Package: MsBackendSql
Authors: Johannes Rainer [aut, cre] (ORCID: https://orcid.org/0000-0002-6977-7147), Chong Tang
[ctb], Laurent Gatto [ctb] (ORCID: https://orcid.org/0000-0002-1520-2268)
Compiled: Mon Mar 17 07:51:40 2025
Introduction
The Spectra
Bioconductor package provides a flexible and expandable infrastructure
for Mass Spectrometry (MS) data. The package supports interchangeable
use of different backends that provide additional file support
or different ways to store and represent MS data. The MsBackendSql
package provides backends to store data from whole MS experiments in SQL
databases. The data in such databases can be easily (and efficiently)
accessed using Spectra objects that use the
MsBackendSql class as an interface to the data in the
database. Such Spectra objects have a minimal memory
footprint and hence allow analysis of very large data sets even on
computers with limited hardware capabilities. For certain operations,
the performance of this data representation is superior to that of other
low-memory (on-disk) data representations such as
Spectra’s MsBackendMzR backend. Finally, the
MsBackendSql supports also remote data access to e.g. a
central database server hosting several large MS data sets.
Installation
The package can be installed with the BiocManager
package. To install BiocManager use
install.packages("BiocManager") and, after that,
BiocManager::install("MsBackendSql") to install this
package.
Creating and using MsBackendSql SQL databases
MsBackendSql SQL databases can be created either by
importing (raw) MS data from MS data files using the
createMsBackendSqlDatabase() or using the
backendInitialize() function by providing in addition to
the database connection also the full MS data to import as a
DataFrame. In the first example we use the
createMsBackendSqlDatabase() function to import the full MS
data from the provided MS data files into an (empty) database. Below we
first create an empty SQLite database (in a temporary file) and use the
createMsBackendSqlDatabase() function to create all
necessary tables in that database and import the MS data from two mzML
files (from the r Biocpkg("msdata") package).
library(RSQLite)
dbfile <- tempfile()
con <- dbConnect(SQLite(), dbfile)
library(Spectra)
library(MsBackendSql)
fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
createMsBackendSqlDatabase(con, fls)
dbDisconnect(con)By default (with parameters blob = TRUE and
peaksStorageMode = "blob2") the peaks data matrix of each
spectrum is stored as a BLOB data type into the database (one
entry per spectrum). This has advantages on the performance to extract
the peaks data from the database, but does not allow to filter
individual peaks by their m/z or intensity values directly in
the database. As an alternative (using blob = FALSE) it is
also possible to store the individual m/z and intensity values
in separate columns of the database table. This long table
format results however in considerably larger databases (with
potentially poorer performance). Note also that the code and backend is
optimized for MySQL/MariaDB databases by taking advantage of table
partitioning and specialized table storage options. Any other SQL
database server is however also supported (also portable, self-contained
SQLite databases). In fact, performance for MsBackendSql
databases with peaks data stored as BLOB data type is similar
for SQLite and MySQL/MariaDB databases.
The MsBackendSql package provides two backends to interact
with such databases: the MsBackendSql class and the
MsBackendOfflineSql class, that inherits all properties and
functions from the former, but does not store the connection to the
database within the object. The MsBackendOfflineSql object
thus supports parallel processing and allows to save/load the object
(e.g. using save and saveRDS). The
MsBackendOfflineSql might therefore be used as the
preferred backend to SQL databases for most applications.
To access the data in the database we create below a
Spectra object providing the database connection
information in the constructor call and specifying to use the
MsBackendOfflineSql as backend (parameter
source). We stored the data to a SQLite database, thus we
provide the database name (SQLite database file name) and the SQLite DBI
driver with parameters dbname and drv. Which
parameters are required to connect to the database depends on the SQL
database and the used driver. For a MySQL/MariaDB database we would use
the MariaDB() driver and would have to provide the database
name, user name, password as well as the host name and port through
which the database is accessible.
