hupo-psi / psi-ms-cv Goto Github PK

This term is obsolete https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001016 but no option is provided. The current mzIdnetML and mztab hardcode this information directly into a prop[erty database version. But the term can exist also in case someone want to translate this.

• imports:
  • imports to obo format files will not work in OWL toolchains
  • always use official OBO PURLs in imports. For example, you are using PATO, see products here: http://obofoundry.org/ontology/pato
• xrefs
  • looks like you are using these in an unusual way, OWL may be better suited to your needs

There are some additional issues reported here:
http://obo-dashboard-test.ontodev.com/ms/dashboard.html

I recommend also

• documenting your ontology editing practice in an editors guide. Which tools are used to edit the obo? It says generated by obo-edit, but looks hand edited?
• documenting user expectations of the file. How are the imports used by tools? What would happen if these were omitted? How are the xrefs used?

Thermo recently started selling an ion mobility device that can bolt-on many of its instruments. The resulting files produce a new line in the scan header with the term 'compensationVoltage', which is used to specify the FAIMS setting for that scan. Can we add this term to the controlled vocabulary please?

Describe the question or discussion

It looks like the automatic generation of OWL failed with an out of memory error in the latest build attempt after today's merge.

I wonder if we should remove the import of NCIT. This is such a huge beast and I am doubtful that it is gaining us anything.

Dear PSI-MS CV community,
( I posted this message to the PSI-MS-CV mailing list, but is stuck in the approval queue. Sorry for the duplication, GitHub issues is a better place to have such discussions in any case )

I am writing on behalf of the PSI-QC working group, as we want to get our QC-CV 'into the fold'. Before that, however, we thought it'd be best to start a conversation on how.
We have been developing a separate CV initially to have some freedoms on what/how things work out best for the mzQC format, which relies heavily on CV control.
Our CV holds the metric definitions, relations and few additional 'organisational' terms, so far <300 entries, for which we chose the QC prefix (naturally). We ditched the xref: value-type declarations in favour of defining term values with full CV terms and relations, which works nicely with the format.
The mzQC format is, unlike most PSI formats, JSON based. One of the goals in the design was to bring the format closer to the last miles of analysis (R/pandas/web) but also as something that works between any steps of an MS-based study workflow (lightweight with high automation potential). If you want to know more, check out our specification document draft ( https://hupo-psi.github.io/mzQC/). For mzQC, we have to cover a vast range of QC/MS-related topics in the CV. For that, we've devised a set of templates and rules for adding new term/metrics via GitHub issues. To keep better track of the entries, Nils created a GitHub workflow for obo-to-markup conversion to enhance browsability. QC-CV is not standalone, we base as much as possible on existing definitions, so we imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. So, overall I think QC-CV would fit in nicely, either as big PR or piece-wise. As for the merge, maybe we can follow the same playbook as the PEFF integration did? What do you think?

TL;DR: mzQC folks want to merge their CV into PSI-MS. But before opening a gargantuan PR, we should talk.

Best,

After an update to the new obo we get a lot of:
Warning: while loading term 'MS:1003130' of CV 'MS': parent term name 'proteoform-level Q-value' and id 'MS:1003127' differ.
warnings when reading mzMLs.
Looking at the terms how they stand right now I think it could be an issue that MS:1003130 is a MS:1003127 ! proteoform-level Q-value but MS:1003127 has changed to ProSight:spectral E-value
see:

[Term]
id: MS:1003127
name: ProSight:spectral E-value
def: "ProSight spectrum-level E-value." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1003130
name: ProSight:proteoform Q-value
def: "ProSight proteoform-level Q-value." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1003127 ! proteoform-level Q-value
relationship: has_order MS:1002109 ! lower score better

Can we add lys-n as enzyme under https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001045&viewMode=All&siblings=false

Since the addition of http://purl.obolibrary.org/obo/stato.owl and http://purl.obolibrary.org/obo/ncit.owl to the CV, robot is running out of memory during parsing. Working on diagnosing why.

