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From: Juan A. V. <ju...@eb...> - 2021-04-27 13:22:54
|
Hi Martin, Everything fine. Thanks a lot for this. Cheers, Juan Antionio > On 26 Apr 2021, at 15:05, Martin Eisenacher <mar...@ru...> wrote: > > Dear colleagues, > dear persons interested in the PSI developments, > > a minor update of the PSI DocProc definition has been agreed to by the > steering committee. > > It mentions "online document editing" systems for public review / removed > the mentioning of the > insecure "comment" function on psidev.info website, changes to shortened > public and > invited review phase from 60 to 45 days; changes the license model from > "Copyright" to "CC-BY-NC 4.0". > > It has to go through a 14-day public review, after which its status could be > changed to FINAL. > I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to > 1.1.1, so please add or > comment until May 10th! > > Thank you > Martin > -- > PD DR. MARTIN EISENACHER > Department Leader > DEPARTMENT Medical Bioinformatics > Medizinisches Proteom-Center > Medical Faculty > & > Medical Proteome Analysis > Center for Proteindiagnostics (PRODI) > > Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum > Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496 > E-mail mar...@ru... > www.medizinisches-proteom-center.de > > <20210426_PSI_Document_Process_ver_1.1.2_PREFINAL_DIFF.docx>_______________________________________________ > Psi-announce mailing list > Psi...@eb... > https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce |
From: Eric D. <ede...@sy...> - 2021-04-26 16:42:15
|
This looks good to me, thanks! -----Original Message----- From: Martin Eisenacher via Psidev-ms-dev <psi...@li...> Sent: Monday, April 26, 2021 7:06 AM To: psi...@li...; psi...@li...; psi...@li...; psi...@eb... Cc: Martin Eisenacher <mar...@ru...> Subject: [Psidev-ms-dev] PSI DocProc minor update 1.1.2 Dear colleagues, dear persons interested in the PSI developments, a minor update of the PSI DocProc definition has been agreed to by the steering committee. It mentions "online document editing" systems for public review / removed the mentioning of the insecure "comment" function on psidev.info website, changes to shortened public and invited review phase from 60 to 45 days; changes the license model from "Copyright" to "CC-BY-NC 4.0". It has to go through a 14-day public review, after which its status could be changed to FINAL. I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to 1.1.1, so please add or comment until May 10th! Thank you Martin -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Medical Faculty & Medical Proteome Analysis Center for Proteindiagnostics (PRODI) Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail mar...@ru... www.medizinisches-proteom-center.de |
From: Martin E. <mar...@ru...> - 2021-04-26 14:06:12
|
Dear colleagues, dear persons interested in the PSI developments, a minor update of the PSI DocProc definition has been agreed to by the steering committee. It mentions "online document editing" systems for public review / removed the mentioning of the insecure "comment" function on psidev.info website, changes to shortened public and invited review phase from 60 to 45 days; changes the license model from "Copyright" to "CC-BY-NC 4.0". It has to go through a 14-day public review, after which its status could be changed to FINAL. I attach version 1.1.2 PREFINAL_DIFF with changes marked in comparison to 1.1.1, so please add or comment until May 10th! Thank you Martin -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Medical Faculty & Medical Proteome Analysis Center for Proteindiagnostics (PRODI) Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail mar...@ru... www.medizinisches-proteom-center.de |
From: Martin E. <mar...@ru...> - 2020-10-19 15:05:15
|
Dear colleague, dear member of the Mass Spectrometry community, please forward this message to potentially interested colleagues! The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see <http://www.psidev.info> http://www.psidev.info for an overview of activities). A recommendation document specifying the Universal Spectrum Identifier (USI) has been submitted to the PSI document process. Because it is not a file format, there is neither a Schema definition nor XML / tab example files, but some practical examples of USIs from ProteomeXchange member DBs and others (included in the document). Specification document: https://github.com/HUPO-PSI/usi/blob/master/Specification/USI_SpecDoc_1.0.dr aft07_2020-09-29.docx?raw=true Use case examples: http://www.psidev.info/usi (USIs used in repository URLs). Development background: <https://github.com/HUPO-PSI/usi> https://github.com/HUPO-PSI/usi After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 1.0.0 DRAFT 7 now goes through 60-days public comments and external review phase (end: 18th December 2020). Purpose of the standard (excerpt from the spec. doc.): "This document presents a specification for a multi-part identifier of the form mzspec:<collection>:<msRun>:<indexType>:<indexNumber>:<optional interpretation> for mass spectra so that they may be easily and universally referenced for subsequent access. The Universal Spectrum Identifier (USI) describes a virtual path to locate a spectrum plus a possible interpretation of that spectrum. The USI is being implemented at most ProteomeXchange partner repositories and can be freely used by any other software. While initially implemented for the field of proteomics, its design is amenable to other fields that use mass spectrometers for analyte detection." PLEASE SEND COMMENTS directly to mar...@ru... for example regarding the following criteria: - That it is well formed - that is, it is presented in accordance with the templates and is clearly written. - That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format. This message is to encourage you to contribute to the standards development activity by commenting on the material that is attached as well as available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal. If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI. Many thanks for your valuable time and participation Martin Eisenacher (PSI Editor) -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Medical Faculty & Medical Proteome Analysis Center for Proteindiagnostics (PRODI) Building PRODI E2.269 | Gesundheitscampus 4 | D-44801 Bochum Fon +49 (0)234 32-18104 | Fax +49 (0)234 32-14496 E-mail <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de |
From: Eric D. <eri...@is...> - 2020-08-06 16:49:59
|
Hi everyone, I was trying to access the XLMOD controlled vocabulary through OLS but I’m having trouble. https://www.ebi.ac.uk/ols/ontologies/xlmod OLS knows about it. But it is unbrowsable. And trying to download it yields some weird OWL file that doesn’t seem to include the actual terms. It looks like the OBO file is here: https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo Is someone able to improve the OLS situation? Thanks, Eric |
From: Eric D. <eri...@is...> - 2020-03-05 16:57:27
|
I don’t know much about this instrument itself, but seems reasonable to me. My only suggested change is to remove the apostrophe. It is incorrectly used and unnecessary. But I also notice that all Bruker instruments have this (so Juan was just following the pattern, okay). But I vote that we fix this everywhere in the CV. i.e. s/Daltonics’/Daltonics/g Thermo doesn’t have apostrophes, Waters doesn’t have apostrophes. I assume the intent was to imply a possessive, but I propose we strip that for all Bruker models. It’s only in the definition anyway, so should not affect software. Thanks, Eric *From:* Juan Antonio Vizcaino <ju...@eb...> *Sent:* Thursday, March 5, 2020 3:46 AM *To:* psi...@li... *Cc:* psi...@li...; Mass spectrometry standard development <psi...@li...>; Deepti Jaiswal Kundu < ja...@eb...> *Subject:* [Psidev-ms-dev] New term needed for timsTOF Flex instrument Dear all, We have a submitter that has generated data coming from an timsTOF fleX instrument. This term is not yet in the PSI MS CV. The one that is there is for the timsTOF Pro (MS:1003005). So I am proposing to add it to the CV. [Term] id: MS:1xxxxx name: timsTOF fleX def: "Bruker Daltonics' timsTOF fleX." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model Thanks in advance, Juan |
