Part 1: Loading and annotation

Load the SWATH-MS example data from the package, this is a reduced file in order to limit the file size of the package.

library(SWATH2stats)
library(data.table)
data('Spyogenes', package = 'SWATH2stats')

Alternatively the original file downloaded from the Peptide Atlas can be loaded from the working directory.

data <- data.frame(fread('rawOpenSwathResults_1pcnt_only.tsv', sep='\t', header=TRUE))

Extract the study design information from the file names. Alternatively, the study design table can be provided as an external table.

Study_design <- data.frame(Filename = unique(data$align_origfilename))
Study_design$Filename <- gsub('.*strep_align/(.*)_all_peakgroups.*', '\\1', Study_design$Filename)
Study_design$Condition <- gsub('(Strep.*)_Repl.*', '\\1', Study_design$Filename)
Study_design$BioReplicate <- gsub('.*Repl([[:digit:]])_.*', '\\1', Study_design$Filename)
Study_design$Run <- seq_len(nrow(Study_design))
head(Study_design)

##                                 Filename Condition BioReplicate Run
## 1  Strep0_Repl1_R02/split_hroest_K120808    Strep0            1   1
## 2  Strep0_Repl2_R02/split_hroest_K120808    Strep0            2   2
## 3 Strep10_Repl1_R02/split_hroest_K120808   Strep10            1   3
## 4 Strep10_Repl2_R02/split_hroest_K120808   Strep10            2   4

The SWATH-MS data is annotated using the study design table.

data.annotated <- sample_annotation(data, Study_design, column_file = "align_origfilename")

Remove the decoy peptides for a subsequent inspection of the data.

data.annotated.nodecoy <- subset(data.annotated, decoy==FALSE)

Part 2: Analyze correlation, variation and signal

Count the different analytes for the different injections.

count_analytes(data.annotated.nodecoy)

##        run_id transition_group_id FullPeptideName ProteinName
## 1  Strep0_1_1               10229            8377        1031
## 2  Strep0_2_2                9716            7970        1003
## 3 Strep10_1_3                8692            7138         943
## 4 Strep10_2_4                8424            6941         910

Plot the correlation of the signal intensity.

correlation <- plot_correlation_between_samples(data.annotated.nodecoy, column.values = 'Intensity')

## Warning: Use of `data.plot$value` is discouraged.
## ℹ Use `value` instead.

Plot the correlation of the delta_rt, which is the deviation of the retention time from the expected retention time.

correlation <- plot_correlation_between_samples(data.annotated.nodecoy, column.values = 'delta_rt')

## Warning: Use of `data.plot$value` is discouraged.
## ℹ Use `value` instead.

Plot the variation of the signal across replicates.

variation <- plot_variation(data.annotated.nodecoy)

variation[[2]]

##   Condition   mode_cv   mean_cv median_cv
## 1    Strep0 0.2280372 0.2545450 0.2351859
## 2   Strep10 0.1706934 0.2947144 0.2592725

Plot the total variation versus variation within replicates.

variation_total <- plot_variation_vs_total(data.annotated.nodecoy)

variation_total[[2]]

##       scope   mode_cv   mean_cv median_cv
## 1 replicate 0.2209867 0.2728681 0.2438041
## 2     total 0.2655678 0.3439050 0.3139993

Calculate the summed signal per peptide and protein across samples.

peptide_signal <- write_matrix_peptides(data.annotated.nodecoy)
protein_signal <- write_matrix_proteins(data.annotated.nodecoy)
head(protein_signal)

##                       ProteinName Strep0_1_1 Strep0_2_2 Strep10_1_3 Strep10_2_4
## 1  Spyo_Exp3652_DDB_SeqID_1571119     265206     163326       51831       45021
## 2  Spyo_Exp3652_DDB_SeqID_1579753     185725     150672       21483      144314
## 3  Spyo_Exp3652_DDB_SeqID_1631459     176686     132415       42165       32735
## 4  Spyo_Exp3652_DDB_SeqID_1640263       3310       6617       98550       45169
## 5  Spyo_Exp3652_DDB_SeqID_1709452     852502     747772      503581      504761
## 6 Spyo_Exp3652_DDB_SeqID_17244480      17506      29578        7607        2482

Part 3: FDR estimation

Estimate the overall FDR across runs using a target decoy strategy.

par(mfrow = c(1, 3))
fdr_target_decoy <- assess_fdr_overall(data.annotated, n_range = 10, 
                                       FFT = 0.25, output = 'Rconsole')

According to this FDR estimation one would need to filter the data with a lower mscore threshold to reach an overall protein FDR of 5%.

