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In acyl carrier proteins (ACP) for example, it serves as a \'swinging arm\' for the attachment of activated fatty acid and amino-acid groups. + + + + + + + + + Specific for sidechain of lysine. Does not modify the N-termini except for glycine at a slower rate than the side chain of lysine. + + + A lipid-type modification. HNE forms a Michael addition product on Cysteine, Histidine and Lysines. Unusually, it doesn\'t replace a hydrogen on the amino acid side chain. + + + The addition of a sugar unit to a protein amino acid, e.g. the addition of glycan chains to proteins. Addition of glucuronic acid. Observed for N-term G + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Reduction of Schiff base formed between K amino group and acetaldehyde + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lys modification is formation of Schiff base. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The two glycine residues left on ubiquitinylated lysine after tryptic digestion. + + + + + + + + + + + + + + + Can also be the product of reaction with EZ-Link Sulfo-NHS-SS-Biotin (Sulfosuccinimidyl 2-(biotinamido)-ethyl-1, 3-dithiopropionate) followed by reduction with DTT + + + + + + + + + + + + + + + + + + + + + Found on vision signal transduction proteins + + + + + + Found on vision signal transduction proteins + + + + + + Core structure of high-mannose N-linked oligosaccharides + + + + + + MS/MS experiments of mass spectrometric a-ions (MS^3) can be used for protein identification by library searching. T3-sequencing is such a technique (see reference). Search engines must recognize this \'virtual modification\' for this purpose. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Conversion of glycosylated asparagine residues upon deglycosylation with PGNase F in 18O labelled water. + + + + + + BHT metabolism has been studied in rats and mice in relation to tumor promotion. + + + Phosphoserine to S-ethylcystine\r\nvia Beta elimination/Michael addition of ethylthiol + + + DAET = 2-(dimethylamino)ethanethiol; The phosphorylation to amine is the beta elimination of phosphate and Michael addition of 2-(dimethylamino)ethanethiol to the site. + + + + + + + + + + + + + + + + + + OH-PGO and PGO react with arginine at a stoichiometry of 2:1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Different channels have the same nominal mass but slightly different exact masses. Use this value for all channels for quantitation purposes. mTRAQ heavy is identical to iTRAQ4plex 117 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Cytopiloyne is a polyacetylenic glucoside isolated form Bidens pilosa which can modulate T helper cell differentiation. Biotinylated cytopiloyne might be use to identify its receptor in T cell. + + + Cytopiloyne is a polyacetylenic glucoside isolated form Bidens pilosa which can modulated T helper cell differentiation. Biotinylated cytopiloyne might be use to identify its receptor in T cell. + + + + + + + + + + + + + + + PET = 2-[4-pyridyl]ethanethiol. This modification is a chemical derivative, based on a alkaline catalysed beta-elimination of phosphoserines and phosphothreonines and subsequent 1,4-addition of 2-[4-pyridine]ethanethiol. These modified serines and threonines produce in MS/MS a characteristic fragment which can be used for precursor-ion-scan experiments. + + + N-terminal sulfonation of diglycine to detect ubiquitination sites + + + + + + + + + + + + Potential protein modification when using AEBSF (Pefabloc) as a serine protease inhibitor. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EDC crosslinker is used to couple biotin PEO-amine to carboxyl groups or 5\' phosphate groups + + + The cleavage of a peptide bond between Try-Xxx with oxidation of tryptophan to the oxolactone occurs in the presence of BNPS-skatole. This is a useful method for the chemical cleavage of proteins specifically at tryptophan residues. + + + + + + + + + One note about this chemistry is that for W you have to take care of O2 big time (and extract the I-uracil monophosphate with organics to get rid of residual iodide). