一、软件介绍：
Mascot
- Mascot results can be exported in several different formats. The .dat results format can be converted to PRIDEXML using the PRIDE Converter tool. The mzIdentML format can be uploaded to PRIDE and if the peak list files are also provided then results can be viewed using the PRIDE Inspector.
- Mascot results exported in csv format, along with peak list files, can be uploaded to MS-Viewer.
- Mascot Distiller allows viewing of annotated spectra offline from a Mascot Server. To enable this, authors need to supply the .rov and instrument raw files. Distiller also gives access to MS1 quantification results for this data.
MaxQuant
- MaxQuant creates large results folders that contain many different file formats, including raw, peaklist and several different text format results files.If the whole of this folder is provided (zipped together in the correct arrangement) it is possible to view annotated spectra using MaxQuant Viewer . Authors MUST also provide the MaxQuant software (including Viewer) in the version used to create the results to ensure Viewer compatibility.
- Uploading the msms.txt file (in the ‘combined’ folder) and the .apl files (archived together as a single file; e.g. zip file) to MS-Viewer also allows viewing of annotated spectra.
- Annotated spectra can also be visualized from the ‘combined’ folder and mqpar.xml file from the MaxQuant output using PDV.
MS-GF+
- MS-GF+ can export mzIdentML files which, when submitted with corresponding peak list files, allow viewing of results using PRIDE Inspector.
MyriMatch
- MyriMatch can produce pepXML and mzIdentML files. mzIdentML files can be uploaded to PRIDE, along with peak list files, to allow viewing of annotated spectra using PRIDE Inspector. pepXML files, along with peak list files, could be uploaded to MS-Viewer to facilitate annotated spectra.
PEAKS
- PEAKS can export mzIdentML files which, when submitted with corresponding peak list files, allows viewing of results using PRIDE Inspector.
OMSSA
- OMSSA xml results files can be converted into PRIDEXML using PRIDE Converter or into mzIdentML using the mzidLibrary. The PRIDEXML file or mzIdentML along with peak list files allow viewing of annotated spectra using PRIDE Inspector. PRIDEXML can also be uploaded to MS-Viewer.
ProteinPilot
- ProteinPilot version 5.0 can natively export mzIdentML. Submission of mzIdentML file/s along with corresponding peak list file/s allows viewing of spectra using PRIDE Inspector. ProteinPilot results files (.group) can also be opened using the ProteinPilot software to allow visualization of annotated spectra.
- For earlier versions of ProteinPilot: ProteinPilot .xml files, combined with peak lists, can be viewed using ProteinPilot.
- ProteinPilot tab-delimited output, along with peaklists, need very minor changes before being viewable using MS-Viewer.
Protein Prospector
- Protein Prospector tab-delimited text results files, along with peak list files can be uploaded to MS-Viewer to provide annotated spectra.
ProteomeDiscoverer
- msf results files can be viewed using Proteome Discoverer Viewer or uploaded to MS-Viewer.
- For analyses performed on Proteome Discoverer 2.0 and above, annotated spectra can be viewed from the .pdResult files generated from the consensus workflow output.
- ProCon can convert msf files into mzIdentML files. Submission of mzIdentML file/s along with corresponding peak list file/s allows viewing of spectra using PRIDE Inspector.
Scaffold
- Scaffold results files (.sf3) can be viewed using Scaffold Viewer.
- Scaffold results can be exported as mzIdentML files and then uploaded to PRIDE to allow viewing of annotated spectra using PRIDE Inspector.
TPP/ Protein/Peptide Prophet
- pepXML files, along with peak list files, can be uploaded to MS-Viewer to provide annotated spectra.
X!Tandem
- X!Tandem results files can be converted into PRIDEXML using PRIDE Converter or into mzIdentML using the mzIdLibrary. The PRIDEXML file or mzIdentML along with peak list files allow viewing of annotated spectra using PRIDE Inspector. PRIDEXML can also be uploaded to MS-Viewer.