A new term to describe ion mobility/drift time deconvolution

[Term]
id: MS:XXXXXX
name: ion mobility deconvolution
def: "The separation of m/z over ion mobility signal into discrete bins or features." [PSI:MS]
is_a: MS:1000543 ! data processing action

It is arguable whether this term should derive from peak picking since some approaches involve 2D centroiding m/z by drift time signal.

Several tools exist to do this, including Waters and Bruker software that exports to mzML already. In Waters's case, this is combined with peak picking, charge state deconvolution and deisotoping. In Bruker's, only peak picking is done.

Hi there,

would you be able to add tags to all the releases you have done so far in this repo?

This could be automated with

# inspired by https://gist.github.com/mloberg/3750653

FILE=psi-ms.obo

REVS=`git log --pretty=%H -- $FILE`

# check each revision for checksum
for rev in $REVS; do
    git show $rev:$FILE > _file_to_check
    version="v"`grep data-version _file_to_check | egrep -o "([0-9]{1,}\.)+.{1,}"`
    # if you are on a Linux system, change md5 to md5sum
    # echo $rev `md5 _file_to_check` $version
    echo "Lets tag commit $rev with $version"
    git tag -a $version $rev -m "auto tag version"
    rm _file_to_check
done

followed by a

git push --tags

would be great to pull out versions on demand :)

Additionally, would it be possible to add the older obos as well?

Cheers

.c

Hi,

i am currently using the "ReDU Sample Information Template v3.0" for molecular networking with GNPS. However i can't enter my used MS because it is not part of the controlled vocabulary. I'd like to suggest adding "Shimadzu GCMS-QP2010SE" to the Google sheet.

Best regards

The issue with the wrong id seems to be fixed but now wet get validation errors:
Error: mzML file semantically invalid 'FileHandler_test_282.tmp'
Error - CV term used in invalid element: 'MS:1000497 - zoom scan' at element '/mzML/run/spectrumList/spectrum'

The OBO file is malformed, missing [Term] headers for three new entries related to lipids:

https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo#L19371-L19389

Describe the new term or terms you would like to add.

Dear all,
on behalf of the PSI-QC group I'd like to request some CV terms, albeit not exclusively QC related terms.
Yet, I sketched the terms with accessions that reflect the accession number space in which we will place
(as agreed in the joint telco after #80) our qc-cv terms for a merge with PSI-MS. But that will come next week,
and these terms are somewhat independent.

We noticed there is no value specification for the start and end time of a MS acquisition. So we'd need:

[Term]
id: MS:4000277
name: DateTime value
def: "A date and time specified through ISO 8601 format" [PSI:QC]

for

[Term]
id: MS:4000278
name: DateTime of acquisition start
def: "The datetime string of the acquisition start timepoint in ISO8601 format" [PSI:QC]
comment: Acquisition start time as registered by the instrument.
relationship: has_value_type MS:4000277 ! DateTime value
is_a: MS:1002435 ! data processing start time

and

[Term]
id: MS:4000279
name: DateTime of acquisition end
def: "The datetime string of the acquisition end timepoint in ISO8601 format" [PSI:QC]
comment: Acquisition end time as registered by the instrument.
relationship: has_value_type MS:4000277 ! DateTime value
is_a: MS:1000747 ! completion time

Example value: "2012-01-30T07:30:51"

However, for the relationship: has_value_type there is a DateTime specification in another onto already, idk if we should import and reuse as GENEPIO:0002148 ! date value specification (ISO 8601)

Here HUPO-PSI/mzTab#14 we have some example Reagents that should be move it to PSI-MS ontology.

Moving from here: MICommunity/psimi#17

See owlcs/owlapi#523

You should always use purls for imports, e.g

import: http://purl.obolibrary.org/obo/pato.obo
import: http://purl.obolibrary.org/obo/uo.obo

In fact we recommend that these are OWL.

import: http://purl.obolibrary.org/obo/pato.owl
import: http://purl.obolibrary.org/obo/uo.owl

You can use an OboEdit catalog to have OE resolve these to a local obo cache. But really you should stop using OE, we do not support it any more. Contact me if you have problems

I got the following error while loading psi-ms.obo in OBOEdit

Load Error, line 20055
Badly formatted definition. No dbxref list found. 

