Abstract

This vignette describes the functionality implemented in the QFeatures package. QFeatures provides infrastructure to manage and process quantitative features for high-throughput mass spectrometry assays, including proteomics and metabolomics.

Introduction

The QFeatures package provides infrastructure (that is classes to store data and the methods to process and manipulate them) to manage and analyse quantitative features from mass spectrometry experiments. It is based on the SummarizedExperiment and MultiAssayExperiment classes. Assays in a QFeatures object have a hierarchical relation: proteins are composed of peptides, themselves produced by spectra, as depicted in figure @ref(fig:featuresplot). Throughout the aggregation and processing of these data, the relations between assays are tracked and recorded, thus allowing users to easily navigate across spectra, peptide and protein quantitative data.

Conceptual representation of a `QFeatures` object and the aggregative relation between different assays.

Conceptual representation of a QFeatures object and the aggregative relation between different assays.

In the following sections, we are going to demonstrate how to create a single-assay QFeatures objects starting from a spreadsheet, how to compute the next assays (peptides and proteins), and how these can be manipulated and explored.

Creating QFeatures object

While QFeatures objects can be created manually (see ?QFeatures for details), most users will probably possess quantitative data in a spreadsheet or a dataframe. In such cases, the easiest is to use the readQFeatures function to extract the quantitative data and metadata columns. Below, we load the hlpsms dataframe that contains data for 28 PSMs from the TMT-10plex hyperLOPIT spatial proteomics experiment from (Christoforou et al. 2016). The ecol argument specifies that columns 1 to 10 contain quantitation data, and that the assay should be named psms in the returned QFeatures object, to reflect the nature of the data.

data(hlpsms)
hl <- readQFeatures(hlpsms, ecol = 1:10, name = "psms")
hl
## An instance of class QFeatures containing 1 assays:
##  [1] psms: SummarizedExperiment with 3010 rows and 10 columns

Below, we see that we can extract an assay using its index or its name. The individual assays are stored as SummarizedExperiment object and further access its quantitative data and metadata using the assay and rowData functions

hl[[1]]
## class: SummarizedExperiment 
## dim: 3010 10 
## metadata(0):
## assays(1): ''
## rownames(3010): 1 2 ... 3009 3010
## rowData names(18): Sequence ProteinDescriptions ... RTmin markers
## colnames(10): X126 X127C ... X130N X131
## colData names(0):
hl[["psms"]]
## class: SummarizedExperiment 
## dim: 3010 10 
## metadata(0):
## assays(1): ''
## rownames(3010): 1 2 ... 3009 3010
## rowData names(18): Sequence ProteinDescriptions ... RTmin markers
## colnames(10): X126 X127C ... X130N X131
## colData names(0):
head(assay(hl[["psms"]]))
##         X126      X127C       X127N      X128C       X128N      X129C
## 1 0.12283431 0.08045915 0.070804055 0.09386901 0.051815695 0.13034383
## 2 0.35268185 0.14162381 0.167523880 0.07843497 0.071087436 0.03214548
## 3 0.01546089 0.16142297 0.086938133 0.23120844 0.114664348 0.09610188
## 4 0.04702854 0.09288723 0.102012167 0.11125409 0.067969116 0.14155358
## 5 0.01044693 0.15866147 0.167315736 0.21017494 0.147946673 0.07088253
## 6 0.04955362 0.01215244 0.002477681 0.01297833 0.002988949 0.06253195
##        X129N       X130C      X130N       X131
## 1 0.17540095 0.040068658 0.11478839 0.11961594
## 2 0.06686260 0.031961793 0.02810434 0.02957384
## 3 0.15977819 0.010127118 0.08059400 0.04370403
## 4 0.18015910 0.035329902 0.12166589 0.10014038
## 5 0.17555789 0.007088253 0.02884754 0.02307803
## 6 0.01726511 0.172651119 0.37007905 0.29732174
head(rowData(hl[["psms"]]))
## DataFrame with 6 rows and 18 columns
##      Sequence ProteinDescriptions NbProteins ProteinGroupAccessions
##   <character>         <character>  <integer>            <character>
## 1     SQGEIDk       Tetratrico...          1                 Q8BYY4
## 2     YEAQGDk       Vacuolar p...          1                 P46467
## 3     TTScDTk       C-type man...          1                 Q64449
## 4     aEELESR       Liprin-alp...          1                 P60469
## 5     aQEEAIk       Isoform 2 ...          2               P13597-2
## 6    dGAVDGcR       Structural...          1                 Q6P5D8
##   Modifications    qValue       PEP  IonScore NbMissedCleavages
##     <character> <numeric> <numeric> <integer>         <integer>
## 1 K7(TMT6ple...     0.008   0.11800        27                 0
## 2 K7(TMT6ple...     0.001   0.01070        27                 0
## 3 C4(Carbami...     0.008   0.11800        11                 0
## 4 N-Term(TMT...     0.002   0.04450        24                 0
## 5 N-Term(Car...     0.001   0.00850        36                 0
## 6 N-Term(TMT...     0.000   0.00322        26                 0
##   IsolationInterference IonInjectTimems Intensity    Charge      mzDa      MHDa
##               <integer>       <integer> <numeric> <integer> <numeric> <numeric>
## 1                     0              70    335000         2   503.274   1005.54
## 2                     0              70    926000         2   520.267   1039.53
## 3                     0              70    159000         2   521.258   1041.51
## 4                     0              70    232000         2   531.785   1062.56
## 5                     0              70    212000         2   537.804   1074.60
## 6                     0              70    865000         2   539.761   1078.51
##   DeltaMassPPM     RTmin       markers
##      <numeric> <numeric>   <character>
## 1        -0.38     24.02       unknown
## 2         0.61     18.85       unknown
## 3         1.11     10.17       unknown
## 4         0.35     29.18       unknown
## 5         1.70     25.56 Plasma mem...
## 6        -0.67     21.27 Nucleus - ...

