vignettes/MSiP_tutorial.md

In Babulab-bioc/MSiP: 'MassSpectrometry' Interaction Prediction

title: "Mass Spectrometry interaction Prediction (MSiP)" author: | | Matineh Rahmatbakhsh | [e-mail] email: "[e-mail]" package: "MSiP" output: html_vignette vignette: > %\VignetteEngine{knitr::knitr} %\VignetteIndexEntry{MSiP tutorial} %\usepackage[UTF-8]{inputenc}

Introduction

The MSiP is a computational approach to predict protein-protein interactions (PPIs) from large-scale affinity purification mass spectrometry (AP-MS) data. This approach includes both spoke and matrix models for interpreting AP-MS data in a network context. The "spoke" model considers only bait-prey interactions, whereas the "matrix" model assumes that each of the identified proteins (baits and prey) in a given AP-MS experiment interacts with each of the others. The spoke model has a high false-negative rate, whereas the matrix model has a high false-positive rate. Thus, although both statistical models have merits, a combination of both models has shown to increase the performance of machine learning classifiers in terms of their capabilities in discrimination between true and false positive interactions Drew et al., 2017.

Load the package

library(MSiP)

Sample Data Description:

A demo AP-MS proteomics dataset is provided in this package to guide the users about data structure.

data("SampleDatInput")
head(SampleDatInput)

##    Experiment.id Replicate  Bait   Prey counts
## 1:            14    BN2198  NSP5 Q07065     17
## 2:            23    BN2214 ORF7A O75947      3
## 3:            16    BN2173  NSP7 Q8TCU6      2
## 4:             7    BN2177 NSP11 P30153      2
## 5:            22    BN2186  ORF6 Q8NBM4      1
## 6:             4    BN2190     N P51571      1

Scoring based on "spoke-model":

Comparative Proteomic Analysis Software Suite (CompPASS) is a robust statistical scoring scheme for assigning scores to bait-prey interactions Sowa et al., 2009. The output from CompPASS scoring includes Z-score, S-score, D-score, WD-score and other features. This function was optimized from the source code.

Babulab-bioc/MSiP documentation built on Dec. 17, 2021, 9:52 a.m.