Expand description
§Handle PSM files
Handling many different formats of PSM files. Supports these formats:
- mzTab
- Fasta
- Spectrum Sequence List (SSL)
- mzSpecLib (only with feature
mzannotate)
And output from the following programs:
- BiatNovo
- DeepNovo
- InstaNovo
- MaxQuant
- MetaMorpheus
- MSFragger
- NovoB
- Novor
- OPair
- Peaks
- PepNet
- PGPointNovo
- PLGS
- pLink
- PointNovo
- PowerNovo
- Proteoscape
- pUniFind
- Sage
- π-HelixNovo
- π-PrimeNovo
§Compilation features
mzannotate- Adds mzannotate as a dependency and allow mzSpecLib spectra to be used as PSM and allow other formats to parse annotated spectra
§Changelog
§0.2.1
- Fix mzident being able to be built without feature mzannotate
§0.2.0
- Better InstaNovo parsing and version detection thanks to @BioGeek
- Full mzTab metadata support in reading and writing
- Renamed identified peptidoform to PSM to align better with general terms
- Better protein handling with the trait ProteinMetaData
- All software now have a PSI-MS term
Modules§
- mztab_
writer - Write mzTab files.
- prelude
- A subset of the types and traits that are envisioned to be used the most, importing this is a good starting point for working with the crate
Structs§
- BasicCSV
Format - The type to contain the format description for BasicCSV files.
- BasicCSVPSM
- The data for individual entries in BasicCSV files.
- CVTerm
- Define a parameter for an mzTab file
- Deep
Novo Family Format - The type to contain the format description for DeepNovoFamily files.
- Deep
Novo FamilyPSM - The data for individual entries in DeepNovoFamily files.
- Fasta
Data - A single parsed line of a fasta file
- Insta
Novo Format - The type to contain the format description for InstaNovo files.
- Insta
NovoPSM - The data for individual entries in InstaNovo files.
- MSFragger
Format - The type to contain the format description for MSFragger files.
- MSFraggerPSM
- The data for individual entries in MSFragger files.
- MSFragger
Protein - The data for proteins in MSFragger files.
- MaxQuant
Format - The type to contain the format description for MaxQuant files.
- MaxQuantPSM
- The data for individual entries in MaxQuant files.
This can contain data from the database match and the de novo match at the same time when
run with MaxNovo. In that case the de novo data will not be shown via the methods of the
PSMMetaDatatrait. If access is needed solely to the de novo data and not to the database data the easiest way is detecting this case and overwriting the data in place. - Maybe
Peptidoform - A structure where a peptidoform might be present
- Meta
Morpheus Format - The type to contain the format description for MetaMorpheus files.
- Meta
MorpheusPSM - The data for individual entries in MetaMorpheus files.
- Meta
Morpheus Protein - The data for proteins in MetaMorpheus files.
- MzTabPSM
- Peptidoform data from a mzTab file
- MzTab
Protein - A protein definition from mzTab
- NoProtein
- A basic type to use a placeholder when a PSM format does not contain any protein level information.
- NovoB
Format - The type to contain the format description for NovoB files.
- NovoBPSM
- The data for individual entries in NovoB files.
- Novor
Format - The type to contain the format description for Novor files.
- NovorPSM
- The data for individual entries in Novor files.
- Opair
Format - The type to contain the format description for Opair files.
- OpairPSM
- The data for individual entries in Opair files.
- Opair
Protein - The data for proteins in Opair files.
- PLGS
Format - The type to contain the format description for PLGS files.
- PLGSPSM
- The data for individual entries in PLGS files.
- PLGS
Protein - The data for proteins in PLGS files.
- PLink
Format - The type to contain the format description for PLink files.
- PLinkPSM
- The data for individual entries in PLink files.
- PSM
- A peptidoform that is identified by a de novo or database matching program as matching to a spectrum
- PSMIter
- An iterator returning parsed PSMs
- PUni
Find Format - The type to contain the format description for PUniFind files.
