Question: runInfo returns startTimeStamp -infinity
0
gravatar for pol.soladelossantos
6 weeks ago by
pol.soladelossantos0 wrote:

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

ADD COMMENTlink modified 6 weeks ago by Laurent Gatto1.2k • written 6 weeks ago by pol.soladelossantos0
Answer: runInfo returns startTimeStamp -infinity
0
gravatar for Laurent Gatto
6 weeks ago by
Laurent Gatto1.2k
Belgium
Laurent Gatto1.2k wrote:

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.

ADD COMMENTlink written 6 weeks ago by Laurent Gatto1.2k

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

ADD REPLYlink written 6 weeks ago by pol.soladelossantos0

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.

ADD REPLYlink written 6 weeks ago by Laurent Gatto1.2k

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?

ADD REPLYlink written 6 weeks ago by pol.soladelossantos0

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.

ADD REPLYlink written 6 weeks ago by Laurent Gatto1.2k
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