Line 20055 is
def: "Number of extraneous mantissa bits truncated to improve subsequent compression."
Adding [PSI-MS] to the end of the line 20055 fixes the error - i.e
def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI-MS]

Since I am not quite confident with the ontology format and meaning of all fields. I would like to confirm that it is indeed a valid fix.

@germa we need to add the following CVTerm:

CPTAC accession number

Similar to the term for proteomeXchange:

https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1001919

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

What is the new software's name?

Workflow4Metabolomics

Describe the software briefly.

The collaborative portal dedicated to metabolomics data processing, analysis and annotation for Metabolomics community under Galaxy developed and supported by the French National infrastructure in metabolomics & fluxomics (MetaboHUB) and the French Institute of Bioinformatics (IFB).

Software type

MS:1001455 ! acquisition software, MS:1001456 ! analysis software, MS:1001457 ! data processing software, MS:1002414 ! postprocessing software, MS:1002878 ! small molecule analysis software, MS:1002964 ! lipidomics analysis software

Describe any additional information.

https://workflow4metabolomics.org/

[Term]
id: MS:1000XXX
name: SHA-256
def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000561 ! data file checksum type

We could add (deprecated) to other terms:
NIST formally deprecated use of SHA-1 in 2011 and MD-5 is deprecated even longer.
Yours,
Steffen

Please add enzyme Tryp-N, described in these manuscripts:

• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7857546/
• https://pubmed.ncbi.nlm.nih.gov/25419962/
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7842235/
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7995609/

It is also known as LysargiNase, sold by Millipore:
https://www.emdmillipore.com/US/en/product/LysargiNase,MM_NF-EMS0008

Suggested terms to add (instances of 0000000 need to be changed to valid numbers):

[Term]
id: MS:0000000
name: Tryp-N
def: "Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues." [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7857546/]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:0000000 ! (?=[KR])

[Term]
id: MS:0000000
name: (?=[KR])
def: "Regular expression for Tryp-N." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

Hi,

I wonder if you could point me to a small mzMLb example file?

Cheers
Soren

In the mass spectrometer files we need a Cvterm for apl file (peak list file from Andromeda search engine).

inside here https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000560

1. term: Tandem Mass Spectrometry
   synonyms: MS/MS, MS2
   definition: Technique to isolate ions (peptides) and subject ions to fragmentation.
   xref: http://purl.obolibrary.org/obo/NCIT_C18142

2. term: in-gel digestion
   synonyms: in-gel digest, In-Gel Tryptic Digestion
   definition: Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes.
   (perhaps a subclass of http://purl.obolibrary.org/obo/MS_1000831?)

3. term: in-solution digestion
   synonyms: in-solution digest
   definition: Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes.
   (perhaps a subclass of http://purl.obolibrary.org/obo/MS_1000831?)

-[ ] MaxQuant:protein group-level score
-[ ] MaxQuant:peptide PEP
-[ ] MaxQuant:evidence:score
-[ ] MaxQuant:evidence:PEP

For https://github.com/HUPO-PSI/psi-ms-CV/releases/download/4.1.31/psi-ms.obo , lines end in '\r\n'.
I think we don't want that.

Hi, our validation with fastobo-validator psi-ms.obo
in https://github.com/HUPO-PSI/psi-ms-CV/blob/master/.github/workflows/validate-obo.yml#L27
does not catch duplicated IDs. Unsure if any of the other (non-fast ?!) obolibrary/odkfull tools would catch that,
but the following bash one-liner checks that there are no duplicates:

test "X$(grep '^id:' /data/psi-ms.obo | uniq -d)" == "X" && echo TRUE

Yours, Steffen

Hi, @althonos here, I'm working with @rsalek and @Tomnl on mzML2isa,

I've detected an issue with values deriving from MS:1000465: they're listed as being children of PATO:0002186 (polarity) but PATO:0002186 defines the polarity (polar/nonpolar) and not the electric charge (negative/positive/neutral), that is defined by PATO:0002193.

