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Published
20 hours ago •
sneumann
sneumann
Error in object@backend$getPeakList(scans) : Invalid cvParam accession "1003007"
Dear contributors,
I encountered an error while using XCMS to process a mzML file with combined ion-mobility scans. This data file was converted using "combine ion mobility scans" function in MSconvert (3.0.20133-4ec330cb1).
Here are some info of my R script.
library(xcms)
library(magrittr)
mzml <- dir("./", pattern = "new.mzML")
pd <- data.frame(sample_name = sub(basename(mzml), pattern = ".mzML", replacement = "", fixed = TRUE),
sample_group = rep("new_IM_combined",1),
stringsAsFactors = FALSE)
raw_data <- readMSData(files = mzml, pdata = new("NAnnotatedDataFrame",pd),mode = "onDisk")
raw_data@featureData@data %>% head
cwp <- CentWaveParam(ppm = 20, peakwidth = c(5,40), prefilter = c(3,500), snthresh = 5)
xchr <- findChromPeaks(raw_data, param = cwp)
Error information:
Error in object@backend$getPeakList(scans) :
Invalid cvParam accession "1003007"
traceback():
> traceback()
16: stop(e)
15: value[[3L]](cond)
14: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({
FUN(...)
}, error = handle_error)
11: withCallingHandlers({
tryCatch({
FUN(...)
}, error = handle_error)
}, warning = handle_warning)
10: FUN(...)
9: FUN(X[[i]], ...)
8: lapply(X, FUN_, ...)
7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)
6: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)
5: bplapply(object_mslevel, FUN = findChromPeaks_OnDiskMSnExp, method = "centWave",
param = param, BPPARAM = BPPARAM)
4: bplapply(object_mslevel, FUN = findChromPeaks_OnDiskMSnExp, method = "centWave",
param = param, BPPARAM = BPPARAM)
3: .local(object, param, ...)
2: findChromPeaks(raw_data, param = cwp)
1: findChromPeaks(raw_data, param = cwp)
Session Info:
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_1.5 xcms_3.8.2 MSnbase_2.12.0 ProtGenerics_1.18.0 S4Vectors_0.24.4 mzR_2.20.0 Rcpp_1.0.4.6
[8] BiocParallel_1.20.1 Biobase_2.46.0 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-2 DEoptimR_1.0-8 BiocManager_1.30.10 compiler_3.6.3 pillar_1.4.4 plyr_1.8.6
[7] iterators_1.0.12 zlibbioc_1.32.0 tools_3.6.3 digest_0.6.25 ncdf4_1.17 MALDIquant_1.19.3
[13] lifecycle_0.2.0 tibble_3.0.2 preprocessCore_1.48.0 gtable_0.3.0 lattice_0.20-41 pkgconfig_2.0.3
[19] rlang_0.4.6 Matrix_1.2-18 foreach_1.5.0 rstudioapi_0.11 dplyr_1.0.0 IRanges_2.20.2
[25] generics_0.0.2 vctrs_0.3.1 multtest_2.42.0 grid_3.6.3 tidyselect_1.1.0 robustbase_0.93-6
[31] glue_1.4.1 impute_1.60.0 R6_2.4.1 survival_3.1-12 XML_3.99-0.3 RANN_2.6.1
[37] limma_3.42.2 ggplot2_3.3.2 purrr_0.3.4 splines_3.6.3 scales_1.1.1 pcaMethods_1.78.0
[43] codetools_0.2-16 ellipsis_0.3.1 MASS_7.3-51.6 MassSpecWavelet_1.52.0 mzID_1.24.0 colorspace_1.4-1
[49] affy_1.64.0 doParallel_1.0.15 munsell_0.5.0 vsn_3.54.0 crayon_1.3.4 affyio_1.56.0
Does anyone have an idea on how this could be resolved? I have had no trouble running this before but could no longer make it work after MSConvert updated at some point. The only thing I could notice being changed was the "spectrumId" column in the OnDiskMSnExp object.
> raw_data@featureData@data %>% head
fileIdx spIdx smoothed seqNum acquisitionNum msLevel polarity originalPeaksCount totIonCurrent retentionTime basePeakMZ basePeakIntensity
F1.S001 1 1 NA 1 1 1 1 100188 1420588 3.417 0 0
F1.S002 1 2 NA 2 2 1 1 93503 1420733 4.562 0 0
F1.S003 1 3 NA 3 3 1 1 99532 1440382 5.706 0 0
F1.S004 1 4 NA 4 4 1 1 111433 1475069 6.851 0 0
F1.S005 1 5 NA 5 5 1 1 101443 1466774 7.995 0 0
F1.S006 1 6 NA 6 6 1 1 97472 1456877 9.140 0 0
collisionEnergy ionisationEnergy lowMZ highMZ precursorScanNum precursorMZ precursorCharge precursorIntensity mergedScan
F1.S001 NA 0 103.0579 1677.330 NA NA NA NA NA
F1.S002 NA 0 104.3075 1617.811 NA NA NA NA NA
F1.S003 NA 0 106.2480 1654.061 NA NA NA NA NA
F1.S004 NA 0 104.9191 1636.054 NA NA NA NA NA
F1.S005 NA 0 156.7585 1686.527 NA NA NA NA NA
F1.S006 NA 0 124.2497 1647.860 NA NA NA NA NA
mergedResultScanNum mergedResultStartScanNum mergedResultEndScanNum injectionTime filterString spectrumId centroided
F1.S001 NA NA NA 0 <NA> merged=1 frame=1 TRUE
F1.S002 NA NA NA 0 <NA> merged=2 frame=2 TRUE
F1.S003 NA NA NA 0 <NA> merged=3 frame=3 TRUE
F1.S004 NA NA NA 0 <NA> merged=4 frame=4 TRUE
F1.S005 NA NA NA 0 <NA> merged=5 frame=5 TRUE
F1.S006 NA NA NA 0 <NA> merged=6 frame=6 TRUE
ionMobilityDriftTime isolationWindowTargetMZ isolationWindowLowerOffset isolationWindowUpperOffset scanWindowLowerLimit
F1.S001 29.9618 NA NA NA 99.89902
F1.S002 29.9618 NA NA NA 99.89902
F1.S003 29.9618 NA NA NA 99.89902
F1.S004 29.9618 NA NA NA 99.89902
F1.S005 29.9618 NA NA NA 99.89902
F1.S006 29.9618 NA NA NA 99.89902
scanWindowUpperLimit spectrum
F1.S001 1699.315 1
F1.S002 1699.315 2
F1.S003 1699.315 3
F1.S004 1699.315 4
F1.S005 1699.315 5
F1.S006 1699.315 6
There was a related issue at mzR package a while ago that seems to rely on this column for spectra processing. [https://github.com/sneumann/mzR/issues/44] I will keep everyone posted if I figure out what is going on here.
Thanks for helping on this in advance.
Best, Lingjue
I guess the solution to this would be to update the proteowizard version within mzR - and if I'm not wrong @sneumann tried to do that already but stumbled across some problems.