From: Juan A. V. <ju...@eb...> - 2020-03-05 11:46:03
|
Dear all, We have a submitter that has generated data coming from an timsTOF fleX instrument. This term is not yet in the PSI MS CV. The one that is there is for the timsTOF Pro (MS:1003005). So I am proposing to add it to the CV. [Term] id: MS:1xxxxx name: timsTOF fleX def: "Bruker Daltonics' timsTOF fleX." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model Thanks in advance, Juan |
From: Gerhard M. <may...@ru...> - 2020-02-17 14:48:18
|
Dear proteomics/metabolomics community, following are the new and changed terms for the version 4.1.35 of the psi-ms.obo file, which can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo New CV terms in version 4.1.35 of psi-ms.obo: ============================================= [Term] id: MS:1003083 name: raw data file def: "Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file)." [PSI:MS] is_a: MS:1000577 ! source data file [Term] id: MS:1003084 name: processed data file def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000577 ! source data file [Term] id: MS:1003085 name: previous MSn-1 scan precursor intensity def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001141 ! intensity of precursor ion is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003086 name: precursor apex intensity def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001141 ! intensity of precursor ion is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003087 name: supported by repository but incomplete data and/or metadata def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1003088 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] id: MS:1003089 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] id: MS:1003090 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 Changed CV terms in version 4.1.35 of psi-ms.obo: ================================================= ************ Added is_a relation [Term] id: MS:1000224 name: molecular mass def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000861 ! molecular entity property relationship: has_units UO:0000002 ! mass unit ************ renamed and added relationship: part_of MS:1002806 ! ion [Term] id: MS:1000507 name: ion property def: "Nonphysical characteristic attributed to an ion." [PSI:MS] relationship: part_of MS:1002806 ! ion ************ Added is_a relation [Term] id: MS:1002959 name: isomer def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000859 ! molecule ************ renamed and added is_a relation [Term] id: MS:1000577 name: source data file def: "Data file from which an entity is sourced." [PSI:MS] synonym: "source file" EXACT [] relationship: part_of MS:1001458 ! spectrum generation information is_a: MS:1000499 ! spectrum attribute ************ changed the definition [Term] id: MS:1002856 name: Supported dataset by repository def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002857 name: Unsupported dataset by repository def: "Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Gerhard M. <may...@ru...> - 2020-01-21 12:54:25
|
Dear proteomics/metabolomics community, following are the new terms for the version 4.1.33 of the psi-ms.obo file, which can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains new terms for spectral libraries and a term for the MS-DIAL software. We also reorganized part of the CV, renamed some terms, reactivated some obsolete terms and made some definitions more clear. New CV terms in version 4.1.33 of psi-ms.obo: ============================================= [Term] id: MS:1003033 name: molecular entity attribute def: "Non-inherent characteristic attributed to a molecular entity." [PSI:PI] relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1003034 name: atom def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] is_a: MS:1000881 ! molecular entity [Term] id: MS:1003035 name: small molecule def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule] is_a: MS:1000859 ! molecule [Term] id: MS:1003036 name: metabolite def: "Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite] is_a: MS:1003035 ! small molecule [Term] id: MS:1003037 name: ribonucleotide def: "Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003038 name: deoxyribonucleotide def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003039 name: amino acid def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] is_a: MS:1003035 ! small molecule [Term] id: MS:1003040 name: monosaccharide def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003041 name: nucleic acid def: "Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid] is_a: MS:1000859 ! molecule [Term] id: MS:1003042 name: polysaccharide def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide] is_a: MS:1000859 ! molecule [Term] id: MS:1003043 name: number of residues def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003044 name: number of missed cleavages def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003045 name: peptide-to-protein mapping def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003046 name: peptide-to-protein mapping attribute def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] is_a: MS:1003045 ! peptide-to-protein mapping [Term] id: MS:1003047 name: protein sequence offset def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute [Term] id: MS:1003048 name: number of enzymatic termini def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute [Term] id: MS:1003049 name: peptidoform def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] is_a: MS:1000860 ! peptide [Term] id: MS:1003050 name: peptidoform attribute def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI] relationship: part_of MS:1003049 ! peptidoform [Term] id: MS:1003051 name: peptidoform ion def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] is_a: MS:1003049 ! peptidoform synonym: "precursor" RELATED [] synonym: "precursor ion" RELATED [] synonym: "parent ion" RELATED [] [Term] id: MS:1003052 name: peptidoform ion property def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI] relationship: part_of MS:1003051 ! peptidoform ion [Term] id: MS:1003053 name: theoretical monoisotopic m/z def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property [Term] id: MS:1003054 name: theoretical average m/z def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property [Term] id: MS:1003055 name: adduct def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct] is_a: MS:1000859 ! molecule [Term] id: MS:1003056 name: adduct ion property def: "Physical measurable characteristic of an adduct ion." [PSI:PI] relationship: part_of MS:1000353 ! adduct ion [Term] id: MS:1003057 name: scan number def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] is_a: MS:1000503 ! scan attribute [Term] id: MS:1003058 name: spectrum property def: "Inherent or measurable characteristic of a spectrum." [PSI:PI] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1003059 name: number of peaks def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] is_a: MS:1003058 ! spectrum property [Term] id: MS:1003060 name: number of data points def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] is_a: MS:1003058 ! spectrum property [Term] id: MS:1003061 name: spectrum name def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003062 name: spectrum index def: "Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003063 name: universal spectrum identifier def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003064 name: spectrum aggregation attribute def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003065 name: spectrum aggregation type def: "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003066 name: singleton spectrum def: "Spectrum that is not the result of some aggregation process." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003067 name: consensus spectrum def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003068 name: best replicate spectrum def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003069 name: number of replicate spectra available def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003070 name: number of replicate spectra used def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003071 name: spectrum origin attribute def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003072 name: spectrum origin type def: "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI] is_a: MS:1003071 ! spectrum origin attribute [Term] id: MS:1003073 name: observed spectrum def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003074 name: predicted spectrum def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003075 name: demultiplexed spectrum def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003076 name: uninterpreted spectrum def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003077 name: interpreted spectrum def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003078 name: interpreted spectrum attribute def: "Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI] relationship: part_of MS:1003077 ! interpreted spectrum [Term] id: MS:1003079 name: total unassigned intensity fraction def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003080 name: top 20 peak unassigned intensity fraction def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003081 name: unidentified modification monoisotopic mass delta def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML." [PSI:PI] is_a: MS:1001471 ! peptide modification details xref: value-type:xsd\:double "The allowed value-type for this CV term." relationship: has_units UO:0000221 ! dalton [Term] id: MS:1003082 name: MS-DIAL def: "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372] is_a: MS:1002878 ! small molecule software is_a: MS:1001457 ! data processing software Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Eric D. <eri...@is...> - 2020-01-16 21:52:34
|
Many thanks for putting this together, Gerhard. Here are some suggested refinements or corrections: [Term] id: MS:1003065 name: spectrum aggregation type def: "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003072 name: spectrum origin type def: "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI-PI] is_a: MS:1003071 ! spectrum origin attribute [Term] id: MS:1003033 name: molecular entity attribute def: "Non-inherent characteristic attributed to a molecular entity." [PSI:PI] relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1003050 name: peptidoform attribute def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI] relationship: part_of MS:1003049 ! peptidoform [Term] id: MS:1003052 name: peptidoform ion property def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI] relationship: part_of MS:1003051 ! peptidoform ion [Term] id: MS:1003058 name: spectrum property def: " Inherent or measurable characteristic of a spectrum." [PSI:PI] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1003064 name: spectrum aggregation attribute def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003071 name: spectrum origin attribute def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003078 name: interpreted spectrum attribute def: "Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI] relationship: part_of MS:1003077 ! interpreted spectrum [Term] id: MS:1003082 name: MS-DIAL def: "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372] is_a: MS:1002878 ! small molecule software is_a: MS:1001457 ! data processing software *From:* Gerhard Mayer via Psidev-ms-dev <psi...@li...> *Sent:* Thursday, January 16, 2020 12:10 AM *To:* psi...@li...; psi...@li...; psi...@li... *Cc:* Gerhard Mayer <may...@ru...> *Subject:* [Psidev-ms-dev] Release candidate 4.1.33_rc1 of psi-ms.obo Dear proteomics/metabolomics community, following are the new terms for the release version 4.1.33_rc1 of the psi-ms.obo file. It contains new terms for spectral libraries and a term for the MS-DIAL software. We also reorganized part of the CV, renamed some terms, reactivated some obsolete terms and made some definitions more clear. Please unpack and diff the two files to see the detailed changes. New CV terms in version 4.1.33_rc1 of psi-ms.obo: ================================================= [Term] id: MS:1003033 name: molecular entity attribute def: "A nonphysical characteristic attributed to a molecular entity." [PSI:PI] relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1003034 name: atom def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] is_a: MS:1000881 ! molecular entity [Term] id: MS:1003035 name: small molecule def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [ https://en.wikipedia.org/wiki/Small_molecule] is_a: MS:1000859 ! molecule [Term] id: MS:1003036 name: metabolite def: "Small molecule that is the intermediate end product of metabolism." [ https://en.wikipedia.org/wiki/Metabolite] is_a: MS:1003035 ! small molecule [Term] id: MS:1003037 name: ribonucleotide def: "Nucleotide containing ribose as its pentose component." [ https://en.wikipedia.org/wiki/Ribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003038 name: deoxyribonucleotide def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [ https://en.wikipedia.org/wiki/Deoxyribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003039 name: amino acid def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] is_a: MS:1003035 ! small molecule [Term] id: MS:1003040 name: monosaccharide def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [ https://en.wikipedia.org/wiki/Monosaccharide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003041 name: nucleic acid def: "Molecule composed of a chain of nucleotides." [ https://en.wikipedia.org/wiki/Nucleic_acid] is_a: MS:1000859 ! molecule [Term] id: MS:1003042 name: polysaccharide def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [ https://en.wikipedia.org/wiki/Polysaccharide] is_a: MS:1000859 ! molecule [Term] id: MS:1003043 name: number of residues def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003044 name: number of missed cleavages def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003045 name: peptide-to-protein mapping def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003046 name: peptide-to-protein mapping attribute def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] is_a: MS:1003045 ! peptide-to-protein mapping [Term] id: MS:1003047 name: protein sequence offset def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute [Term] id: MS:1003048 name: number of enzymatic termini def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute [Term] id: MS:1003049 name: peptidoform def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] is_a: MS:1000860 ! peptide [Term] id: MS:1003050 name: peptidoform attribute def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI] relationship: part_of MS:1003049 ! peptidoform [Term] id: MS:1003051 name: peptidoform ion def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] is_a: MS:1003049 ! peptidoform synonym: "precursor" RELATED [] synonym: "precursor ion" RELATED [] synonym: "parent ion" RELATED [] [Term] id: MS:1003052 name: peptidoform ion property def: "A physical characteristic of a peptidoform ion." [PSI:PI] relationship: part_of