For further details on how to manipulate such objects, refer to the MultiAssayExperiment (Ramos et al. 2017) and SummerizedExperiment (Morgan et al. 2019) packages.

As illustrated in figure @ref(fig:featuresplot), an central characteristic of QFeatures objects is the aggregative relation between their assays. This can be obtained with the aggregateFeatures function that will aggregate quantitative features from one assay into a new one. In the next code chunk, we aggregate PSM-level data into peptide by grouping all PSMs that were matched the same peptide sequence. Below, the aggregation function is set, as an example, to the mean. The new assay is named peptides.

hl <- aggregateFeatures(hl, "psms", "Sequence", name = "peptides", fun = colMeans)
## Your row data contain missing values. Please read the relevant
## section(s) in the aggregateFeatures manual page regarding the effects
## of missing values on data aggregation.
hl
## An instance of class QFeatures containing 2 assays:
##  [1] psms: SummarizedExperiment with 3010 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 2923 rows and 10 columns
hl[["peptides"]]
## class: SummarizedExperiment 
## dim: 2923 10 
## metadata(0):
## assays(2): assay aggcounts
## rownames(2923): aAADADVSLHNFSAR aAADPSEk ... yYSFFDLNPk YYSIASSSk
## rowData names(7): Sequence ProteinDescriptions ... markers .n
## colnames(10): X126 X127C ... X130N X131
## colData names(0):

Below, we repeat the aggregation operation by grouping peptides into proteins as defined by the ProteinGroupAccessions variable.

hl <- aggregateFeatures(hl, "peptides", "ProteinGroupAccessions", name = "proteins", fun = colMeans)
hl
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 3010 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 2923 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 1596 rows and 10 columns
hl[["proteins"]]
## class: SummarizedExperiment 
## dim: 1596 10 
## metadata(0):
## assays(2): assay aggcounts
## rownames(1596): A2A432 A2A6Q5-3 ... Q9Z2Z9 Q9Z315
## rowData names(3): ProteinGroupAccessions markers .n
## colnames(10): X126 X127C ... X130N X131
## colData names(0):

The sample assayed in a QFeatures object can be documented in the colData slot. The hl data doens’t currently possess any sample metadata. These can be addedd as a new DataFrame with matching names (i.e. the DataFrame rownames must be identical assay’s colnames) or can be added one variable at at time, as shown below.

colData(hl)
## DataFrame with 10 rows and 0 columns
hl$tag <- c("126", "127N", "127C", "128N", "128C", "129N", "129C",
            "130N", "130C", "131")
colData(hl)
## DataFrame with 10 rows and 1 column
##               tag
##       <character>
## X126          126
## X127C        127N
## X127N        127C
## X128C        128N
## X128N        128C
## X129C        129N
## X129N        129C
## X130C        130N
## X130N        130C
## X131          131

Manipulating feature metadata

The QFeatures package provides some utility functions that streamline the accession and manipulation of the feature metadata.