sps <- Spectra(dbname = dbfile, source = MsBackendOfflineSql(), drv = SQLite())
sps## MSn data (Spectra) with 1862 spectra in a MsBackendOfflineSql backend:
## msLevel precursorMz polarity
## <integer> <numeric> <integer>
## 1 1 NA 1
## 2 1 NA 1
## 3 1 NA 1
## 4 1 NA 1
## 5 1 NA 1
## ... ... ... ...
## 1858 1 NA 1
## 1859 1 NA 1
## 1860 1 NA 1
## 1861 1 NA 1
## 1862 1 NA 1
## ... 35 more variables/columns.
## Use 'spectraVariables' to list all of them.
## Database: /tmp/RtmphWJ49j/file839b4774fbe4Spectra objects allow also to change the backend to any
other backend (extending MsBackend) using the
setBackend() function. Below we use this function to first
load all data into memory by changing from the
MsBackendOfflineSql to a MsBackendMemory.
sps_mem <- setBackend(sps, MsBackendMemory())
sps_mem## MSn data (Spectra) with 1862 spectra in a MsBackendMemory backend:
## msLevel rtime scanIndex
## <integer> <numeric> <integer>
## 1 1 0.280 1
## 2 1 0.559 2
## 3 1 0.838 3
## 4 1 1.117 4
## 5 1 1.396 5
## ... ... ... ...
## 1858 1 258.636 927
## 1859 1 258.915 928
## 1860 1 259.194 929
## 1861 1 259.473 930
## 1862 1 259.752 931
## ... 35 more variables/columns.
## Processing:
## Switch backend from MsBackendOfflineSql to MsBackendMemory [Mon Mar 17 07:51:47 2025]With this function it is also possible to change from any backend to
a MsBackendOfflineSql (or MsBackendSql) in
which case a new database is created and all data from the originating
backend is stored in this database. To change the backend to an
MsBackendOfflineSql we need to provide the connection
information to the SQL database as additional parameters. These
parameters are the same that need to be passed to a
dbConnect() call to establish the connection to the
database. These parameters include the database driver (parameter
drv), the database name and eventually the user name, host
etc (see ?dbConnect for more information). In the simple
example below we store the data into a SQLite database and thus only
need to provide the database name, which corresponds SQLite database
file. In our example we store the data into a temporary file.
Optionally, setBackend() supports also the parameters
blob and peaksDataStorage described above for
the createMsBackendSqlDatabase() function.
sps2 <- setBackend(sps_mem, MsBackendOfflineSql(), drv = SQLite(),
dbname = tempfile())
sps2## MSn data (Spectra) with 1862 spectra in a MsBackendOfflineSql backend:
## msLevel precursorMz polarity
## <integer> <numeric> <integer>
## 1 1 NA 1
## 2 1 NA 1
## 3 1 NA 1
## 4 1 NA 1
## 5 1 NA 1
## ... ... ... ...
## 1858 1 NA 1
## 1859 1 NA 1
## 1860 1 NA 1
## 1861 1 NA 1
## 1862 1 NA 1
## ... 35 more variables/columns.
## Use 'spectraVariables' to list all of them.
## Database: /tmp/RtmphWJ49j/file839b577e6036
## Processing:
## Switch backend from MsBackendOfflineSql to MsBackendMemory [Mon Mar 17 07:51:47 2025]
## Switch backend from MsBackendMemory to MsBackendOfflineSql [Mon Mar 17 07:51:47 2025]Similar to any other Spectra object we can retrieve the
available spectra variables using the
spectraVariables() function.
spectraVariables(sps)## [1] "msLevel" "rtime"
## [3] "acquisitionNum" "scanIndex"
## [5] "dataStorage" "dataOrigin"
## [7] "centroided" "smoothed"
## [9] "polarity" "precScanNum"
## [11] "precursorMz" "precursorIntensity"
## [13] "precursorCharge" "collisionEnergy"
## [15] "isolationWindowLowerMz" "isolationWindowTargetMz"
## [17] "isolationWindowUpperMz" "peaksCount"
## [19] "totIonCurrent" "basePeakMZ"
## [21] "basePeakIntensity" "ionisationEnergy"
## [23] "lowMZ" "highMZ"
## [25] "mergedScan" "mergedResultScanNum"
## [27] "mergedResultStartScanNum" "mergedResultEndScanNum"
## [29] "injectionTime" "filterString"
## [31] "spectrumId" "ionMobilityDriftTime"
## [33] "scanWindowLowerLimit" "scanWindowUpperLimit"
## [35] "electronBeamEnergy" "spectrum_id_"The MS peak data can be accessed using either the mz(),
intensity() or peaksData() functions. Below we
extract the peaks matrix of the 5th spectrum and display the first 6
rows.
