MSnID-package


    Extracts MS/MS ID data from mzIdentML (leveraging <a rd-options="" href="/link/mzID?package=MSnID&version=1.6.0" data-mini-rdoc="MSnID::mzID">mzID</a> package) 
    or text files. After collating the search results from multiple datasets 
    it assesses their identification quality and optimize filtering criteria 
    to achieve the maximal identifications at a user specified false discovery 
    rate. Additional utilities include:
    <ol>
<li>
            post-experimental recalibration of mass measurement accuracy 
        
        </li>
<li>
            assessment of irregular and missed cleavages given the 
            enzyme cleavage pattern 
        
        </li>
<li>
            assessment of false discovery rates at peptide-to-spectrum match, 
            unique peptide and protein levels
        
        </li>
<li>
            leverages brute-force and sophisticated optimization routines 
            (Nelder-Mead and simulated annealing) for finding the filtering 
            criteria that provide the maximum spectrum, peptide or protein 
            identifications while not exceeding a corresponding preset 
            threshold of false discovery rate
        </li>
<li>
            converts the results into MSnSet class object as 
            spectral counting data
        
    </li>
</ol><p></p><p></p>

package

Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or
text files. After collating the search results from multiple datasets it
assesses their identification quality and optimize filtering criteria to
achieve the maximum number of identifications while not exceeding a
specified false discovery rate. Also contains a number of utilities to
explore the MS/MS results and assess missed and irregular enzymatic
cleavages, mass measurement accuracy, etc.

Vlad Petyuk

MSnID

Utilities for Exploration and Assessment of Confidence of
LC-MSn Proteomics Identifications.

MSnID-package function

Extracts MS/MS ID data from mzIdentML (leveraging <a href="mzID" rd-options="">mzID</a> package) 
    or text files. After collating the search results from multiple datasets 
    it assesses their identification quality and optimize filtering criteria 
    to achieve the maximal identifications at a user specified false discovery 
    rate. Additional utilities include:
    <ol><li>post-experimental recalibration of mass measurement accuracy</li></ol>
        <item>assessment of irregular and missed cleavages given the 
            enzyme cleavage pattern</item>
        <item>assessment of false discovery rates at peptide-to-spectrum match, 
            unique peptide and protein levels</item>
        <item>leverages brute-force and sophisticated optimization routines 
            (Nelder-Mead and simulated annealing) for finding the filtering 
            criteria that provide the maximum spectrum, peptide or protein 
            identifications while not exceeding a corresponding preset 
            threshold of false discovery rate</item>
        <item>converts the results into MSnSet class object as 
            spectral counting data</item>

MSnID-package: MSnID: Utilities for Handling MS/MS Identifications

Description

Arguments

Details