The feature metadata, more generally referred to as rowData in the Bioconductor ecosystem, is specific to each assay in a QFeatures object. Therefore there are as many rowData tables as there are assays. rowDataNames provides a list where each element contains the name of the rowData columns available in the corresponding assay.

## CharacterList of length 3
## [["psms"]] Sequence ProteinDescriptions NbProteins ... RTmin markers
## [["peptides"]] Sequence ProteinDescriptions NbProteins ... markers .n
## [["proteins"]] ProteinGroupAccessions markers .n

We saw above how to get the rowData from an assay, but we can also extract the rowData for all assays by calling the function on the QFeautures object directly. Similarly to rowDataNames, a list is returned where each element contains the rowData available in the corresponding assay.

rowData(hl)
## DataFrameList of length 3
## names(3): psms peptides proteins

In some cases, we are interested in extracting the rowData as a single data table. This is easily performed using the rbindRowData function. The function will automatically select the columns that are common to all selected assays.

rbindRowData(hl, i = c("peptides", "proteins"))
## DataFrame with 4519 rows and 5 columns
##            assay       rowname ProteinGroupAccessions       markers        .n
##      <character>   <character>            <character>   <character> <integer>
## 1       peptides aAADADVSLH...                 P0C7N9       unknown         1
## 2       peptides      aAADPSEk                 Q6P9Q6       unknown         1
## 3       peptides aAAQFLTSTW...                 Q9D7Z3 Nucleus - ...         1
## 4       peptides aAASGAAGDk...                 A2AGT5       unknown         1
## 5       peptides     AAAVSTEGk                 Q9ERE8       unknown         1
## ...          ...           ...                    ...           ...       ...
## 4515    proteins        Q9Z2V5                 Q9Z2V5       unknown         1
## 4516    proteins        Q9Z2W0                 Q9Z2W0       unknown         1
## 4517    proteins        Q9Z2X1                 Q9Z2X1       unknown         1
## 4518    proteins        Q9Z2Z9                 Q9Z2Z9       unknown         3
## 4519    proteins        Q9Z315                 Q9Z315       unknown         1

We can also replace and add columns in the rowData. This requires to provide a List where the names of the List point to the assay to be updated and the elements of the List contain DataFrames with the replacement values. If the DataFrame contains a column that is not present in the rowData, that column will get added to the rowData. For instance, let’s add a rowData variables with the mean protein expression as well as the associated standard deviation. First, we need to create the DataFrame with the mean expression.

dF <- DataFrame(mean = rowSums(assay(hl[["proteins"]])),
                sd = rowSds(assay(hl[["proteins"]])))

Then, we create the list and name the element proteins so that the new data is added to the rowData of the proteins assay. To add the list, we insert it back into the rowData.

rowData(hl) <- List(proteins = dF)

As shown below, the new mean and sd variables have been added to the rowData of the proteins assay.

rowData(hl)[["proteins"]]
## DataFrame with 1596 rows and 5 columns
##          ProteinGroupAccessions     markers        .n      mean        sd
##                     <character> <character> <integer> <numeric> <numeric>
## A2A432                   A2A432     unknown         1         1 0.0822395
## A2A6Q5-3               A2A6Q5-3     unknown         1         1 0.0891478
## A2A8L5                   A2A8L5     unknown         2         1 0.1009041
## A2AF47                   A2AF47     unknown         1         1 0.0749159
## A2AGT5                   A2AGT5     unknown         6         1 0.1065126
## ...                         ...         ...       ...       ...       ...
## Q9Z2V5                   Q9Z2V5     unknown         1         1 0.0882136
## Q9Z2W0                   Q9Z2W0     unknown         1         1 0.0565321
## Q9Z2X1                   Q9Z2X1     unknown         1         1 0.1539930
## Q9Z2Z9                   Q9Z2Z9     unknown         3         1 0.0930030
## Q9Z315                   Q9Z315     unknown         1         1 0.1234534

Note that you can also replace an existing column in the rowData by naming the column name in the DataFrame after the column to replace.

