output box found in **Run Progress** tab. By checking the “Verbose” option on “Settings” tab the user can see more information on run progress | ||
+ | * Errors - Any errors encountered during the processing of a run will be displayed in the error box found in “Run Progress” tab. | ||
+ | |||
+ | </ | ||
+ | </ | ||
+ | |||
+ | ==== Reports / Logs ==== | ||
+ | |||
+ | <WRAP group> | ||
+ | <WRAP half column> | ||
+ | {{: | ||
+ | <wrap lo> | ||
+ | </ | ||
+ | |||
+ | <WRAP half column> | ||
+ | |||
+ | * Every run generates a number of different logs and reports. These reports can be viewed in “Reports / Logs” tab. The top list displays the name of the report. The report name is identical to the name of the folder selected in output directory path. Clicking on a report name will populate the bottom list which contains list of files generated during a run | ||
+ | * The list of report files can be filtered to view only the desired files. | ||
+ | |||
+ | </ | ||
+ | </ | ||
+ | ---- | ||
+ | |||
+ | ===== Additional Information ===== | ||
+ | |||
+ | This document is intended to provide instructions on how to run the NIST MSQC software on your computer. The metrics and benchmark values have been reported in two publications (PubMed IDs: [[http:// | ||
+ | |||
+ | For more background information, | ||
+ | |||
+ | <WRAP center round important 60%> | ||
+ | **Attention**: | ||
+ | </ | ||
+ | |||
+ | |||