Chapter 2 MS Introduction

2.2.1 From the ProteomeXchange database

MS-based proteomics data is disseminated through the ProteomeXchange infrastructure, which centrally coordinates submission, storage and dissemination through multiple data repositories, such as the PRoteomics IDEntifications (PRIDE) database at the EBI for mass spectrometry-based experiments (including quantitative data, as opposed as the name suggests), PASSEL at the ISB for Selected Reaction Monitoring (SRM, i.e. targeted) data and the MassIVE resource. These data can be downloaded within R using the rpx package.

library("rpx")
pxannounced()

## 15 new ProteomeXchange annoucements

##     Data.Set    Publication.Data Message
## 1  PXD009823 2021-01-11 19:53:23     New
## 2  PXD023182 2021-01-11 19:31:53     New
## 3  PXD009823 2021-01-11 19:15:50     New
## 4  PXD023119 2021-01-11 09:15:33     New
## 5  PXD020322 2021-01-11 08:36:51     New
## 6  PXD016960 2021-01-11 08:22:53     New
## 7  PXD002178 2021-01-11 08:22:32     New
## 8  PXD014445 2021-01-11 08:01:54     New
## 9  PXD022245 2021-01-11 07:58:24     New
## 10 PXD002177 2021-01-11 07:49:00     New
## 11 PXD014230 2021-01-11 07:48:20     New
## 12 PXD010554 2021-01-11 07:48:03     New
## 13 PXD014720 2021-01-11 07:36:09     New
## 14 PXD019257 2021-01-11 07:32:22     New
## 15 PXD021916 2021-01-11 07:29:21     New

Using the unique PXD000001 identifier, we can retrieve the relevant metadata that will be stored in a PXDataset object. The names of the files available in this data can be retrieved with the pxfiles accessor function.

px <- PXDataset("PXD000001")
px

## Object of class "PXDataset"
##  Id: PXD000001 with 11 files
##  [1] 'F063721.dat' ... [11] 'erwinia_carotovora.fasta'
##  Use 'pxfiles(.)' to see all files.

pxfiles(px)

##  [1] "F063721.dat"                                                         
##  [2] "F063721.dat-mztab.txt"                                               
##  [3] "PRIDE_Exp_Complete_Ac_22134.xml.gz"                                  
##  [4] "PRIDE_Exp_mzData_Ac_22134.xml.gz"                                    
##  [5] "PXD000001_mztab.txt"                                                 
##  [6] "README.txt"                                                          
##  [7] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML" 
##  [8] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML"
##  [9] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"         
## [10] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw"           
## [11] "erwinia_carotovora.fasta"

Other metadata for the px data set:

pxtax(px)

## [1] "Erwinia carotovora"

pxurl(px)

## [1] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001"

pxref(px)

## [1] "Gatto L, Christoforou A. Using R and Bioconductor for proteomics data analysis. Biochim Biophys Acta. 2013 May 18. doi:pii: S1570-9639(13)00186-6. 10.1016/j.bbapap.2013.04.032"

Data files can then be downloaded with the pxget function. Below, we retrieve the raw data file. The file is downloaded11 If the file is already available, it is not downloaded a second time. in the working directory and the name of the file is return by the function and stored in the mzf variable for later use.22 This and other files are also availabel in the msdata package, described below

fn <- "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
mzf <- pxget(px, fn)

## Loading TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML from cache.

mzf

## [1] "/home/lgatto/.cache/rpx/79d8694e5060_TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"

2.2.2 From AnnotationHub

AnnotationHub is a cloud resource set up and managed by the Bioconductor project that serves various omics datasets. It is possible to contribute and access (albeit currently only a limited number of) proteomics data.

library("AnnotationHub")
ah <- AnnotationHub()

## snapshotDate(): 2020-10-27

query(ah, "proteomics")

## AnnotationHub with 4 records
## # snapshotDate(): 2020-10-27
## # $dataprovider: PRIDE
## # $species: Erwinia carotovora
## # $rdataclass: mzRpwiz, mzRident, MSnSet, AAStringSet
## # additional mcols(): taxonomyid, genome, description,
## #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## #   rdatapath, sourceurl, sourcetype 
## # retrieve records with, e.g., 'object[["AH49006"]]' 
## 
##             title                                                         
##   AH49006 | PXD000001: Erwinia carotovora and spiked-in protein fasta file
##   AH49007 | PXD000001: Peptide-level quantitation data                    
##   AH49008 | PXD000001: raw mass spectrometry data                         
##   AH49009 | PXD000001: MS-GF+ identiciation data

ms <- ah[["AH49008"]]
ms

## Mass Spectrometry file handle.
## Filename:  ab7777b09e8_55314 
## Number of scans:  7534

The data contains 7534 spectra - 1431 MS1 spectra and 6103 MS2 spectra. The file name, ab7777b09e8_55314, is not very descriptive because the data originates from the AnnotationHub cloud repository. If the data was read from a local file, is would be named as the mzML (or mzXML) file (see below).

2.2.3 Data packages

Some data are also distributed through dedicated packages. The msdata, for example, provides some general raw data files relevant for both proteomics and metabolomics.

library("msdata")
## proteomics raw data
proteomics()

## [1] "MRM-standmix-5.mzML.gz"                                                
## [2] "MS3TMT10_01022016_32917-33481.mzML.gz"                                 
## [3] "MS3TMT11.mzML"                                                         
## [4] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML.gz"
## [5] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz"

## proteomics identification data
ident()

## [1] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"

## quantitative data
quant()

## [1] "cptac_a_b_peptides.txt"

More often, such experiment packages distribute processed data; an example of such is the pRolocdata package, that offers quantitative proteomics data.

pRolocdata::pRolocdata()