mscore4protfdr(data, FFT = 0.25, fdr_target = 0.05)

## Target protein FDR:0.05

## Required overall m-score cutoff:0.0017783
## achieving protein FDR =0.0488

## [1] 0.001778279

Part 4: Filtering

Filter data for values that pass the 0.001 mscore criteria in at least two replicates of one condition.

data.filtered <- filter_mscore_condition(data.annotated, 0.001, n_replica = 2)

## Fraction of peptides selected: 0.67

## Dimension difference: 7226, 0

Select only the 10 peptides showing strongest signal per protein.

data.filtered2 <- filter_on_max_peptides(data.filtered, n_peptides = 10)

## Before filtering: 
##   Number of proteins: 884
##   Number of peptides: 6594
## 
## Percentage of peptides removed: 29.6%
## 
## After filtering: 
##   Number of proteins: 884
##   Number of peptides: 4642

Filter for proteins that are supported by at least two peptides.

data.filtered3 <- filter_on_min_peptides(data.filtered2, n_peptides = 2)

## Before filtering: 
##   Number of proteins: 884
##   Number of peptides: 4642
## 
## Percentage of peptides removed: 3.6%
## 
## After filtering: 
##   Number of proteins: 717
##   Number of peptides: 4475

Part 5: Conversion

Convert the data into a transition-level format (one row per transition measured).

data.transition <- disaggregate(data.filtered3)

## The library contains 6 transitions per precursor.
##                   
## The data table was transformed into a table containing one row per transition.

Convert the data into the format required by MSstats.

MSstats.input <- convert4MSstats(data.transition)

## One or several columns required by MSstats were not in the data. 
##                 The columns were created and filled with NAs.
## Missing columns: ProductCharge, IsotopeLabelType

## IsotopeLabelType was filled with light.

## Warning in convert4MSstats(data.transition): Intensity values that were 0, were
## replaced by NA

head(MSstats.input)

##                      ProteinName    PeptideSequence PrecursorCharge
## 1 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR               3
## 2 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR               3
## 3 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR               3
## 4 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR               3
## 5 Spyo_Exp3652_DDB_SeqID_1571119        AHIAYLPSDGR               2
## 6 Spyo_Exp3652_DDB_SeqID_1571119        AHIAYLPSDGR               2
##                      FragmentIon ProductCharge IsotopeLabelType Intensity
## 1 105801_AEAAIYQFLEAIGENPNR/3_y6            NA            light      4752
## 2 105801_AEAAIYQFLEAIGENPNR/3_y6            NA            light      6144
## 3 105801_AEAAIYQFLEAIGENPNR/3_y6            NA            light      3722
## 4 105801_AEAAIYQFLEAIGENPNR/3_y6            NA            light      6624
## 5        118149_AHIAYLPSDGR/2_y8            NA            light      4036
## 6        118149_AHIAYLPSDGR/2_y8            NA            light      1642
##   BioReplicate Condition Run
## 1            2    Strep0   2
## 2            1   Strep10   3
## 3            2   Strep10   4
## 4            1    Strep0   1
## 5            1    Strep0   1
## 6            1   Strep10   3

Convert the data into the format required by mapDIA.

mapDIA.input <- convert4mapDIA(data.transition)
head(mapDIA.input)

##                      ProteinName      PeptideSequence
## 1 Spyo_Exp3652_DDB_SeqID_1571119   AEAAIYQFLEAIGENPNR
## 2 Spyo_Exp3652_DDB_SeqID_1571119          AHIAYLPSDGR
## 3 Spyo_Exp3652_DDB_SeqID_1571119             EEFTAVFK
## 4 Spyo_Exp3652_DDB_SeqID_1571119 EKAEAAIYQFLEAIGENPNR
## 5 Spyo_Exp3652_DDB_SeqID_1571119           EQHEDVVIVK
## 6 Spyo_Exp3652_DDB_SeqID_1571119     LTSQIADALVEALNPK
##                       FragmentIon Strep0_1 Strep0_2 Strep10_1 Strep10_2
## 1  105801_AEAAIYQFLEAIGENPNR/3_y6     6624     4752      6144      3722
## 2         118149_AHIAYLPSDGR/2_y8     4036     2405      1642       720
## 3             35179_EEFTAVFK/2_y5     2307     1541      1561       NaN
## 4 28903_EKAEAAIYQFLEAIGENPNR/3_y6     3410     2185       NaN      1984
## 5           73581_EQHEDVVIVK/2_b6     2423     1343       NaN       NaN
## 6   115497_LTSQIADALVEALNPK/2_y11     6553     6349       NaN       NaN