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + usually major adduct formed from malondialdehyde (MDA) with the amino group of lysine residues + + + + + + + + + + + + Discontinued Invitrogen X-link reagent + + + imidoester cross-linker + + + FP-biotin was designed to label the active site serine of serine esterases/proteases. + + + + + + Commercially available from Toronto Research Chemicals Inc, as of 2005. Designed to label the active site serine of serine esterases/proteases. + + + Michael addition adduct of 4-hydroxynonenal with histidine, cystein and lysine residues stabilized by reduction with NaBH4 + + + + + + + + + A selective label for the active site serine of the serine esterase/protease family. It has also been shown to label tyrosine in serum albumin. + + + Created by auto-catalytic dealkylation of the O-Diisopropylphosphate adduct. + + + Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied. + + + + + + Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied. + + + Observed + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + phycocyanobilin and phycobiliviolin have different structures but the same empirical formula + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescent derivative + + + + + + + + + + + + + + + Modification procedure used for phosphopeptide mapping + + + Found in canned food products + + + For SILAC experiments + + + + + + + + + + + + BHTOH is formed upon metabolism of BHT with P450 enzymes. The BHTOH is further metabolized to its quinone methide (electrophile) which reacts with -SH and -NH2 groups + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lactosylation of bovine Beta-Lactoglobulin + + + + + + + + + Dethiobiotin-FP was designed to label the active site serine of serine hydrolases (e.g. esterases, peptidases, lipases) + + + CLIP-TRAQ-2 H(17) C(10) C13 N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 141.0983 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 113 or 114 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. in preparation). + + + + + + + + + + + + + + + In a recent publication (see reference), we have shown that family 84 glycoside hydrolases contain a deep pocket beneath the 2-acetamido group of its substrate (N-acetyl-glucosamine). With this strucual feature in mind, we have designed a specific inhibitor that contains a chloride group appended to the end of the propyl chain on a known inhibitor termed propyl-NAG-thiazoline. We have shown kinetically that this molecule is a potent suicide inhibitor of this enzyme famiy and now wish to know the precise residue which is acting as the nucleophile to dispace the choride atom. We have included all residues that are in the vacinity of the chloride atom that could potentially act in a nucleophilic manner. + + + More commonly seen as a neutral loss + + + Different channels have the same nominal mass but slightly different exact masses. + + + Different channels have the same nominal mass but slightly different exact masses. + + + + + + + + + CLIP_TRAQ_3 (H(20) C(11) C13 N(3) O(4) is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 155.1 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 127 or 128 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. in preparation). + + + CLIP_TRAQ_4 is an in-house made compound that reacts with primary amines through a N-hydroxysuccinimide group leading to a 128.1 Da mass shift (monoisotopic) in MS mode. The reporter ion in MS/MS mode can either be 100 or 101 m/z depending on the position of isotopic C13 in the molecule. (Fahlman, R. and Overall, C.M. in preparation). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Reversible post-translational modification of proteins by nitrated fatty acids + + + Reversible post-translational modification of proteins by nitrated fatty acids + + + Attention: As the digest is typically applied AFTER ICPL_light/heavy labeling, only ProteinN-term labeling and Lys-specific labeling is applied. + + + + + + Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use this entry for all channels + + + + + + + + + Mass Spectroscopic Characterization of Protein Modification by 4-Hydroxy-2-(E)-nonenal and 4-Oxo-2-(E)-nonenal. + + + Covalent adduction of nucleophilic amino acids by 4-hydroxynonenal and 4-oxononenal + + + + + + Created by auto-catalytic dealkylation of the O-Dimethylphosphate adduct. + + + + + + Created by auto-catalytic dealkylation of the O-Diethylphosphate adduct. + + + + + + Created by auto-catalytic dealkylation of either the O-pinacolylmethylphosphonate adduct, or the O-isopropylmethylphosphonate adduct. + + + + + + Other 4 channels have the same nominal mass but slightly different exact mass. For quantitation purposes, use iTRAQ8plex for all channels + + + Beta-elimination and Michael addition of dithiothreitol (DTT) to serine and threonine adds a weight of approximately 136.2. + + + Carbodiimide mediated blocking of free carboxylic acids (Asp/Glu sidechains and C-termini) with ethanolamine; reaction yields an amide-bond between the