## mz intensity
## [1,] 105.0347 0
## [2,] 105.0362 164
## [3,] 105.0376 0
## [4,] 105.0391 0
## [5,] 105.0405 328
## [6,] 105.0420 0All data (peaks data or spectra variables) are
always retrieved on-the-fly from the database resulting
thus in a minimal memory footprint for the Spectra
object.
print(object.size(sps), units = "KB")## 114.6 KbThe backend supports also adding additional spectra variables or changing their values. Below we add 10 seconds to the retention time of each spectrum.
sps$rtime <- sps$rtime + 10Such operations do however not change the data in the database (which is always considered read-only) but are cached locally within the backend object (in memory). The size in memory of the object is thus higher after changing that spectra variable.
print(object.size(sps), units = "KB")## 129.2 KbSuch $<- operations can also be used to
cache spectra variables (temporarily) in memory which can
eventually improve performance. Below we test the time it takes to
extract the MS level from each spectrum from the database, then cache
the MS levels in memory using $msLevel <- and test the
timing to extract these cached variable.
system.time(msLevel(sps))## user system elapsed
## 0.01 0.00 0.01
sps$msLevel <- msLevel(sps)
system.time(msLevel(sps))## user system elapsed
## 0.005 0.000 0.005We can also use the reset() function to reset
the data to its original state (this will cause any local spectra
variables to be deleted and the backend to be initialized with the
original data in the database).
sps <- reset(sps)Performance comparison with other backends
The need to retrieve any spectra data on-the-fly from the database
has an impact on the performance of data access functions of
Spectra objects using
MsBackendSql/MsBackendOfflineSql backends. To
evaluate this we compare below the performance of the
MsBackendSql to other Spectra backends,
specifically, the MsBackendMzR which is the default backend
to read and represent raw MS data, and the MsBackendMemory
backend that keeps all MS data in memory (and is thus not suggested for
larger MS experiments). Similar to the MsBackendMzR, also
the MsBackendSql keeps only a limited amount of data in
memory. These on-disk backends need thus to retrieve spectra
and MS peaks data on-the-fly from either the original raw data files (in
the case of the MsBackendMzR) or from the SQL database (in
the case of the MsBackendSql). The in-memory backend
MsBackendMemory is supposed to provide the fastest data
access since all data is kept in memory.
Below we thus create Spectra objects from the same data
but using the different backends.
con <- dbConnect(SQLite(), dbfile)
sps <- Spectra(con, source = MsBackendSql())
sps_mzr <- Spectra(fls, source = MsBackendMzR())
sps_im <- setBackend(sps_mzr, backend = MsBackendMemory())At first we compare the memory footprint of the 3 backends.
print(object.size(sps), units = "KB")## 112.9 Kb
print(object.size(sps_mzr), units = "KB")## 401.4 Kb
print(object.size(sps_im), units = "KB")## 54509.1 KbThe MsBackendSql has the lowest memory footprint of all
3 backends because it does not keep any data in memory. The
MsBackendMzR keeps all spectra variables, except the MS
peaks data, in memory and has thus a larger size. The
MsBackendMemory keeps all data (including the MS peaks
data) in memory and has thus the largest size in memory.
Next we compare the performance to extract the MS level for each
spectrum from the 4 different Spectra objects.
library(microbenchmark)
microbenchmark(msLevel(sps),
msLevel(sps_mzr),
msLevel(sps_im))## Unit: microseconds
## expr min lq mean median uq max
## msLevel(sps) 5096.138 5248.6570 5628.30519 5449.4260 5838.2555 9299.301
## msLevel(sps_mzr) 377.363 412.8245 436.82355 428.8495 457.6535 629.122
## msLevel(sps_im) 10.790 13.3950 22.34694 21.7255 26.8050 73.968
## neval
## 100
## 100
## 100Extracting MS levels is thus slowest for the
MsBackendSql, which is not surprising because both other
backends keep this data in memory while the MsBackendSql
needs to retrieve it from the database.