- PUni
FindPSM - The data for individual entries in PUniFind files.
- Peaks
Family Id - The scans identifier for a peaks identification
- Peaks
Format - The type to contain the format description for Peaks files.
- PeaksPSM
- The data for individual entries in Peaks files.
- PepNet
Format - The type to contain the format description for PepNet files.
- PepNetPSM
- The data for individual entries in PepNet files.
- Peptidoform
Present - A structure where a peptidoform definitely is present
- PiHelix
Novo Format - The type to contain the format description for PiHelixNovo files.
- PiHelix
NovoPSM - The data for individual entries in PiHelixNovo files.
- PiPrime
Novo Format - The type to contain the format description for PiPrimeNovo files.
- PiPrime
NovoPSM - The data for individual entries in PiPrimeNovo files.
- Power
Novo Format - The type to contain the format description for PowerNovo files.
- Power
NovoPSM - The data for individual entries in PowerNovo files.
- Proteoscape
Format - The type to contain the format description for Proteoscape files.
- ProteoscapePSM
- The data for individual entries in Proteoscape files.
- Sage
Format - The type to contain the format description for Sage files.
- SagePSM
- The data for individual entries in Sage files.
- Spectrum
Sequence List Format - The type to contain the format description for SpectrumSequenceList files.
- Spectrum
Sequence ListPSM - The data for individual entries in SpectrumSequenceList files.
Enums§
- BasicCSV
Version - All possible basic CSV versions
- Deep
Novo Family Version - All possible DeepNovoFamily versions
- Fasta
Identifier - A fasta identifier following the NCBI identifier definition
- File
Format - A file format that might not be (fully) known
- Insta
Novo Version - All possible InstaNovo versions
- Known
File Format - A file format that is fully known
- MSFragger
Open Modification - A MSFragger open search modification
- MSFragger
Version - All possible MSFragger versions
- MaxQuant
Version - All possible MaxQuant versions
- Meta
Morpheus Match Kind - Meta
Morpheus Version - All possible peaks versions
- NovoB
Version - All possible NovoB versions
- Novor
Version - All available Novor versions
- Opair
Version - All possible peaks versions
- PLGS
Version - All possible PLGS versions
- PLink
Peptide Type - The different types of peptides a cross-link experiment can result in
- PLink
Version - All possible pLink versions
- PSMData
- The definition of all special metadata for all types of PSM that can be read
- PUni
Find Version - All possible pUniFind versions
- Peaks
Version - All possible peaks versions
- PepNet
Version - All possible PepNet versions
- PiHelix
Novo Version - All possible π-HelixNovo versions
- PiPrime
Novo Version - All possible π-PrimeNovo versions
- Power
Novo Version - All possible PowerNovo versions
- Protein
Data - The definition of all special metadata for all types of Proteins that can be read
- Proteoscape
Version - All available Novor versions
- Reliability
- The reliability of a PSM
- Sage
Version - All possible Sage versions
- Spectrum
Id - A spectrum identifier
- Spectrum
Ids - Multiple spectrum identifiers
- Spectrum
Sequence List Version - All possible SpectrumSequenceList versions
- Used
Model - The model that produced the final prediction for an InstaNovoPlus
Constants§
- AB
- Version Ab of PEAKS export
- BASIC
- msms.txt
- DB_
PEPTIDE - Version DB peptide of PEAKS export