- X!Tandem tab-delimited file (spreadsheet format), along with peak list files, can be uploaded to MS-Viewer.
Scaffold DIA
Scaffold DIA produces a publication report listing all parameters and settings used in the analysis, as well as a supplementary data export that reports all quantitative results and the parameters used in any statistical analysis performed. Scaffold DIA results files (.sdia), which retain all MS1 and MS2 XIC information for quantified peptides, can be viewed using the free Scaffold DIA Viewer.
Skyline
Results in .sky files can be viewed using Skyline, or be made available via deposition to PanoramaPublic. Results as a .blib spectral library can also be viewed in Skyline following these instructions.
Spectronaut
A finalized Spectronaut analysis can be exported as a .SNE file. SNE files can be loaded by the standard Spectronaut software or using the Spectronaut Viewer. Among other information .SNE files contain all the scoring and peak integration information. Optionally, all the MS1 and MS2 ion traces (XIC data) can be saved with an .SNE file. After loading an .SNE file, the original raw files can also be mapped back to the experiment. This is needed to visualize apex MS1 and MS2 spectra. Further, if the ion traces have not been saved to the .SNE files they can also be re extracted from the raw files to the loaded experiment. Hence, with the .SNE file and the corresponding raw files one can browse through the apex MS1/MS2 spectra as well as MS1/MS2 ion traces.
二、下载链接
Mascot Distiller: The latest version of Mascot Distiller can be downloaded from Matrix Science here:
http://www.matrixscience.com/distiller_download.html
The software will operate as a viewer of existing Mascot Distiller projects without a license, but a license is required to create new projects.
MS-Viewer: MS-Viewer is part of the Protein Prospector package. This is a web-based software (no installation required) and can be accessed here:
http://prospector2.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer
Authors MUST upload their spectra to MS-Viewer in the formats as described above. Upon successful upload, a unique permanent search key to access the spectra will be generated, which will need to be included in the manuscript.
Instructions and links to video tutorials on the use of this software can be found here:
http://prospector2.ucsf.edu/prospector/html/instruct/viewerman.htm
mzidLibrary:This software can be downloaded from:
https://code.google.com/p/mzidentml-lib/
PDV: PDV is an integrative proteomics data viewer that can be downloaded from https://github.com/wenbostar/PDV
PRIDE Converter: The latest version of the Converter can be downloaded from here:
https://code.google.com/p/pride-converter-2/
PRIDE Inspector: The latest version of PRIDE Inspector can be downloaded from here:
https://github.com/PRIDE-Toolsuite/pride-inspector/releases
ProCon: This tool can be downloaded from:
http://www.ruhr-uni-bochum.de/mpc/software/ProCon/
Protein Pilot: A trial version of Protein Pilot can be downloaded from Sciex here:
https://licensing.absciex.com/download/index
A license is required to use the full package, but it can be used as a viewer without a license.
Proteome Discoverer Viewer: Go to http://portal.thermo-brims.com and create an account. After the account has been created, go to the Proteome Discoverer tab, downloads, update existing software if needed (be sure to follow instructions on prerequisite software required to run Proteome Discoverer) and download Proteome Discoverer. A trial version of Proteome Discoverer will be installed on your computer which is fully functional. After 30 days the trial version will only act as a viewer of output files.
Scaffold Viewer: Proteome Software’s free viewer can be downloaded from here:
http://www.proteomesoftware.com/products/free-viewer/
Skyline: Skyline can be downloaded for free at: https://skyline.ms
Panorama can be accessed here: https://panoramaweb.org
Spectronaut: To download Spectronaut Viewer please visit
https://www.biognosys.com/technology/spectronaut-viewer and apply for a free license.
参考文章：
1.https://www.mcponline.org/page/content/annotated-spectra
2.https://www.mcponline.org/page/DIA-guidelines