MS:1003051 ! peptidoform ion [Term] id: MS:1003053 name: theoretical monoisotopic m/z def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property [Term] id: MS:1003054 name: theoretical average m/z def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property [Term] id: MS:1003055 name: adduct def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [ https://en.wikipedia.org/wiki/Adduct] is_a: MS:1000859 ! molecule [Term] id: MS:1003056 name: adduct ion property def: "Physical measurable characteristic of an adduct ion." [PSI:PI] relationship: part_of MS:1000353 ! adduct ion [Term] id: MS:1003057 name: scan number def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] is_a: MS:1000503 ! scan attribute [Term] id: MS:1003058 name: spectrum property def: "Physical measurable characteristic of a spectrum." [PSI:PI] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1003059 name: number of peaks def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] is_a: MS:1003058 ! spectrum property [Term] id: MS:1003060 name: number of data points def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] is_a: MS:1003058 ! spectrum property [Term] id: MS:1003061 name: spectrum name def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003062 name: spectrum index def: "Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003063 name: universal spectrum identifier def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003064 name: spectrum aggregation attribute def: "Nonphysical characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003065 name: spectrum aggregation type def: "Categorization of a spectrum based on the type of aggregation it is based on (e.g., an individual spectrum, a consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003066 name: singleton spectrum def: "Spectrum that is not the result of some aggregation process." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003067 name: consensus spectrum def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003068 name: best replicate spectrum def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003069 name: number of replicate spectra available def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003070 name: number of replicate spectra used def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003071 name: spectrum origin attribute def: "Nonphysical characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003072 name: spectrum origin type def: "Categorization of a spectrum based on its type of aggregation (e.g., an individual spectrum, a consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003071 ! spectrum origin attribute [Term] id: MS:1003073 name: observed spectrum def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003074 name: predicted spectrum def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003075 name: demultiplexed spectrum def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003076 name: uninterpreted spectrum def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003077 name: interpreted spectrum def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003078 name: interpreted spectrum attribute def: "Nonphysical characteristic attributed to an interpreted spectrum." [PSI:PI] relationship: part_of MS:1003077 ! interpreted spectrum [Term] id: MS:1003079 name: total unassigned intensity fraction def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003080 name: top 20 peak unassigned intensity fraction def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003081 name: unidentified modification monoisotopic mass delta def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML." [PSI:PI] is_a: MS:1001471 ! peptide modification details xref: value-type:xsd\:double "The allowed value-type for this CV term." relationship: has_units UO:0000221 ! dalton [Term] id: MS:1003082 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 is_a: MS:1001457 ! data processing software Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... *Web: *www.ruhr-uni-bochum.de/mpc |
From: Gerhard M. <may...@ru...> - 2020-01-16 08:10:21
|
Dear proteomics/metabolomics community, following are the new terms for the release version 4.1.33_rc1 of the psi-ms.obo file. It contains new terms for spectral libraries and a term for the MS-DIAL software. We also reorganized part of the CV, renamed some terms, reactivated some obsolete terms and made some definitions more clear. Please unpack and diff the two files to see the detailed changes. New CV terms in version 4.1.33_rc1 of psi-ms.obo: ================================================= [Term] id: MS:1003033 name: molecular entity attribute def: "A nonphysical characteristic attributed to a molecular entity." [PSI:PI] relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1003034 name: atom def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] is_a: MS:1000881 ! molecular entity [Term] id: MS:1003035 name: small molecule def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule] is_a: MS:1000859 ! molecule [Term] id: MS:1003036 name: metabolite def: "Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite] is_a: MS:1003035 ! small molecule [Term] id: MS:1003037 name: ribonucleotide def: "Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003038 name: deoxyribonucleotide def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003039 name: amino acid def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] is_a: MS:1003035 ! small molecule [Term] id: MS:1003040 name: monosaccharide def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003041 name: nucleic acid def: "Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid] is_a: MS:1000859 ! molecule [Term] id: MS:1003042 name: polysaccharide def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide] is_a: MS:1000859 ! molecule [Term] id: MS:1003043 name: number of residues def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003044 name: number of missed cleavages def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003045 name: peptide-to-protein mapping def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003046 name: peptide-to-protein mapping attribute def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] is_a: MS:1003045 ! peptide-to-protein mapping [Term] id: MS:1003047 name: protein sequence offset def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute [Term] id: MS:1003048 name: number of enzymatic termini def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute [Term] id: MS:1003049 name: peptidoform def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] is_a: MS:1000860 ! peptide [Term] id: MS:1003050 name: peptidoform attribute def: "Nonphysical characteristic attributed to a peptidoform." [PSI:PI] relationship: part_of MS:1003049 ! peptidoform [Term] id: MS:1003051 name: peptidoform ion def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] is_a: MS:1003049 ! peptidoform synonym: "precursor" RELATED [] synonym: "precursor ion" RELATED [] synonym: "parent ion" RELATED [] [Term] id: MS:1003052 name: peptidoform ion property def: "A physical characteristic of a peptidoform ion." [PSI:PI] relationship: part_of MS:1003051 ! peptidoform ion [Term] id: MS:1003053 name: theoretical monoisotopic m/z def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property [Term] id: MS:1003054 name: theoretical average m/z def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property [Term] id: MS:1003055 name: adduct def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct] is_a: MS:1000859 ! molecule [Term] id: MS:1003056 name: adduct ion property def: "Physical measurable characteristic of an adduct ion." [PSI:PI] relationship: part_of MS:1000353 ! adduct ion [Term] id: MS:1003057 name: scan number def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] is_a: MS:1000503 ! scan attribute [Term] id: MS:1003058 name: spectrum property def: "Physical measurable characteristic of a spectrum." [PSI:PI] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1003059 name: number of peaks def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] is_a: MS:1003058 ! spectrum property [Term] id: MS:1003060 name: number of data points def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] is_a: MS:1003058 ! spectrum property [Term] id: MS:1003061 name: spectrum name def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003062 name: spectrum index def: "Integer index value associated with a spectrum within a collection of spectra, often in a spectral library. By custom, index counters should begin with 0." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003063 name: universal spectrum identifier def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003064 name: spectrum aggregation attribute def: "Nonphysical characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003065 name: spectrum aggregation type def: "Categorization of a spectrum based on the type of aggregation it is based on (e.g., an individual spectrum, a consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003066 name: singleton spectrum def: "Spectrum that is not the result of some aggregation process." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003067 name: consensus spectrum def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003068 name: best replicate spectrum def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003069 name: number of replicate spectra available def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003070 name: number of replicate spectra used def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003071 name: spectrum origin attribute def: "Nonphysical characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003072 name: spectrum origin type def: "Categorization of a spectrum based on its type of aggregation (e.g., an individual spectrum, a consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003071 ! spectrum origin attribute [Term] id: MS:1003073 name: observed spectrum def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003074 name: predicted spectrum def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003075 name: demultiplexed spectrum def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003076 name: uninterpreted spectrum def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003077 name: interpreted spectrum def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003078 name: interpreted spectrum attribute def: "Nonphysical characteristic attributed to an interpreted spectrum." [PSI:PI] relationship: part_of MS:1003077 ! interpreted spectrum [Term] id: MS:1003079 name: total unassigned intensity fraction def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003080 name: top 20 peak unassigned intensity fraction def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003081 name: unidentified modification monoisotopic mass delta def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the <Modification> element in mzIdentML." [PSI:PI] is_a: MS:1001471 ! peptide modification details xref: value-type:xsd\:double "The allowed value-type for this CV term." relationship: has_units UO:0000221 ! dalton [Term] id: MS:1003082 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 is_a: MS:1001457 ! data processing software Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Jones, A. <And...@li...> - 2019-12-05 17:04:58
|
Dear all, We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020, and registration is now open: http://www.psidev.info/hupo-psi-meeting-2020 There is no cost to attend the workshop, with lunches, coffee/tea and a workshop dinner included. You will have to cover your own costs for travel and hotels. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the Universal Spectrum Identifier, quality control and capturing study metadata, and on the molecular interactions side on mapping standards to Cytoscape. We will be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP). We are also planning a new session related to standards for glycoproteomics, to scope out the community need in this area. The PSI is always keen to recruit new members, so please join if you think you may be interested in data sharing and standards for proteomics. Please also get in touch, if you are interested to join PSI activities in general but cannot travel to San Diego. Best wishes Andy Jones (PSI Chair) |
From: Zaia, J. <jz...@bu...> - 2019-11-27 15:31:26
|
I have been in touch with Nathan Edwards (Georgetown University, copied). He expressed interest in attending the session to discuss supporting glycoproteomics data. Best regards, Joe From: Eric Deutsch <eri...@is...> Sent: Tuesday, November 26, 2019 7:40 PM To: Robert Chalkley <cha...@cg...>; Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... Subject: Re: [Psidev-pi-dev] [CompMS] Re: [Psi-announce] PSI2020 - Save the Date Hi Robert, great, thanks for contributing! We will try to schedule a specific session for this and announce it so that everyone knows when it is in advance. Thanks, Eric From: co...@go...<mailto:co...@go...> <co...@go...<mailto:co...@go...>> On Behalf Of Robert Chalkley Sent: Monday, November 25, 2019 9:01 AM To: Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>>; Jones, Andy <And...@li...<mailto:And...@li...>>; psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...> Subject: [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date I would also be keen to be involved in discussions about supporting glycopeptide data. Robert On 11/22/2019 11:21 AM, Zaia, Joseph wrote: Dear All, I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation. Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite. In addition, the glycan dissociates during tandem MS experiments. The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation. At present, quantitative software (Skyline and others) do not recognize glycosylation. Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user. Therefore, there is need to expand the manner by which peptides are represented informatically. It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant. It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins. Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? Thank you. Joe Zaia From: Jones, Andy <And...@li...><mailto:And...@li...> Sent: Thursday, November 21, 2019 11:29 AM To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...><mailto:psi...@li...>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...> Subject: [Psidev-pi-dev] PSI2020 - Save the Date Hi all, We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP). Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks. Best wishes Andy Jones on behalf of the PSI steering committee _______________________________________________ Psi-announce mailing list Psi...@eb...<mailto:Psi...@eb...> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- Robert Chalkley PhD Adjunct Professor Genentech Hall, N474A Tel: 415 476 5189 Fax: 415 502 1655 Mass Spectrometry Facility University of California San Francisco 600 16th Street, Genentech Hall, suite N472A San Francisco, CA 94143-2240 -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go...<mailto:com...@go...>. To view this discussion on the web visit https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu<https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer>. |
From: Eric D. <eri...@is...> - 2019-11-27 02:20:09
|