- DB_
PROTEIN_ PEPTIDE - Version DB protein peptide of PEAKS export protein group, protein id, protein accession, unique, start, end,
- DB_PSM
- Version DB psm of PEAKS export
- DEEPNOVO_
V0_ 0_ 1 - The only known version of DeepNovo
- FRAGPIPE_
V22 - v22
- FRAGPIPE_
V20_ OR_ 21 - v20 or v21
- INSTANOVOPLUS_
V1_ 1_ 4 - The known InstaNovoPlus 1.1.4 output schema
- INSTANOVOPLUS_
V1_ 2_ 2 - InstaNovoPlus version 1.2.2 standalone output
- INSTANOVO_
COMBINED_ V1_ 2_ 2 - InstaNovo version 1.2.2 combined transformer and InstaNovoPlus refined output
- INSTANOVO_
V1_ 0_ 0 - InstaNovo version 1.0.0
- INSTANOVO_
V1_ 1_ 0 - InstaNovo version 1.1.0
- INSTANOVO_
V1_ 1_ 4 - InstaNovo version 1.1.4
- INSTANOVO_
V1_ 2_ 2 - InstaNovo version 1.2.2 transformer output
- META_
MORPHEUS - The only supported format for [
MetaMorpheus] data - MSMS
- msms.txt
- MSMS_
SCANS - msmsScans.txt
- NEW_
DENOVO - denovo:
# id, scanNum, RT, mz(data), z, pepMass(denovo), err(data-denovo), ppm(1e6*err/(mz*z)), score, peptide, aaScore, - NEW_PSM
- PSM:
#id, spectraId, scanNum, RT, mz, z, pepMass, err, ppm, score, protein, start, length, origin, peptide, noPTMPeptide, aac, allProteins - NOVOB_
V0_ 0_ 1 - The only known version of NovoB
- NOVO_
MSMS_ SCANS - MaxNovo msmsScans.txt
- OLD_
DENOVO - The older supported format for denovo.csv files from Novor
- O_PAIR
- The only supported format for Opair data
- PEPNET_
V1_ 0 - The only known version of PepNet
- PHILOSOPHER
- Philosopher
- PIHELIXNOVO_
V1_ 1 - The only known version of π-HelixNovo
- PIPRIMENOVO_
V0_ 1 - The only known version of π-PrimeNovo
- POINTNOVOFAMILY
- The only known version of the PointNovo Family
- POWERNOVO_
V1_ 0_ 17 - The only known version of PowerNovo
- PSM202305
- The older supported format (202305) for psms.csv files from Novor ID,Fraction,Scan #,m/z,z,Score,Mass,Error (ppm),“# Proteins”,Sequence
- PSM202308
- The older supported format (202308) for psms.csv files from Novor
- PUNIFIND_
V0_ 1 - The only version of pUniFind
- SILAC
- MaxQuant v2.4.14.0 SILAC evidence.txt
- SSL
- General type of SSL files
- V2_3
- The only built in version of pLink export
- V11
- Version 11 of PEAKS export
- V12
- Version 12 of PEAKS export
- V11_
FEATURES - Version 11 of PEAKS export
- V13_DIA
- Version 13 Dia de novo missing: Delta RT, MS2 correlation, #precursors, gene, database, ion intensity, positional confidence
- V2025B
- Version 2025b
- VERSION_
0_ 14 - An older version of a Sage export
- VERSION_
3_ 0 - An older version of a PLGS export
- VERSION_
V4_ 2 - The only supported format for MSFragger data
- X
- An older version of a PEAKS export
- XPLUS
- Version X+ of PEAKS export (made for build 20 November 2019)
- X_
PATCHED - Version X of PEAKS export (made for build 31 January 2019)
Traits§
- PSMFile
Format Version - A version for an PSM file format
- PSMMeta
Data - Generalised access to meta data of PSMs
- PSMSource
- The required methods for any source of PSMs
- Peptidoform
Availability - A trait to mark all options for availability of peptidoforms
- Protein
Meta Data - Generalised access to meta data of identified peptidoforms
Functions§
- open_
psm_ file - Open the selected path and automatically determine the filetype. It will decompress gzipped files automatically.
Type Aliases§
- Boxed
Identified Peptide Iter - Convenience type to not have to type out long iterator types
- GeneralPS
Ms - A general generic PSM iterator from any source format