Package: seq-to-first-iso
Seq-to-first-isoCompute first two isotopologues intensity from peptide sequenceSeq-to-first-iso computes isotopologues M0 and M1 of peptides with a 99.99 % 12C enrichment for quantification bySLIM-labeling.It simulates auxotrophies by differentiating labelled and unlabelled amino acids.The documentation can be foundhere.Try the demo with Binder:InstallationWith pip$ pip install seq-to-first-isoWith conda$ conda install seq-to-first-iso -c biocondaDeveloper modeInstallcondaClone repo:$ git clone https://github.com/pierrepo/seq-to-first-iso
$ cd seq-to-first-isoCreate conda environment:$ conda env create -f environment.ymlRemark: for a fully reproducible environment, you could also use:$ conda env create -f environment.lock.ymlActivate conda environment:$ conda activate seq-to-first-isoInstall local package:$ pip install -e .UsageThe script takes a file with one sequence of amino acids per line and returns a tsv of the file with columns:sequencemassformulaformula_XM0_NCM1_NCM0_12CM1_12COnce installed, the script can be called with:$seq-to-first-isofilename[-ooutput_name][-namino_acids...]Optional arguments are in square bracketsThis will createfilename_stfi.tsvif filename is a correct file0.3.0 :The input file can have annotations separated by a tabulation before the sequences0.4.0 :Support forX!TandemPost-Translational Modifications addedOptions-h, --help:Provide a help page-v, --version:Provide the version-o, --output:Change the name of the output file-n, --non-labelled-aa:Take 1 or more amino acid separated by a commaExamplesYou can provide a list of amino acids which will keep default isotopic abundance:Supposingpeptides.txt:YAQEISR
VGFPVLSVKEHK
LAMVIIKEFVDDLKThe command$seq-to-first-isopeptides.txt-nV,Wwill createpeptides_stfi.tsv:sequencemassformulaformula_XM0_NCM1_NCM0_12CM1_12CYAQEISR865.42938099921C37H59O13N11C37H59O13N110.62064141405751790.2808708233682760.92065612317980330.05161907174495234VGFPVLSVKEHK1338.7659712609C63H102O16N16C48H102O16N16X150.45503589853771360.345060329281908550.75895583936629440.18515489894512063LAMVIIKEFVDDLK1632.91606619252C76H128O21N16S1C66H128O21N16S1X100.369940214812306270.33731883476142640.74750905586989470.15292723586285323Where, in 12C enrichment conditions, the isotopologue intensity M0_12C and M1_12C are computed with unlabelled Valine and Tryptophan (V and W have default isotopic abundance)You can change the name of the output file:$seq-to-first-isopeptides.txt-osequencewill create a file namedsequence.tsvCreditsBinderJupyter et al., "Binder 2.0 - Reproducible, Interactive, Sharable Environments for Science at Scale." Proceedings of the 17th Python in Science Conference. 2018. 10.25080/Majora-4af1f417-011Bioconda:Grüning, Björn, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, the Bioconda Team, and Johannes Köster. 2018. “Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences”.Nature Methods, 2018 doi:10.1038/s41592-018-0046-7.MIDAs:Alves G, Ogurtsov AY, Yu YK (2014) Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.J Am Soc Mass Spectrom, 25: 57-70. DOI: 10.1007/s13361-013-0733-7Pyteomics:Goloborodko, A.A.; Levitsky, L.I.; Ivanov, M.V.; and Gorshkov, M.V. (2013) “Pyteomics - a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics”,Journal of The American Society for Mass Spectrometry, 24(2), 301–304. DOI: 10.1007/s13361-012-0516-6Levitsky, L.I.; Klein, J.; Ivanov, M.V.; and Gorshkov, M.V. (2018) “Pyteomics 4.0: five years of development of a Python proteomics framework”,Journal of Proteome Research. DOI: 10.1021/acs.jproteome.8b00717SLIM-labeling:Léger T, Garcia C, Collomb L, Camadro JM. A Simple Light Isotope Metabolic Labeling (SLIM-labeling) Strategy: A Powerful Tool to Address the Dynamics of Proteome Variations In Vivo.Mol Cell Proteomics. 2017;16(11):2017–2031. doi:10.1074/mcp.M117.066936ChangelogDev1.1.0(2019-12-19)Add export_to_knime() function1.0.0(2019-12-05)Simplify interfaceTake .tsv as input fileTake peptide sequence and charge as input data (from input file)Check input file and input dataframeComply with PEP 8 and PEP 257Update API and CLI demo notebooks0.5.1(2019-07-10)Fixedseq_to_xcomp() can now correctly take a pyteomics.mass.Composition object as the second parameter0.5.0(2019-07-03)AddedFlag for version number in CLIJupyter notebook with Binder environment for demonstrationsDocumentation on Read the DocsConda availabilityChangedBreaking change: changed seq_to_midas() to seq_to_xcomp()Breaking change: changed seq_to_tsv() to seq_to_df()0.4.3(2019-06-26)FixedFix requirements not being installed withpip install0.4.2(2019-06-25)FixedFixsetup.cfg's installation requirements0.4.1(2019-06-24)Extend numpydoc style to all functions inseq_to_first_iso.py0.4.0(2019-06-21)ChangedAdd support for Xtandem ParsingBreaking change:sequence_parser() now returns a dict with "annotations", "raw_sequences", "sequences", "modifications" and "ignored_lines"Add get_mods_composition() that returns a composition from a list of Unimod PTMsRemove the appended "_stfi" if -o flag is provided0.3.0(2019-04-18)ChangedAdd support for files with annotations before the sequencesBreaking change:sequence_parser() now returns (annotations, sequences, ignored_lines)seq_to_tsv() now accepts (sequences, unlabelled_aa, annotations=None)FixedOutput files now have "_stfi" appended to differentiate from .tsv input files with the same name0.2.1(2019-04-17)Format CHANGELOG0.2.0(2019-04-17)Add bumpversionChangedseq_to_tsv() no longer writes a file, instead it returns a dataframe0.1.0(2019-04-08)First releaseBSD 3-Clause LicenseCopyright (c) 2019, Lilian Yang-crosson All rights reserved.
Copyright (c) 2019, Pierre Poulain All rights reserved.Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.