Hence is it a tad strange to have "negative scan" as a children of "polarity" as PATO's polarity and MS's scan polarity are not representing the same idea.

As such,

[Term]
id: MS:1000129
name: negative scan
def: "Polarity of the scan is negative." [PSI:MS]
is_a: PATO:0002186 ! polarity
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

[Term]
id: MS:1000130
name: positive scan
def: "Polarity of the scan is positive." [PSI:MS]
is_a: PATO:0002186 ! polarity
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

sould be changed to

[Term]
id: MS:1000129
name: negative scan
def: "Polarity of the scan is negative." [PSI:MS]
is_a: PATO:0002193 ! electric charge
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

[Term]
id: MS:1000130
name: positive scan
def: "Polarity of the scan is positive." [PSI:MS]
is_a: PATO:0002193 ! electric charge
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

or completely removed as I don't feel they are really appropriate here.

Describe the new term or terms you would like to add.

Would it be possible to update the MS ontology terms with:

1. Synapt XS
2. SELECT SERIES Cyclic IMS
3. SELECT SERIES MRT

Synapt XS and SELECT SERIES Cyclic IMS can be described in terms of configuration as a Synapt G2-Si geometry.

SELECT SERIES MRT is a multi-reflecting time-of flight analyzer.

What is the new software's name?

PeakForest

Describe the software briefly.

A comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB).

Software type

MS:1003207 ! library creation software, MS:1002878 ! small molecule analysis software

Describe any additional information.

https://peakforest.org/

for proper activation element representation in mzML

@germa @edeutsch :

Can we make sure the following files are included in the PSI-MS ontology, for the file types:

• Quantification file URI
• FASTA file URI
• Spectrum Library file URI
• MS Image file URI

These terms are used in PRIDE submission pipeline, would be great to have them.

Hi;

We need terms for the following tools and their scores:

MSFragger

PeptideProphet

• peptideprophet probability

ProteinProphet

• proteinprophet score
• protein group probability
• protein probability
• peptide probability
• peptide weight
• peptide group weight

InterProphet

• interprophet probability

PTMProphet

• ptmprophet site localization predictions.

We also need a term to describe if a certain peptide was classified as razor. I noticed that some terms incorporate that into their description but they are for MaxQuant and Mascot, we need a generic term for
different pipelines.

Thanks

A while back some terms for our new mzMLb hybrid HDF5/XML file format were incorporated into the obo. Now that the manuscript is uploaded to bioRxiv (https://www.biorxiv.org/content/10.1101/2020.02.13.947218v1), we would like to add three further terms. These were specifically designed for mzMLb but also work fine with mzML etc. They require one integer parameter that specifies the level of truncation. They do not help if no compression is used, so I think it would be best to incorporate them into the obo in the same form as the MS-Numpress ones. i.e.:

[Term]
name: truncation and zlib compression
def: "Compression using truncation and zlib." [https://github.com/biospi/pwiz]
xref: value-type:xsd:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
name: truncation, delta prediction and zlib compression
def: "Compression using truncation, delta prediction and zlib." [https://github.com/biospi/pwiz]
xref: value-type:xsd:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

[Term]
name: truncation, linear prediction and zlib compression
def: "Compression using truncation, linear prediction and zlib." [https://github.com/biospi/pwiz]
xref: value-type:xsd:int "The number of mantissa bits truncated."
is_a: MS:1000572 ! binary data compression type

Best wishes,
Andy

Title says it all. Maybe README is sufficient as a start.
Do we want to have 1) An issue template for new terms,
and/or simply ask for pull requests ? Add a remark where IDs come from
(in case of 2) self chosen ?).
My main difficulty is that we can't have N simultaneously open PR each appending one Term at the end, and we can't have one big PR adding N terms if we want to be able to reject just one of the terms.
Yours, Steffen

Describe the question or discussion

Hi,

Is there a small example file using the PSI-MS ontology? I'm interested in how the binary data array class is populated, specifically for m/z array and intensity array. For example, the m/z array has the relationship has_units->m/z. So there is the m/z class. But I don't see a class specifying the definition of "array". Would something along the lines of rdf:Seq (ordered) suffice?