Hi Robert, great, thanks for contributing! We will try to schedule a specific session for this and announce it so that everyone knows when it is in advance. Thanks, Eric *From:* co...@go... <co...@go...> *On Behalf Of *Robert Chalkley *Sent:* Monday, November 25, 2019 9:01 AM *To:* Zaia, Joseph <jz...@bu...>; Jones, Andy <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... *Subject:* [CompMS] Re: [Psi-announce] [Psidev-pi-dev] PSI2020 - Save the Date I would also be keen to be involved in discussions about supporting glycopeptide data. Robert On 11/22/2019 11:21 AM, Zaia, Joseph wrote: Dear All, I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation. Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite. In addition, the glycan dissociates during tandem MS experiments. The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation. At present, quantitative software (Skyline and others) do not recognize glycosylation. Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user. Therefore, there is need to expand the manner by which peptides are represented informatically. It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant. It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins. Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? Thank you. Joe Zaia *From:* Jones, Andy <And...@li...> <And...@li...> *Sent:* Thursday, November 21, 2019 11:29 AM *To:* psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...> <psi...@li...>; psi...@li...; Co...@go... *Subject:* [Psidev-pi-dev] PSI2020 - Save the Date Hi all, We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP). Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks. Best wishes Andy Jones on behalf of the PSI steering committee _______________________________________________ Psi-announce mailing list Psi...@eb... https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- Robert Chalkley PhD Adjunct Professor Genentech Hall, N474A Tel: 415 476 5189 Fax: 415 502 1655 Mass Spectrometry Facility University of California San Francisco 600 16th Street, Genentech Hall, suite N472A San Francisco, CA 94143-2240 -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu <https://groups.google.com/d/msgid/compms/53fa5771-c50a-6f0d-5d17-de723112a016%40cgl.ucsf.edu?utm_medium=email&utm_source=footer> . |
From: Robert C. <cha...@cg...> - 2019-11-25 17:54:03
|
I would also be keen to be involved in discussions about supporting glycopeptide data. Robert On 11/22/2019 11:21 AM, Zaia, Joseph wrote: > > Dear All, > > I would like to initiate discussion for expanding the use cases for > proteomics to include complex protein glycosylation. Glycosylation is > as a rule heterogeneous, with 30 or so glycoforms per glycosite. In > addition, the glycan dissociates during tandem MS experiments. The > software and data standards need to be expanded to include the > glycosylation size, heterogeneity, and tandem MS dissociation. At > present, quantitative software (Skyline and others) do not recognize > glycosylation. Without this recognition the quantitative tools > developed for peptides cannot be adapted without tedious effort on the > part of the user. Therefore, there is need to expand the manner by > which peptides are represented informatically. It is important that > glycopeptides be included in the use cases for mzIdentML and mzQuant. > It is also important that spectral library generating software be > expanded to allow glycosylated peptides to facilitate use of data > independent experiments for glycoproteins. > > Would it be possible for me to communicate these ideas at the PSI > Workshop in San Diego? > > Thank you. > > Joe Zaia > > *From:* Jones, Andy <And...@li...> > *Sent:* Thursday, November 21, 2019 11:29 AM > *To:* psi...@eb...; ps...@eb...; Mass spectrometry > standard development <psi...@li...>; > psi...@li...; Co...@go... > *Subject:* [Psidev-pi-dev] PSI2020 - Save the Date > > Hi all, > > We are pleased to announce that the 2020 Annual workshop for the > Proteomics Standards Initiative (PSI) will take place in San Diego > USA, Mon 23^rd to Thurs 26^th March 2020. The workshop will focus on > developing data standards related to mass spectrometry for spectral > libraries, the universal spectrum identifier, quality control and > capturing study metadata, and in the molecular interactions side on > mapping standards to Cytoscape. We will also be welcoming the new PSI > work group – Intrinsically Disordered Proteins (IDP). > > Please save the date if you might be interested to attend, we are > always pleased to welcome new groups into the PSI. The registration > page will be made available in the coming weeks. > > Best wishes > > Andy Jones on behalf of the PSI steering committee > > > _______________________________________________ > Psi-announce mailing list > Psi...@eb... > https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce -- Robert Chalkley PhD Adjunct Professor Genentech Hall, N474A Tel: 415 476 5189 Fax: 415 502 1655 Mass Spectrometry Facility University of California San Francisco 600 16th Street, Genentech Hall, suite N472A San Francisco, CA 94143-2240 |
From: Zaia, J. <jz...@bu...> - 2019-11-25 15:12:57
|
Thanks, Juan. I look forward to attending the spring HUPO-PSI meeting. Joe From: Juan Antonio Vizcaino <ju...@eb...> Sent: Monday, November 25, 2019 8:04 AM To: Zaia, Joseph <jz...@bu...> Cc: Andy Jones <And...@li...>; psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... Subject: Re: [CompMS] [Psidev-pi-dev] PSI2020 - Save the Date Dear Joe, Thanks for your e-mail. You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot. Best regards, Juan On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...<mailto:jz...@bu...>> wrote: Dear All, I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation. Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite. In addition, the glycan dissociates during tandem MS experiments. The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation. At present, quantitative software (Skyline and others) do not recognize glycosylation. Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user. Therefore, there is need to expand the manner by which peptides are represented informatically. It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant. It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins. Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? Thank you. Joe Zaia From: Jones, Andy <And...@li...<mailto:And...@li...>> Sent: Thursday, November 21, 2019 11:29 AM To: psi...@eb...<mailto:psi...@eb...>; ps...@eb...<mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li...<mailto:psi...@li...>>; psi...@li...<mailto:psi...@li...>; Co...@go...<mailto:Co...@go...> Subject: [Psidev-pi-dev] PSI2020 - Save the Date Hi all, We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP). Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks. Best wishes Andy Jones on behalf of the PSI steering committee -- You received this message because you are subscribed to the Google Groups "CompMS" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go...<mailto:com...@go...>. To view this discussion on the web visit https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com<https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com?utm_medium=email&utm_source=footer>. |
From: Juan A. V. <ju...@eb...> - 2019-11-25 13:04:24
|