carboxylic acid of the peptide/protein and the primary amine of ethanolamine; reaction irreversibly modifies carboxylic acids. Shown above is the composition of the mass adduct, after substraction of water. + + + m/z values of the TMT® fragment ions to be quantified for 6plex and 10plex: 126.12773 127.12476 128.13443 129.13147 130.14114 131.13818. Additional m/z values for 10plex: 127.13108 128.12811 129.13779 130.13482 + + + When the beta-elimination and Michael addition of dithiothreitol (DTT) (BEMAD) reaction is used with alkylated cysteine a sulfur group is lost leaving the addition of approximately 120.2 in the chemical reaction. + + + Duplex-TMT® reagents 2TMT-126, 2TMT-127. m/z values of the TMT® fragment ions to be quantified: 126.12773 127.13108 + + + This modification describes the \"native\" TMT Reagent without isotopic label. + + + Accurate mass for Exactag Thiol labels + + + Accurate mass for Exactag Amine labels. Includes the mass of the conjugation reagent + + + Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity. + + + Mass Spectorscopic Characterization of Protein Modification by 4-hydroxy-2-(E)-nonenal and 4-oxo-2-(E)-nonenal + + + Methionine is substituted in culture with azidohomoalanine. The azide group reacts with the alkyne group of DADPS Biotin Alkyne. + + + Synthesis and Reactions of Nitroso Sulphamethoxazole with Biological Nucleophiles: Implications for Immune Mediated Toxicity. + + + + + + + + + + + + + + + phenacyl bromide conjugated with a linker and biotin tag, details not published yet + + + Can be used for quantitative analysis of cysteine-containing peptides. Same reaction can be used for quantitative analysis of O-linked post-translational modifications to serines and threonines, but then the modification is 16 Da more in mass; i.e. isotopically labeled reagent adds 142 Da in mass. + + + + + + + + + + + + Modified peptides identified by isotope pattern. Restriction to cysteine-containing peptides combined with high mass accuracy allows peptide identification. + + + Can be used for quantitative analysis of O-linked post-translational modifications. Same reaction can be used for quantitative analysis of cysteine-containing peptides, but then the modification is 16 Da less in mass; i.e. isotopically labeled reagent adds 126 Da in mass. + + + N-terminal initiator methionine is removed by a methionine aminopeptidase from proteins where the residue following the methionine is Ala, Cys, Gly, Pro, Ser, Thr or Val. This is generally the final N-terminal state for proteins where the following residue was a Cys, Pro or Val. + + + The N-terminal initiator methionine is removed by a methionine aminopeptidase from proteins whose residue following the methionine is Ala, Cys, Gly, Pro, Ser, Thr or Val. Proteins whose following residue was Ala, Gly, Ser or Thr are then acetylated by an N(alpha)-acetyltransferase on the new N-terminus. + + + + + + + + + + + + + + + The formula has been reduced from H(34) to H(33) on 13 May 2009 so as to give correct observed m/z values. The charge on the TMPP means that ions have one less proton than would be expected + + + The two glycine residues left on SILAC labeled ubiquitinylated lysine after tryptic digestion + + + + + + For SILAC experiments, + PTM + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Protein which is posttranslationally modified by the attachment of cGMP on the sulfur atom of Cys or hydroxyl group of Ser residues. + + + Protein which is posttranslationally modified by the attachment of cGMP that has lost ribose 3\',5\'-cyclic monophosphate moiety on the sulfur atom of Cys or hydroxyl group of Ser. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Attention: As the digest is typically applied AFTER ICPL labeling, only ProteinN-term labeling and Lys-specific labeling is applied. + + + + + + + + + + + + MDCC is used extensively as a fluorescent probe to report changes in protein conformation. + + + + + + + + + + + + + + + + + + This modification describes the Super Heavy TMTpro Reagent. Upon HCD, this reagent releases a reporter ion of 135.151600 (monoisotopic mass) + + + Methionine (C5H11NO2S) is substituted in cell culture by Azidohomoalanine (C4H8N4O2). The azido group reacts with an alkyne group attached to a linker (PEO) with a biotin group at the end (C27H45N5O7S). As a result the side chain of Met (C3H7S) is substitued by C29H49N8O7S. + + + + + + + + + + + + + + + + + + Protein from animals exposed to organoarsenicals + + + for Brad Strader + + + for Brad Strader + + + for Brad Strader + + + for Brad Strader + + + + + + + + + + + + + + + for