Subsetting

One particularity of the QFeatures infrastructure is that the features of the constitutive assays are linked through an aggregative relation. This relation is recorded when creating new assays with aggregateFeatures and is exploited when subsetting QFeature by their feature names.

In the example below, we are interested in the Stat3B isoform of the Signal transducer and activator of transcription 3 (STAT3) with accession number P42227-2. This accession number corresponds to a feature name in the proteins assay. But this protein row was computed from 8 peptide rows in the peptides assay, themselves resulting from the aggregation of 8 rows in the psms assay.

stat3 <- hl["P42227-2", , ]
stat3
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 9 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 8 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 1 rows and 10 columns

We can easily visualise this new QFeatures object using ggplot2 once converted into a data.frame. See the visualization vignette for more details about data exploration from a QFeatures object.

stat3_df <- data.frame(longFormat(stat3))
stat3_df$assay <- factor(stat3_df$assay,
                        levels = c("psms", "peptides", "proteins"))
library("ggplot2")
ggplot(data = stat3_df,
       aes(x = colname,
           y = value,
           group = rowname)) +
    geom_line() + geom_point() +
    facet_grid(~ assay)

Below we repeat the same operation for the Signal transducer and activator of transcription 1 (STAT1) and 3 (STAT3) accession numbers, namely P42227-2 and P42225. We obtain a new QFeatures instance containing 2 proteins, 9 peptides and 10 PSMS. From this, we can readily conclude that STAT1 was identified by a single PSM/peptide.

stat <- hl[c("P42227-2", "P42225"), , ]
stat
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 10 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 9 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 2 rows and 10 columns

Below, we visualise the expression profiles for the two proteins.

stat_df <- data.frame(longFormat(stat))
stat_df$stat3 <- ifelse(stat_df$rowname %in% stat3_df$rowname,
                        "STAT3", "STAT1")
stat_df$assay <- factor(stat_df$assay,
                        levels = c("psms", "peptides", "proteins"))

ggplot(data = stat_df,
       aes(x = colname,
           y = value,
           group = rowname)) +
    geom_line() + geom_point() +
    facet_grid(stat3 ~ assay)

The subsetting by feature names is also available as a call to the subsetByFeature function, for use with the pipe operator.

## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 9 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 8 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 1 rows and 10 columns
hl %>%
    subsetByFeature(c("P42227-2", "P42225"))
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 10 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 9 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 2 rows and 10 columns

and possibly

hl %>%
    subsetByFeature("P42227-2") %>%
    longFormat() %>%
    as.data.frame %>%
    ggplot(aes(x = colname,
               y = value,
               group = rowname)) +
    geom_line() +
    facet_grid(~ assay)

to reproduce the line plot.

Filtering

QFeatures is assays can also be filtered based on variables in their respective row data slots using the filterFeatures function. The filters can be defined using the formula interface or using AnnotationFilter objects from the AnnotationFilter package (Morgan and Rainer 2019). In addition to the pre-defined filters (such as SymbolFilter, ProteinIdFilter, … that filter on gene symbol, protein identifier, …), this package allows users to define arbitrary character or numeric filters using the VariableFilter.

mito_filter <- VariableFilter(field = "markers",
                              value = "Mitochondrion",
                              condition = "==")
mito_filter
## class: CharacterVariableFilter 
## condition: == 
## value: Mitochondrion
qval_filter <- VariableFilter(field = "qValue",
                              value = 0.001,
                              condition = "<=")
qval_filter
## class: NumericVariableFilter 
## condition: <= 
## value: 0.001

These filter can then readily be applied to all assays’ row data slots. The mito_filter will return all PSMs, peptides and proteins that were annotated as localising to the mitochondrion.

filterFeatures(hl, mito_filter)
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 167 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 162 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 113 rows and 10 columns

The qval_filter, on the other hand, will only return a subset of PSMs, because the qValue variable is only present in the psms assays. The q-values are only relevant to PSMs and that variable was dropped from the other assays.