Cheers
David

The term MS:1002479, "regular expression" currently has 9 children (one of whom has several children of its own, MS:1001180, "Cleavage agent regular expression"). No specific flavor of regular expression is specified, though given that many different implementations all cover several common features, this is not usually an issue.

Three patterns use POSIX character class syntax, however, which are note widely supported or require specific flags:

MS:1002505 "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})." [PSI:PI]
MS:1002812 "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI]
MS:1002665 "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))." [PSI:PI]

While not specified in the controlled vocabulary, the mzIdentML specification does state in section 7.9 Enzyme definition that the regular expression used should be compatible with PCRE. While PCRE may use POSIX character classes, they must be placed within an extra pair of [ ] ([[:digit:]]) http://www.pcre.org/current/doc/html/pcre2syntax.html#SEC8, which is not the case here either.

Legalese aside, do these patterns still work for people? Are they in active use? What breaks if we replace [:digit:]with [0-9] or \d?

@edeutsch @germa

As we discussed in Beijing the Unimod Library has been added to OLS http://www.ebi.ac.uk/ols/ontologies/unimod This is one of the steps to move forward UNIMOD as a central place for Mass spectrometry Modifications. The guys from OLS would like that we improve the obo representation of unimod. But this is up to us.

Regards
Yasset

Describe the question or discussion

While checking activation methods provided by Thermo, I found several that aren't covered in current CV.
I am not sure if all of them require a separate CV term and, thus, decided to discuss it, before making a request for new term(s).
Please, share your thoughts on the following terms. Any help is much appreciated.

• Proton Transfer Reaction - PTR is an activation method introduced in latest generation of tribrid instruments (see, for example, PMC7008508). It is in fact ion-ion reaction, but in the world of Thermo it is considered an activation method.
• Negative Proton Transfer Reaction - I assume that is PTR of a negative precursor, thus, it should (probably) be covered by general PTR (the previous one). It is however, two different values for the activation method (according to Thermo's internal representation).
• Negative Electron Transfer Dissociation - again, I assume it is ETD of a negative precursor, and, thus, likely, a version of ETD (MS:1000598), but it is represented by a separate value.
• Ultraviolet Photodissociation - is it a type of multiphoton dissociation (MS:1000435)? Should it have a separate term?
• "SActivation" - don't know what it can be? Any suggestions?
• CardNanoSprayIonization - could not find any references for that ionization method. Is it just a type of nanoelectrospray or something significantly different?

mzMLb is a simplified HDF5 version of mzML which strips the base64 out of mzML and stores both the remainin mzML and the native floating point data as HDF5 datasets. For more info and download a pwiz version with mzMLb support please see here. I'd like to request the following terms be added to the ms CV to support it. In particular, so that the mzML is still valid we use a design very similar to imzML. Consequently, the CV params are very similar too, although not exactly the same as imzML as it stores all binary data in a single external file, whereas in mzMLb the BinaryDataArrays can be split amongst multiple HDF5 datasets (which is necessary as, for example, you can't mix 32bit and 64bit floats in a single HDF5 dataset).

