runInfo returns startTimeStamp -infinity
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@polsoladelossantos-14182
Last seen 19 months ago

Hi, When loading a mzML file through:

library(MSnbase)
library(mzR)
ms <- openMSfile('path/to/file.mzML')

Trying to access injection time I get in some files the following:

ms$startTimeStamp
[1] "-infinity"

What does it mean? Any workaround? Thanks

lcms mzR metabolomics xcms MSnbase • 208 views
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@laurent-gatto-5645
Last seen 1 day ago
Belgium

I think you are missing some bits of code in your example - it probably should be

ms <- openMSfile('path/to/file.mzML')
info <- runInfo(ms)
ms$startTimeStamp

The reason you read "-infinity" is probably because that's what is encoded in your mzML file. You can check for yourself in R with

grep("startTimeStamp", readLines('path/to/file.mzML'), value = TRUE)

or on the command line with

grep startTimeStamp path/to/file.mzML

In the future, could you please add the output of sessionInfo() to make sure we are talking about the latest version.

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Thanks, As you said -infinity it's written on the mzML file. Any workaround to get the time of injection of the sample? Best,

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I don't think there is from that mzML file. You might have to check in the raw binary file, or try to convert it again and see if it was missed out in the first place.

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Moreover, Case of one study MTBLS404, samples of Batch1 have this information, Batch 2 does not.

Batch 2: grep startTimeStamp HUneg070_b2.mzML <run id="HU_neg_070" defaultinstrumentconfigurationref="IC1" starttimestamp="-infinity" defaultsourcefileref="RAW1">

Batch 1: grep startTimeStamp HUneg086.mzML <run id="HU_neg_086" defaultinstrumentconfigurationref="IC1" starttimestamp="2009-05-08T17:17:26Z" defaultsourcefileref="RAW1">

Any idea?

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The only advise I can give you is to download the RAW files and check in there and/or reconvert them to mzML. Other then that, you can try to contact the authors.

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