APEX_ORBI

APEX_LCQ

This dataset contains training ThermoFinnigan LTQ-OrbiTrap (ORBI) and ThermoFinnigan Surveyor/DecaXP+ iontrap (LCQ) data for training of an <code><a href="/link/APEX?package=aLFQ&version=1.0" rd-options="" data-mini-rdoc="aLFQ::APEX">APEX</a></code> classifier. The dataset was generated by Christine Vogel and Edward M. Marcotte (see references).

datasets

APEX

APEXMS

Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample. 

George Rosenberger

aLFQ

aLFQ: An R-package for estimating absolute protein quantities
        from label-free LC-MS/MS proteomics data

APEXMS function

A data.frame with the following components:
 <ol><li>peptide_sequence</li></ol>{ character vector: Peptide sequence. }
  <item>apex</item>{ character vector: observed in experiment: 0 = no; 1 = yes. }

format

<squote>The dataset</squote> was obtained from:<url>http://marcottelab.org/APEX_Protocol/</url>.

APEXMS: Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.

Description

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Examples