We next compare the performance to access the full peaks data from
each Spectra object.
microbenchmark(peaksData(sps, BPPARAM = SerialParam()),
peaksData(sps_mzr, BPPARAM = SerialParam()),
peaksData(sps_im, BPPARAM = SerialParam()),
times = 10)## Unit: microseconds
## expr min lq mean
## peaksData(sps, BPPARAM = SerialParam()) 47724.511 50630.737 136997.25
## peaksData(sps_mzr, BPPARAM = SerialParam()) 443313.699 473775.566 698526.08
## peaksData(sps_im, BPPARAM = SerialParam()) 352.406 369.679 2262.72
## median uq max neval
## 66394.486 296287.223 337742.8 10
## 487093.151 1086863.412 1133045.8 10
## 598.375 872.055 17392.0 10As expected, the MsBackendMemory has the fasted access
to the full peaks data. The MsBackendSql outperforms
however the MsBackendMzR providing faster access to the m/z
and intensity values.
Performance can be improved for the MsBackendMzR using
parallel processing. Note that the MsBackendSql does
not support parallel processing and thus parallel
processing is (silently) disabled in functions such as
peaksData().
m2 <- MulticoreParam(2)
microbenchmark(peaksData(sps, BPPARAM = m2),
peaksData(sps_mzr, BPPARAM = m2),
peaksData(sps_im, BPPARAM = m2),
times = 10)## Unit: microseconds
## expr min lq mean median
## peaksData(sps, BPPARAM = m2) 46378.242 55116.357 60882.6762 60141.8370
## peaksData(sps_mzr, BPPARAM = m2) 428571.292 486742.013 708184.1580 661306.4715
## peaksData(sps_im, BPPARAM = m2) 421.696 835.187 827.6728 868.9195
## uq max neval
## 68905.855 74470.497 10
## 834908.611 1119557.942 10
## 935.384 1028.056 10We next compare the performance of subsetting operations.
microbenchmark(filterRt(sps, rt = c(50, 100)),
filterRt(sps_mzr, rt = c(50, 100)),
filterRt(sps_im, rt = c(50, 100)))## Unit: microseconds
## expr min lq mean median
## filterRt(sps, rt = c(50, 100)) 1948.632 1995.860 2230.2510 2027.4285
## filterRt(sps_mzr, rt = c(50, 100)) 1244.629 1313.572 1466.7465 1350.6075
## filterRt(sps_im, rt = c(50, 100)) 398.333 433.258 465.0411 449.8285
## uq max neval
## 2076.5600 14737.826 100
## 1480.9600 9395.300 100
## 482.4595 1141.708 100The two on-disk backends MsBackendSql and
MsBackendMzR show a comparable performance for this
operation. This filtering does involves access to a spectra variables
(the retention time in this case) which, for the
MsBackendSql needs first to be retrieved from the backend.
The MsBackendSql backend allows however also to
cache spectra variables (i.e. they are stored within the
MsBackendSql object). Any access to such cached spectra
variables can eventually be faster because no dedicated SQL query is
needed.
To evaluate the performance of a pure subsetting operation
we first define the indices of 10 random spectra and subset the
Spectra objects to these.
idx <- sample(seq_along(sps), 10)
microbenchmark(sps[idx],
sps_mzr[idx],
sps_im[idx])## Unit: microseconds
## expr min lq mean median uq max neval
## sps[idx] 134.220 143.8035 152.9504 152.3395 159.6530 226.753 100
## sps_mzr[idx] 674.848 699.9240 723.7425 710.0985 721.6550 1686.854 100
## sps_im[idx] 236.922 247.3460 256.4294 255.7365 260.1395 327.320 100Here the MsBackendSql outperforms the other backends
because it does not keep any data in memory and hence does not need to
subset these. The two other backends need to subset the data they keep
in memory which is in both cases a data frame with either a reduced set
of spectra variables or the full MS data.
At last we compare also the extraction of the peaks data from the
such subset Spectra objects.
sps_10 <- sps[idx]
sps_mzr_10 <- sps_mzr[idx]
sps_im_10 <- sps_im[idx]
microbenchmark(peaksData(sps_10),
peaksData(sps_mzr_10),
peaksData(sps_im_10),
times = 10)## Unit: microseconds
## expr min lq mean median uq
## peaksData(sps_10) 1900.351 1993.435 2505.0174 2202.2290 3159.238
## peaksData(sps_mzr_10) 74106.808 76473.491 80682.8475 79040.6980 83277.198
## peaksData(sps_im_10) 369.468 393.463 535.7353 570.7885 653.417
## max neval
## 3193.532 10
## 97232.225 10
## 688.263 10The MsBackendSql outperforms the
MsBackendMzR while, not unexpectedly, the
MsBackendMemory provides fasted access.
