Pyteomics protocols

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Pyteomics specifications


Unique identifier OMICS_03361
Name Pyteomics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for Pyteomics

Pyteomics in pipeline

PMCID: 4425483
PMID: 25955586
DOI: 10.1371/journal.pone.0125068

[…] of all spectra was performed to find peptides undiscovered by sequest. two home-built programs, written in python 2.7.5, were used to assist de novo sequencing. except when standard python packages pyteomics [] was used, the gui was built using the pyqt4 (v. 4.9.6) package. the first program (mass2aa) was used to fit the mass provided by the user, to an amino acid composition, consisting […]

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Pyteomics in publications

PMCID: 5937359
PMID: 29528219
DOI: 10.1021/acs.analchem.7b05157

[…] followed two separate strategies, a regression and a classification approach. in the regression case, a simple linear model (lm) with a length correction parameter (lcp) was used. the python package pyteomics with lcp optimization was used for the lm implementation. in the classification case, a logistic regression (lr) and a feedforward neural network (fnn) were used. in both cases, […]

PMCID: 5726658
PMID: 29232402
DOI: 10.1371/journal.pone.0189647

[…] than 0.01%. in order to identify the vertebrate species to which the amino acid peptide sequences matched, protein entries from the database were subjected to in silico tryptic cleavage using the pyteomics [] python tools and library. taxonomic lineage for each protein was collected from the ncbi taxonomy database [] (20 january 2016). peptides were associated with the parent protein […]

PMCID: 5417831
PMID: 28302922
DOI: 10.1074/mcp.O117.067728

[…] for diffacto are freely available at under apache 2.0 license. package dependences: scipy, numpy, pandas (, networkx, pyteomics (), and scikit-learn ()., the aim of diffacto is to detect proteins that have different concentrations between samples and to quantify such differences. by comparing each sample to a common […]

PMCID: 4223503
PMID: 25100859
DOI: 10.1074/mcp.O114.038877

[…] product monoisotopic peaks. the masses of reliably identified (in terms of fdr) peptides were used as “software lock mass” for ms scale recalibration. a python script written in house and utilizing pyteomics package () was used for theoretical mass calculation. the rt-dependent calibration curve was calculated by the method of multivariate adaptive regression splines (mars) () based on the rt […]

PMCID: 4125726
PMID: 24895383
DOI: 10.1074/mcp.O113.035915

[…] regarded the most used file format for storing ms/ms data (). the mgf input files can be generated through standard proteomics software tools such as mascot distiller, massmatrix (), raw2msm (), pyteomics (), or msconvert (proteowizard) (). notably, the apl peak lists generated by maxquant are also supported. first (i) the user loads the mgf file into the spiid program by clicking “add mgf […]

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