Convert the data into the format required by aLFQ.

aLFQ.input <- convert4aLFQ(data.transition)

## Checking the integrity of the transitions takes a lot of time. 
##                 To speed up consider changing the option.

head(aLFQ.input)

##        run_id                     protein_id         peptide_id
## 1  Strep0_2_2 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR
## 2 Strep10_1_3 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR
## 3 Strep10_2_4 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR
## 4  Strep0_1_1 Spyo_Exp3652_DDB_SeqID_1571119 AEAAIYQFLEAIGENPNR
## 5  Strep0_1_1 Spyo_Exp3652_DDB_SeqID_1571119        AHIAYLPSDGR
## 6 Strep10_1_3 Spyo_Exp3652_DDB_SeqID_1571119        AHIAYLPSDGR
##                                       transition_id   peptide_sequence
## 1 AEAAIYQFLEAIGENPNR 105801_AEAAIYQFLEAIGENPNR/3_y6 AEAAIYQFLEAIGENPNR
## 2 AEAAIYQFLEAIGENPNR 105801_AEAAIYQFLEAIGENPNR/3_y6 AEAAIYQFLEAIGENPNR
## 3 AEAAIYQFLEAIGENPNR 105801_AEAAIYQFLEAIGENPNR/3_y6 AEAAIYQFLEAIGENPNR
## 4 AEAAIYQFLEAIGENPNR 105801_AEAAIYQFLEAIGENPNR/3_y6 AEAAIYQFLEAIGENPNR
## 5               AHIAYLPSDGR 118149_AHIAYLPSDGR/2_y8        AHIAYLPSDGR
## 6               AHIAYLPSDGR 118149_AHIAYLPSDGR/2_y8        AHIAYLPSDGR
##   precursor_charge transition_intensity concentration
## 1                3                 4752             ?
## 2                3                 6144             ?
## 3                3                 3722             ?
## 4                3                 6624             ?
## 5                2                 4036             ?
## 6                2                 1642             ?

Session info on the R version and packages used.

sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [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       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] data.table_1.16.2  SWATH2stats_1.37.0
## 
## loaded via a namespace (and not attached):
##  [1] KEGGREST_1.47.0         gtable_0.3.6            ggplot2_3.5.1          
##  [4] xfun_0.49               bslib_0.8.0             httr2_1.0.7            
##  [7] Biobase_2.67.0          vctrs_0.6.5             tools_4.4.2            
## [10] generics_0.1.3          curl_6.0.1              stats4_4.4.2           
## [13] tibble_3.2.1            fansi_1.0.6             AnnotationDbi_1.69.0   
## [16] RSQLite_2.3.8           blob_1.2.4              pkgconfig_2.0.3        
## [19] dbplyr_2.5.0            S4Vectors_0.45.2        lifecycle_1.0.4        
## [22] GenomeInfoDbData_1.2.13 farver_2.1.2            compiler_4.4.2         
## [25] stringr_1.5.1           Biostrings_2.75.1       progress_1.2.3         
## [28] munsell_0.5.1           GenomeInfoDb_1.43.2     htmltools_0.5.8.1      
## [31] sys_3.4.3               buildtools_1.0.0        sass_0.4.9             
## [34] yaml_2.3.10             pillar_1.9.0            crayon_1.5.3           
## [37] jquerylib_0.1.4         cachem_1.1.0            tidyselect_1.2.1       
## [40] digest_0.6.37           stringi_1.8.4           reshape2_1.4.4         
## [43] dplyr_1.1.4             labeling_0.4.3          maketools_1.3.1        
## [46] grid_4.4.2              biomaRt_2.63.0          fastmap_1.2.0          
## [49] colorspace_2.1-1        cli_3.6.3               magrittr_2.0.3         
## [52] utf8_1.2.4              withr_3.0.2             scales_1.3.0           
## [55] filelock_1.0.3          prettyunits_1.2.0       UCSC.utils_1.3.0       
## [58] rappdirs_0.3.3          bit64_4.5.2             rmarkdown_2.29         
## [61] XVector_0.47.0          httr_1.4.7              bit_4.5.0              
## [64] png_0.1-8               hms_1.1.3               memoise_2.0.1          
## [67] evaluate_1.0.1          knitr_1.49              IRanges_2.41.1         
## [70] BiocFileCache_2.15.0    rlang_1.1.4             Rcpp_1.0.13-1          
## [73] glue_1.8.0              DBI_1.2.3               xml2_1.3.6             
## [76] BiocGenerics_0.53.3     jsonlite_1.8.9          plyr_1.8.9             
## [79] R6_2.5.1                zlibbioc_1.52.0