Suggested terms:

[Term]
name: mzMLb format
def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
name: Conversion to mzMLb
def: "Conversion of a file format to Proteomics Standards Initiative mzML file format." [PSI:MS]
is_a: MS:1000530 ! file format conversion

[Term]
name: external HDF5 dataset
def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the <binary> section of the BinaryDataArray." [PSI:IMS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
name: external offset
def: "The position in the external data where the array begins." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: has_units UO:0000189 ! Count

[Term]
name: external array length
def: "Describes how many fields an array contains." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for this CV term."
relationship: has_units UO:0000189 ! Count

The following is an example of how the bottom three terms are used:

  <spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="0">
        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
        <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
        <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
        <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>
        <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="102.0338376" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
        <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1.75451e06" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
        <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="9.57907e06"/>
        <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="69.30234975236" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
        <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1414.143143938053" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
        <scanList count="1">
          <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
          <scan>
            <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="0.00660605" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
            <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="FTMS {1,1}  + p ESI Full lock ms [70.00-1400.00]"/>
            <scanWindowList count="1">
              <scanWindow>
                <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="70.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1400.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
              </scanWindow>
            </scanWindowList>
          </scan>
        </scanList>
        <binaryDataArrayList count="2">
          <binaryDataArray encodedLength="0">
            <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
            <userParam name="external HDF5 dataset" value="spectrum_MS_1000514_double"/>
            <userParam name="external array length" value="11944"/>
            <userParam name="external offset" value="0"/>
            <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
            <binary/>
          </binaryDataArray>
          <binaryDataArray encodedLength="0">
            <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
            <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
            <userParam name="external HDF5 dataset" value="spectrum_MS_1000515_float"/>
            <userParam name="external array length" value="11944"/>
            <userParam name="external offset" value="0"/>
            <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
            <binary/>
          </binaryDataArray>
        </binaryDataArrayList>
      </spectrum>

I would like to request a new software term added for MS-DIAL

http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/

I think it belongs below MS:1002878 (small molecule software) since it is described to apply to both metabolomics and lipidomics.

id MS:XXXXXXX
name MS-DIAL
def "MS-DIAL is a universal program for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372]
is_a MS:1002878 small molecule software ! small molecule software
is_a MS:1001457 data processing software ! data processing software

Hi, psi-ms is missing the quantification datatype(s) for xcms
as child of http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1002735

[Term]
id: MS:100XXXX
name: XCMS:into
def: "The data type feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:100XXXX
name: XCMS:intf
def: "The data type feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:100XXXX
name: XCMS:maxo
def: "The data type feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:100XXXX
name: XCMS:area
def: "The data type feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:MS]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

Hi!

Declaring that MS:1000266 (Laser Desorption) has been replaced by MS:1000393 is currently not done correctly: the current version of psi-ms.obo uses an alt_id, which actually assigns the MS:1000393 identifier to the MS:1000266, which is the opposite of what you want to do.

The right way to replace a term is to use the replaced_by clause (hopefully OBO-Edit lets you do that correctly):

[Term]
id: MS:1000266
name: Laser Desorption
def: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS]
comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393).
synonym: "Laser Ionization MERGE" EXACT []
synonym: "LD" EXACT []
is_obsolete: true
replaced_by: MS:1000393

[Term]
id: MS:1000393
name: laser desorption ionization
is_a: MS:1000247 ! desorption ionization

Hi,

http://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000465 says
"scan polarity is An acquisition mode to which specifies weather polarity is negative, positive or alternating.",
but the children are only positive and negative. We are missing alternating.
Problem is that this is a single scan attribute, and a single scan can't be both.
Second question is if this is still a is_a: MS:1000808 ! chromatogram attribute,
as an alternating polarity SRM or MRM is pretty useless.

[Term]
id: MS:1000XXX
name: alternating polarity scans
def: "Polarity of the scans is alternating, i.e. both positive and negative scans present [PSI:MS]
is_a: MS:1000465 ! scan polarity
is_a: MS:1000808 ! chromatogram attribute

Hi,
currently the timsTOF Pro is a singleton below Bruker Daltonics instrument model
https://www.ebi.ac.uk/ols/ontologies/ms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMS_1000122&viewMode=All&siblings=false

=> ask Bruker for a list of models and create a new Series.

Yours,
Steffen

We need a Probability Peptide score for Andromeda search engine:

[MS, MS:xxx, Andromeda:PEP,]

Can you @germa included this. Please is urgent .

Regards
Yasset