Bindu Abraham + + + + + + structural isomer to succinyl + + + The electrophilic moiety of the chemical forms a direct bond with the thiol bond of the cysteine. As a result, there are no losses of elements and the final adduct has the monoisotopic mass of the chemical at 820.3360 added to a cysteine at SH side chain. + + + + + + + + + + + + product of beta elimination of phospho- or glycosylated-Ser with addition of ethylamine + + + product of beta elimination of phospho- or glycosylated-Ser with addition of beta Mercapto Ethanol + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Created for Bindu Abraham 12/22/09 + + + Created for Bindu Abraham 12/22/09 + + + Created for Michael (Brad) Strader 2/12/10 + + + + + + + + + This modification describes the native cysteine-reactive cysTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ion of 126.127725 (monoisotopic mass). + + + This modification describes the isobaric sixplex cysteine-reactive cysTMT6 Reagents with isotopic labels. Upon CID, these reagents release reporter ions of 126.127725, 127.131079, 128.134433, 129.137787, 130.141141, and 131.138176 (monoisotopic mass). + + + + + + sometimes observed after elution of phosphopeptides from TiO2 with ammonium hydroxide + + + + + + + + + + + + + + + + + + Methionine (C5H11NO2S) is substituted in culture with azidohomoalanine (AHA - C4H8N4O2). The azide group reacts with the alkyne group propargylglycine-NH2. As a result the side chain of methionine (C3H7S) is substituted by C7H12N5O. + + + Methionine (C5H11NO2S) is substituted in culture with azidohomoalanine (AHA - C4H8N4O2). The azide group reacts with the alkyne group DDDDK-propargylglycine-NH2. As a result the side chain of methionine (C3H7S) is substituted by C29H44N11O14. + + + Created for Bindu Abraham 2010-10-05 + + + Created for Bindu Abraham 2010-10-05 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Created for Bindu Abraham 2011-01-25 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + TAMRA-FP was designed to label the active site serine of serine hydrolases (e.g. esterases, peptidases, lipases) + + + + + + Deoxyhypusine synthase catalyzes the formation of a deoxyhypusine by transferring an aminobutyl moiety from spermidine onto a conserved lysine residue within the eIF5A + + + Regulation of eIF5A by deoxyhypusine acetylation/deacetylation + + + Regulation of eIF5A by hypusine acetylation/deacetylation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Believed to be created in a secondary reaction after initial formation of an adduct between the organophosphate 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one and Tyr or Ser in proteins. + + + Created by hydrolysis of the product of the reaction of 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one with amino acids residues in proteins. + + + Created by reaction of 2-(o-cresyl)-4H-1,3,2-benzodioxaphosphorane-2-one with amino acid residues in proteins. + + + + + + + + + Unpublished chemically synthesized protein modification tool. + + + + + + Occasionally used as chemical tag. In most cases, +57 is actually over-alkylation with iodoacetamide + + + + + + + + + + + + + + + Side product of the three component Ugi-Joullie reaction. Pirrolidine is reacted with a isocianide modificated peptide (CNGGHHHHHH) to get a Pro-Gly-GGHHHHHH. The main product is the C-terminal modified protein. Unlikely Asp and Glu can react. + + + + + + Side product of the three component Ugi-Joullie reaction. Pirrolidine is reacted with a isocianide modificated glycine to get Protein-Pro-Gly. The main product is the C-terminal modified protein. Unlikely Asp and Glu can react. + + + Cysteine residue reacts with a chlorinated dipyridyl ligand to get a monoalkylated Cys-L1. The only product is this single cys mutant modified on that position. + + + + + + + + + + + + Side product of the three component Ugi-Joullie reaction. Pirrolidine is reacted with a isocianide modificated glycine to get Protein-Pro-Gly-Pro-Gly. The main product is the C-terminal modified protein. Unlikely Asp and Glu can react. + + + + + + + + + Modification by Hex(2) NeuAc using IME coupling to get glycosylated proteins + + + + + + Mentioned by Marshall Bern + + + + + + + + + + + + + + + + + + + + + + + + For SILAC experiments + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Different channels have the same nominal mass but slightly different exact masses. + + + Different channels have the same nominal mass but slightly different exact masses. + + + Different channels have the same nominal mass but slightly different