Dear Joe, Thanks for your e-mail. You are very welcome to present in San Diego. We are still discussing the agenda, but we will make sure you get a slot. Best regards, Juan > On 22 Nov 2019, at 19:21, Zaia, Joseph <jz...@bu...> wrote: > > Dear All, > > I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation. Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite. In addition, the glycan dissociates during tandem MS experiments. The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation. At present, quantitative software (Skyline and others) do not recognize glycosylation. Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user. Therefore, there is need to expand the manner by which peptides are represented informatically. It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant. It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins. > > Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? > > Thank you. > > Joe Zaia > From: Jones, Andy <And...@li... <mailto:And...@li...>> > Sent: Thursday, November 21, 2019 11:29 AM > To: psi...@eb... <mailto:psi...@eb...>; ps...@eb... <mailto:ps...@eb...>; Mass spectrometry standard development <psi...@li... <mailto:psi...@li...>>; psi...@li... <mailto:psi...@li...>; Co...@go... <mailto:Co...@go...> > Subject: [Psidev-pi-dev] PSI2020 - Save the Date > > Hi all, > > We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group – Intrinsically Disordered Proteins (IDP). > > Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks. > > Best wishes > Andy Jones on behalf of the PSI steering committee > > > -- > You received this message because you are subscribed to the Google Groups "CompMS" group. > To unsubscribe from this group and stop receiving emails from it, send an email to com...@go... <mailto:com...@go...>. > To view this discussion on the web visit https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com <https://groups.google.com/d/msgid/compms/BN7PR03MB38755FF1B30AC07417844AB8CE490%40BN7PR03MB3875.namprd03.prod.outlook.com?utm_medium=email&utm_source=footer>. |
From: Zaia, J. <jz...@bu...> - 2019-11-22 19:54:56
|
Dear All, I would like to initiate discussion for expanding the use cases for proteomics to include complex protein glycosylation. Glycosylation is as a rule heterogeneous, with 30 or so glycoforms per glycosite. In addition, the glycan dissociates during tandem MS experiments. The software and data standards need to be expanded to include the glycosylation size, heterogeneity, and tandem MS dissociation. At present, quantitative software (Skyline and others) do not recognize glycosylation. Without this recognition the quantitative tools developed for peptides cannot be adapted without tedious effort on the part of the user. Therefore, there is need to expand the manner by which peptides are represented informatically. It is important that glycopeptides be included in the use cases for mzIdentML and mzQuant. It is also important that spectral library generating software be expanded to allow glycosylated peptides to facilitate use of data independent experiments for glycoproteins. Would it be possible for me to communicate these ideas at the PSI Workshop in San Diego? Thank you. Joe Zaia From: Jones, Andy <And...@li...> Sent: Thursday, November 21, 2019 11:29 AM To: psi...@eb...; ps...@eb...; Mass spectrometry standard development <psi...@li...>; psi...@li...; Co...@go... Subject: [Psidev-pi-dev] PSI2020 - Save the Date Hi all, We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP). Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks. Best wishes Andy Jones on behalf of the PSI steering committee |
From: Jones, A. <And...@li...> - 2019-11-21 16:29:25
|
Hi all, We are pleased to announce that the 2020 Annual workshop for the Proteomics Standards Initiative (PSI) will take place in San Diego USA, Mon 23rd to Thurs 26th March 2020. The workshop will focus on developing data standards related to mass spectrometry for spectral libraries, the universal spectrum identifier, quality control and capturing study metadata, and in the molecular interactions side on mapping standards to Cytoscape. We will also be welcoming the new PSI work group - Intrinsically Disordered Proteins (IDP). Please save the date if you might be interested to attend, we are always pleased to welcome new groups into the PSI. The registration page will be made available in the coming weeks. Best wishes Andy Jones on behalf of the PSI steering committee |
From: Gerhard M. <may...@ru...> - 2019-11-21 07:49:51
|
Dear Joseph, at the moment we plan for Mon 23^rd to Thurs 26^th March 2020 at UCSD in San Diego. The official announcement and registration page will be posted soon on our HUPO-PSI website on http://www.psidev.info/events Cheers, Gerhard On 20.11.2019 21:54, Zaia, Joseph wrote: > > Dear Gerhard, > > Thank you for your reply. I have subscribed to the PSI-PI mailing list. > > In principle, I am interested in attending the HUPO-PSI spring > meeting. But I cannot find information about the date and location. > Could you send me a link? > > Many thanks. > > Joe > > *From:*Gerhard Mayer <may...@ru...> > *Sent:* Wednesday, November 20, 2019 10:52 AM > *To:* Zaia, Joseph <jz...@bu...>; psi...@li... > *Cc:* Klein, Joshua, Adam <ja...@bu...>; Hackett, William, Edwin > <weh...@bu...> > *Subject:* Re: Proteomics standards for glycosylated proteins > > Dear Joseph, > > yes, support for glycoproteomics is still missing in mzIdentML and > I agree that this would be an important extension for a future version > of mzIdentML. > > Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) > is a community effort > of the Proteomics Informatics (PI) group of the HUPO-PSI > (http://www.psidev.info), > I forward your request to the PSI-PI mailing list > (psi...@li... > <mailto:psi...@li...>). > You are invited to subscribe to that list at > https://sourceforge.net/projects/psidev/lists/psidev-pi-dev > <https://sourceforge.net/projects/psidev/lists/psidev-pi-dev> > > Maybe you and/or your associates can attend to the next HUPO-PSI > spring meeting to discuss glycoproteomics support in more details? > HUPO-PSI always welcomes new contributors for further development of > their standard formats. > > Best regards > Gerhard Mayer > HUPO-PSI ontology coordinator > > On 20.11.2019 16:26, Zaia, Joseph wrote: > > Dear Gerhard, > > I am writing to initiate discussion of proteomics exchange > standards for glycosylated proteins. My research group develops > mass spectrometry based methods and bioinformatics for > quantification of glycoprotein glycosylation. We suggest that the > use cases for mzIdentML standard be expanded to include > site-specific protein glycosylation. We note that the use cases > for the mzIdentML1 2.0 release include protein cross-linking and > molecular interaction data that can be inferred from > cross-linking. There is a growing need to expand this to include > glycosylation. > > Many cell surface and extracellular proteins undergo glycosylation > as they pass through the secretory pathway. The glycosylation > reactions do not go to completion, resulting in microheterogeneity > at each protein glycosylation site. Glycans are relatively large > chemical modifications that undergo dissociation during tandem MS > events. Therefore, it is necessary to modify mzIdentML and/or > other exchange standards to include this reality. > > We are eager to engage you and other HUPO Proteome Standards > Initiative members in discussing how to expand the scope or > exchange standards to include glycoproteins. Can you suggest > stake holders who should be included in this conversation? > > Many thanks! > > Joe Zaia > > Joseph Zaia (he/his/him) > > Professor, Biochemistry > > Member, Bioinformatics Program > > Associate Director, Center for Biomedical Mass Spectrometry > > Boston University Medical Campus > > 670 Albany St., Rm. 509 > > Boston, MA 02118 > > USA > > Office: 1-617-358-2429 > > -- > > *----------------------------------------------------------------------* > > *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* > > *Research associate* > > *Ruhr-Universität Bochum, Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* > > *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 > > *E-Mail: *ger...@ru... <mailto:ger...@ru...> > > *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> > -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Zaia, J. <jz...@bu...> - 2019-11-20 21:28:09
|