filterFeatures(hl, qval_filter)
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 2466 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 0 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 0 rows and 10 columns

The same filters can be created using the forumla interface:

filterFeatures(hl, ~ markers == "Mitochondrion")
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 167 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 162 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 113 rows and 10 columns
filterFeatures(hl, ~ qValue <= 0.001)
## An instance of class QFeatures containing 3 assays:
##  [1] psms: SummarizedExperiment with 2466 rows and 10 columns 
##  [2] peptides: SummarizedExperiment with 0 rows and 10 columns 
##  [3] proteins: SummarizedExperiment with 0 rows and 10 columns

Session information

## R Under development (unstable) (2021-11-16 r81199)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] magrittr_2.0.1              ggplot2_3.3.5              
##  [3] QFeatures_1.5.2             MultiAssayExperiment_1.21.3
##  [5] SummarizedExperiment_1.25.2 Biobase_2.55.0             
##  [7] GenomicRanges_1.47.5        GenomeInfoDb_1.31.1        
##  [9] IRanges_2.29.1              S4Vectors_0.33.4           
## [11] BiocGenerics_0.41.2         MatrixGenerics_1.7.0       
## [13] matrixStats_0.61.0          BiocStyle_2.23.0           
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.0               jsonlite_1.7.2           bslib_0.3.1             
##  [4] BiocManager_1.30.16      highr_0.9                GenomeInfoDbData_1.2.7  
##  [7] yaml_2.2.1               pillar_1.6.4             lattice_0.20-45         
## [10] glue_1.5.0               digest_0.6.28            XVector_0.35.0          
## [13] colorspace_2.0-2         htmltools_0.5.2          Matrix_1.3-4            
## [16] pkgconfig_2.0.3          bookdown_0.24            zlibbioc_1.41.0         
## [19] purrr_0.3.4              scales_1.1.1             tibble_3.1.6            
## [22] generics_0.1.1           farver_2.1.0             AnnotationFilter_1.19.0 
## [25] ellipsis_0.3.2           cachem_1.0.6             withr_2.4.2             
## [28] lazyeval_0.2.2           crayon_1.4.2             memoise_2.0.0           
## [31] evaluate_0.14            fs_1.5.0                 fansi_0.5.0             
## [34] MASS_7.3-54              textshaping_0.3.6        tools_4.2.0             
## [37] lifecycle_1.0.1          stringr_1.4.0            munsell_0.5.0           
## [40] cluster_2.1.2            DelayedArray_0.21.2      compiler_4.2.0          
## [43] pkgdown_1.9000.9000.9000 jquerylib_0.1.4          systemfonts_1.0.3       
## [46] rlang_0.4.12             grid_4.2.0               RCurl_1.98-1.5          
## [49] MsCoreUtils_1.7.0        igraph_1.2.8             bitops_1.0-7            
## [52] labeling_0.4.2           rmarkdown_2.11           gtable_0.3.0            
## [55] R6_2.5.1                 knitr_1.36               dplyr_1.0.7             
## [58] fastmap_1.1.0            utf8_1.2.2               clue_0.3-60             
## [61] rprojroot_2.0.2          ragg_1.2.0               ProtGenerics_1.27.0     
## [64] desc_1.4.0               stringi_1.7.5            vctrs_0.3.8             
## [67] tidyselect_1.1.1         xfun_0.28

References

Christoforou, Andy, Claire M Mulvey, Lisa M Breckels, Aikaterini Geladaki, Tracey Hurrell, Penelope C Hayward, Thomas Naake, et al. 2016. “A Draft Map of the Mouse Pluripotent Stem Cell Spatial Proteome.” Nat Commun 7: 8992. https://doi.org/10.1038/ncomms9992.
Morgan, Martin, Valerie Obenchain, Jim Hester, and Hervé Pagès. 2019. SummarizedExperiment: SummarizedExperiment Container.
Morgan, Martin, and Johannes Rainer. 2019. AnnotationFilter: Facilities for Filtering Bioconductor Annotation Resources. https://github.com/Bioconductor/AnnotationFilter.
Ramos, Marcel, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez Cabrera, Tiffany Chan, et al. 2017. “Software for the Integration of Multi-Omics Experiments in Bioconductor.” Cancer Research 77(21); e39-42.