Considerations for database systems/servers
The backends from the MsBackendSql package use standard SQL calls to retrieve MS data from the database and hence any SQL database system (for which an R package is available) is supported. SQLite-based databases would represent the easiest and most user friendly solution since no database server administration and user management is required. Indeed, performance of SQLite is very high, even for very large data sets. Server-based databases on the other hand have the advantage to enable a centralized storage and control of MS data (inclusive user management etc). Also, such server systems would also allow data set or server-specific configurations to improve performance.
A comparison between a SQLite-based with a MariaDB-based MsBackendSql database for a large data set comprising over 8,000 samples and over 15,000,000 spectra is available here. In brief, performance to extract data was comparable and for individual spectra variables even faster for the SQLite database. Only when more complex SQL queries were involved (combining several primary keys or data fields) the more advanced MariaDB database outperformed SQLite.
Other properties of the MsBackendSql
The MsBackendSql backend does not support parallel
processing since the database connection can not be shared across the
different (parallel) processes. Thus, all methods on
Spectra objects that use a MsBackendSql will
automatically (and silently) disable parallel processing even if a
dedicated parallel processing setup was passed along with the
BPPARAM method.
Some functions on Spectra objects require to load the MS
peak data (i.e., m/z and intensity values) into memory. For very large
data sets (or computers with limited hardware resources) such function
calls can cause out-of-memory errors. One example is the
lengths() function that determines the number of peaks per
spectrum by loading the peak matrix first into memory. Such functions
should ideally be called using the peaksapply() function
with parameter chunkSize (e.g.,
peaksapply(sps, lengths, chunkSize = 5000L)). Instead of
processing the full data set, the data will be first split into chunks
of size chunkSize that are stepwise processed. Hence, only
data from chunkSize spectra is loaded into memory in one
iteration.
Summary
The MsBackendSql provides an MS data representations and
storage mode with a minimal memory footprint (in R) that is still
comparably efficient for standard processing and subsetting operations.
This backend is specifically useful for very large MS data sets, that
could even be hosted on remote (MySQL/MariaDB) servers. A potential use
case for this backend could thus be to set up a central storage place
for MS experiments with data analysts connecting remotely to this server
to perform initial data exploration and filtering. After subsetting to a
smaller data set of interest, users could then retrieve/download this
data by changing the backend to e.g. a MsBackendMemory,
which would result in a download of the full data to the user
computer’s memory.
Session information
## R Under development (unstable) (2025-02-24 r87814)
## 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=en_US.UTF-8
## [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: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] microbenchmark_1.5.0 RSQLite_2.3.9 MsBackendSql_1.7.4
## [4] Spectra_1.17.9 BiocParallel_1.41.2 S4Vectors_0.45.4
## [7] BiocGenerics_0.53.6 generics_0.1.3 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 MsCoreUtils_1.19.1 stringi_1.8.4
## [4] hms_1.1.3 digest_0.6.37 evaluate_1.0.3
## [7] bookdown_0.42 blob_1.2.4 fastmap_1.2.0
## [10] jsonlite_1.9.1 ProtGenerics_1.39.2 progress_1.2.3
## [13] mzR_2.41.4 DBI_1.2.3 BiocManager_1.30.25
## [16] codetools_0.2-20 textshaping_1.0.0 jquerylib_0.1.4
## [19] cli_3.6.4 rlang_1.1.5 crayon_1.5.3
## [22] Biobase_2.67.0 bit64_4.6.0-1 cachem_1.1.0
## [25] yaml_2.3.10 tools_4.5.0 parallel_4.5.0
## [28] memoise_2.0.1 ncdf4_1.23 fastmatch_1.1-6
## [31] vctrs_0.6.5 R6_2.6.1 lifecycle_1.0.4
## [34] fs_1.6.5 htmlwidgets_1.6.4 IRanges_2.41.3
## [37] bit_4.6.0 clue_0.3-66 MASS_7.3-65
## [40] ragg_1.3.3 cluster_2.1.8.1 pkgconfig_2.0.3
## [43] desc_1.4.3 pkgdown_2.1.1.9000 bslib_0.9.0
## [46] Rcpp_1.0.14 data.table_1.17.0 systemfonts_1.2.1
## [49] xfun_0.51 knitr_1.50 htmltools_0.5.8.1
## [52] rmarkdown_2.29 compiler_4.5.0 prettyunits_1.2.0
## [55] MetaboCoreUtils_1.15.0