Dear Gerhard, Thank you for your reply. I have subscribed to the PSI-PI mailing list. In principle, I am interested in attending the HUPO-PSI spring meeting. But I cannot find information about the date and location. Could you send me a link? Many thanks. Joe From: Gerhard Mayer <may...@ru...> Sent: Wednesday, November 20, 2019 10:52 AM To: Zaia, Joseph <jz...@bu...>; psi...@li... Cc: Klein, Joshua, Adam <ja...@bu...>; Hackett, William, Edwin <weh...@bu...> Subject: Re: Proteomics standards for glycosylated proteins Dear Joseph, yes, support for glycoproteomics is still missing in mzIdentML and I agree that this would be an important extension for a future version of mzIdentML. Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) is a community effort of the Proteomics Informatics (PI) group of the HUPO-PSI (http://www.psidev.info), I forward your request to the PSI-PI mailing list (psi...@li...<mailto:psi...@li...>). You are invited to subscribe to that list at https://sourceforge.net/projects/psidev/lists/psidev-pi-dev Maybe you and/or your associates can attend to the next HUPO-PSI spring meeting to discuss glycoproteomics support in more details? HUPO-PSI always welcomes new contributors for further development of their standard formats. Best regards Gerhard Mayer HUPO-PSI ontology coordinator On 20.11.2019 16:26, Zaia, Joseph wrote: Dear Gerhard, I am writing to initiate discussion of proteomics exchange standards for glycosylated proteins. My research group develops mass spectrometry based methods and bioinformatics for quantification of glycoprotein glycosylation. We suggest that the use cases for mzIdentML standard be expanded to include site-specific protein glycosylation. We note that the use cases for the mzIdentML1 2.0 release include protein cross-linking and molecular interaction data that can be inferred from cross-linking. There is a growing need to expand this to include glycosylation. Many cell surface and extracellular proteins undergo glycosylation as they pass through the secretory pathway. The glycosylation reactions do not go to completion, resulting in microheterogeneity at each protein glycosylation site. Glycans are relatively large chemical modifications that undergo dissociation during tandem MS events. Therefore, it is necessary to modify mzIdentML and/or other exchange standards to include this reality. We are eager to engage you and other HUPO Proteome Standards Initiative members in discussing how to expand the scope or exchange standards to include glycoproteins. Can you suggest stake holders who should be included in this conversation? Many thanks! Joe Zaia Joseph Zaia (he/his/him) Professor, Biochemistry Member, Bioinformatics Program Associate Director, Center for Biomedical Mass Spectrometry Boston University Medical Campus 670 Albany St., Rm. 509 Boston, MA 02118 USA Office: 1-617-358-2429 -- ---------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER Research associate Ruhr-Universität Bochum, Medizinisches Proteom-Center DEPARTMENT Medical Bioinformatics Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum Fon: +49 (0)234 32-18110 | Fax: +49 (0)234 32-14496 E-Mail: ger...@ru...<mailto:ger...@ru...> Web: www.ruhr-uni-bochum.de/mpc<http://www.ruhr-uni-bochum.de/mpc> |
From: Gerhard M. <may...@ru...> - 2019-11-20 15:51:59
|
Dear Joseph, yes, support for glycoproteomics is still missing in mzIdentML and I agree that this would be an important extension for a future version of mzIdentML. Since the mzIdentML standard (https://github.com/HUPO-PSI/mzIdentML) is a community effort of the Proteomics Informatics (PI) group of the HUPO-PSI (http://www.psidev.info), I forward your request to the PSI-PI mailing list (psi...@li...). You are invited to subscribe to that list at https://sourceforge.net/projects/psidev/lists/psidev-pi-dev Maybe you and/or your associates can attend to the next HUPO-PSI spring meeting to discuss glycoproteomics support in more details? HUPO-PSI always welcomes new contributors for further development of their standard formats. Best regards Gerhard Mayer HUPO-PSI ontology coordinator On 20.11.2019 16:26, Zaia, Joseph wrote: > > Dear Gerhard, > > I am writing to initiate discussion of proteomics exchange standards > for glycosylated proteins. My research group develops mass > spectrometry based methods and bioinformatics for quantification of > glycoprotein glycosylation. We suggest that the use cases for > mzIdentML standard be expanded to include site-specific protein > glycosylation. We note that the use cases for the mzIdentML1 2.0 > release include protein cross-linking and molecular interaction data > that can be inferred from cross-linking. There is a growing need to > expand this to include glycosylation. > > Many cell surface and extracellular proteins undergo glycosylation as > they pass through the secretory pathway. The glycosylation reactions > do not go to completion, resulting in microheterogeneity at each > protein glycosylation site. Glycans are relatively large chemical > modifications that undergo dissociation during tandem MS events. > Therefore, it is necessary to modify mzIdentML and/or other exchange > standards to include this reality. > > We are eager to engage you and other HUPO Proteome Standards > Initiative members in discussing how to expand the scope or exchange > standards to include glycoproteins. Can you suggest stake holders who > should be included in this conversation? > > Many thanks! > > Joe Zaia > > Joseph Zaia (he/his/him) > > Professor, Biochemistry > > Member, Bioinformatics Program > > Associate Director, Center for Biomedical Mass Spectrometry > > Boston University Medical Campus > > 670 Albany St., Rm. 509 > > Boston, MA 02118 > > USA > > Office: 1-617-358-2429 > -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Gerhard M. <may...@ru...> - 2019-11-19 12:42:47
|
Dear proteomics/metabolomics community, following are the new terms for the version 4.1.32 of the psi-ms.obo file, which can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo New CV terms in version 4.1.32 of psi-ms.obo: ============================================= [Term] id: MS:1003032 name: compound identification confidence code in MS-DIAL def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Gerhard M. <may...@ru...> - 2019-11-13 14:21:23
|
Dear proteomics/metabolomics community, following are the new terms for the release candidate 4.1.32_rc1 of the psi-ms.obo file. New CV terms in version 4.1.32_rc1 of psi-ms.obo: ================================================= [Term] id: MS:1003032 name: compound identification confidence code in MS-DIAL def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute Best Regards, Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |
From: Gerhard M. <may...@ru...> - 2019-10-31 13:10:43
|
Dear proteomics/metabolomics community, following are the new and modified terms from the version 4.1.31 of the psi-ms.obo file. It can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo New CV terms version 4.1.31_rc1 of psi-ms.obo: ============================================== [Term] id: MS:1003031 name: CPTAC accession number def: "Main identifier of a CPTAC dataset." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier Modified CV terms version 4.1.31_rc1 of psi-ms.obo: =================================================== [Term] id: MS:1002810 name: adduct ion mass X m/z def: "Theoretical m/z of the X component in the adduct M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabeled as 'Mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [DOI:10.1016/S1044-0305(99)00089-6, http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002809 ! adduct ion attribute Best regards Gerhard -- *----------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *Research associate* *Ruhr-Universität Bochum, Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building ProDi E2.234 | Gesundheitscampus 4 | D-44801 Bochum* *Fon: *+49 (0)234 32-18110 | *Fax: *+49 (0)234 32-14496 *E-Mail: *ger...@ru... <mailto:ger...@ru...> *Web: *www.ruhr-uni-bochum.de/mpc <http://www.ruhr-uni-bochum.de/mpc> |