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1. Peptideshaker Github
2. Peptideshaker

PeptideShaker is a feature-packed piece of software aimed at chemists, biologists, physicists and other profesionalls that need to analyze proteins and peptides. PeptideShaker 1.1.3: 蛋白数据库获取和显示蛋白序列识别结果软件: VPLG 20150917: 可视化的蛋白质-配体相互作用图软件: 以上软件，除特别注明外，均在生物软件DVD光盘1中。. In PeptideShaker the 'confidence' is just 1-PEP. So if you got FDR, FNR, and PEP the most difficult is done! When you set a 95% confidence threshold, the tool goes from the best scoring hits to the worse, and stops just before the first one going under 95%. A colleague just SearchGUI/Peptideshaker using the latest Galaxy wrapper and got: java.lang.IllegalArgumentException: Only one site found in peptide score to position map when estimating the A-score for spectrum 20180613HPChloroMeOHC8.

Released:

MS²ReScore: Sensitive PSM rescoring with predicted MS² peak intensities and retention times.

Project description

Sensitive peptide identification rescoring with predicted spectra usingMS²PIP,DeepLC, andPercolator.

• Usage

About MS²ReScore

MS²ReScore performs sensitive peptide identification rescoring with predictedspectra using MS²PIP,DeepLC, andPercolator. This results in more confidentpeptide identifications, which allows you to get more peptide IDs at the same falsediscovery rate (FDR) threshold, or to set a more stringent FDR threshold while stillretaining a similar number of peptide IDs. MS²ReScore is ideal for challengingproteomics identification workflows, such as proteogenomics, metaproteomics, orimmunopeptidomics.

MS²ReScore uses identifications from aPercolator IN (PIN) file,or from the output of one of these search engines:

• MaxQuant: Start from msms.txt identificationfile and directory with .mgf files. (Be sure to export without FDRfiltering!)
• MSGFPlus: Start with an .mzididentification file and corresponding .mgf.
• X!Tandem: Start with an X!Tandem .xmlidentification file and corresponding .mgf.
• PeptideShaker: Start with aPeptideShaker Extended PSM Report and corresponding .mgf file.

If you use MS²ReScore for your research, please cite the following article:

Accurate peptide fragmentation predictions allow data driven approaches to replaceand improve upon proteomics search engine scoring functions. Ana S C Silva, RobbinBouwmeester, Lennart Martens, and Sven Degroeve. Bioinformatics (2019)doi:10.1093/bioinformatics/btz383

To replicate the experiments described in this article, check out thepub branch of this repository.

Installation

MS²ReScore requires:

• Python 3.7 or higher on Linux, macOS, orWindows Subsystem for Linux
• If the option run_percolator is set to True,Percolator needs to be callable with thepercolator command (tested withversion 3.02.1)
• Some pipelines require the Percolator converters, such as tandem2pin, as well. Theseare usually installed alongside Percolator.

Minimal installation:

Recommended installation, including DeepLC for retention time prediction:

We recommend using a venv orconda virtual environment.

Usage

Command line interface

Run MS²ReScore from the command line as follows:

Run ms2rescore --help to see all command line options.

Configuration file

MS²ReScore can be further configured through a JSON configuration file. A correctconfiguration is required to, for example, correctly parse the peptide modificationsfrom the search engine output. If no configuration file is passed, or some options arenot configured, thedefault valuesfor these settings will be used. Options passed from the command line will overridethe configuration file. The full configuration is validated against aJSON Schema.

A full example configuration file can be found inms2rescore/package_data/config_default.json.

The config file contains three top level categories (general, ms2pip andpercolator) and an additional categories for specific search engines(e.g. maxquant). The most important options in general are:

• pipeline(string): Pipeline to use, depending on input format. Must be one of:['infer', 'pin', 'tandem', 'maxquant', 'msgfplus', 'peptideshaker']. Default: infer.
• feature_sets(array): Feature sets for which to generate PIN files andoptionally run Percolator. Default: ['all'].
  • Items(string): Must be one of:['all', 'ms2pip_rt', 'searchengine', 'rt', 'ms2pip'].

An overview of all options can be found in configuration.md

Notes for specific search engines

• MSGFPlus: Run MSGFPlus in a concatenated target-decoy search, with the-addFeatures 1 flag.
• MaxQuant:
  • Run MaxQuant without FDR filtering (set to 1)
  • MaxQuant requires additional options in the configuration file:
    • modification_mapping: Maps MaxQuant output to MS²PIP modifications list.Keys must contain MaxQuant's two-letter modification codes and values must matchone of the modifications listed in the MS²PIP configuration (seeMS2PIP config).
    • fixed_modifications: Must list all modifications set as fixed during theMaxQuant search (as this is not denoted in the msms.txt file). Keys refer to theamino acid, values to the modification name used in the MS²PIP configuration.

Peptideshaker Github

Output

Several intermediate files are created when the entire pipeline is run. These can beaccessed by specifying the tmp_dir option. Depending on whether or not Percolator isrun, the following output files can be expected:

For each feature set (e.g. all, ms2pip, searchengine...):

Peptideshaker

• <file>.pin Percolator IN file
• <file>.pout Percolator OUT file with target PSMs
• <file>.pout_dec Percolator OUT file with decoy PSMs
• <file>.weights Internal feature weights used by Percolator's scoring function.

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2.0.0b5 pre-release

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2.0.0b3 pre-release

2.0.0b2 pre-release

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