exact masses. + + + Different channels have the same nominal mass but slightly different exact masses. + + + + + + + + + Chemical reaction with 2,4-dinitro-1-chloro benzene (DNCB) by nucleophilic attack on electrophilic amino acid side chains + + + + + + + + + + + + + + + + + + + + + Lab based observation that D5 NEM hydrolyses in an analogous way to NEM + + + + + + Adduct formed upon reaction of the organophosphate tabun with the active site serine of serine esterases/proteases such as butyrylcholinestease. + + + This adduct is a consequence of hydrolysis of the initial adduct formed by tabun (aging) on the active site serine of serine esterases/proteases such as butyrylcholinesterase. + + + + + + + + + + + + This modification describes the native iodoTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ion of 126.127725(monoisotopic mass). + + + This modification describes the native iodoTMT Reagent without isotopic label. Upon CID, this reagent releases a reporter ions of 126.127725, 127.124760, 128.134433, 129.131468, 130.141141, and 131.138176 (monoisotopic mass). + + + For SILAC experiments + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Different tags have the same nominal mass but slightly different exact masses. Use this modification for all tags for quantitation purposes. 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Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition search GlyConnect + + + Composition 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P. 1883–1898. + + + diff --git a/conf/modules.config b/conf/modules.config index 59da97fd..ce8c56d6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -146,6 +146,25 @@ process { ] } + withName: 'EASYPQP_CONVERT' { + publishDir = [ + enabled: false + ] + } + + withName: 'EASYPQP_LIBRARY' { + ext.args = [ + "--perform_rt_calibration False", + "--perform_im_calibration False", + "--nofdr", + ].join(' ').trim() + publishDir = [ + path: {"${params.outdir}/spectrum_library"}, + mode: params.publish_dir_mode, + pattern: '*speclib.tsv' + ] + } + withName: 'OPENMS_IDFILTER_QUANT' { ext.prefix = {"${meta.spectra}_fdr_filtered"} ext.args = "-best:spectrum_per_peptide 'sequence+charge+modification'" diff --git a/modules/local/easypqp/convert.nf b/modules/local/easypqp/convert.nf new file mode 100644 index 00000000..8951b9e5 --- /dev/null +++ b/modules/local/easypqp/convert.nf @@ -0,0 +1,58 @@ +process EASYPQP_CONVERT { + tag "$meta.id" + label 'process_single' + + conda "bioconda::easypqp=0.1.50" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/easypqp:0.1.50--pyhdfd78af_1' : + 'biocontainers/easypqp:0.1.50--pyhdfd78af_1' }" + + input: + tuple val(meta), path(pepxml), path(spectra) + path unimod + + output: + tuple val(meta), path("*.psmpkl") , emit: psmpkl + tuple val(meta), path("*.peakpkl"), emit: peakpkl + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + + """ + export MPLCONFIGDIR=/tmp/matplotlib + export XDG_CACHE_HOME=/tmp/fontconfig-cache + mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME + + easypqp convert \\ + --pepxml $pepxml \\ + --spectra $spectra \\ + --unimod $unimod \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + export MPLCONFIGDIR=/tmp/matplotlib + export XDG_CACHE_HOME=/tmp/fontconfig-cache + mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME + + touch "${prefix}.psmpkl" + touch "${prefix}.peakpkl" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/local/easypqp/library.nf b/modules/local/easypqp/library.nf new file mode 100644 index 00000000..3a10a360 --- /dev/null +++ b/modules/local/easypqp/library.nf @@ -0,0 +1,48 @@ +process EASYPQP_LIBRARY { + tag "$meta.id" + label 'process_single' + + conda "bioconda::easypqp=0.1.50" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/easypqp:0.1.50--pyhdfd78af_1' : + 'biocontainers/easypqp:0.1.50--pyhdfd78af_1' }" + + input: + tuple val(meta), path(psmpkl), path(peakpkl) + + output: + tuple val(meta), path("*.tsv") , emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + easypqp library \ + --out ${prefix}_speclib.tsv \ + $args \ + $psmpkl $peakpkl + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch "${prefix}_speclib.tsv" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + easypqp: \$(easypqp --version 2>&1 | sed 's/easypqp, version //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/workflows/mhcquant.nf b/workflows/mhcquant.nf index 339bb87b..b7e5a3ae 100644 --- a/workflows/mhcquant.nf +++ b/workflows/mhcquant.nf @@ -13,6 +13,8 @@ include { PYOPENMS_CHROMATOGRAMEXTRACTOR } from '../modules/local/pyopenms_chrom include { OPENMS_COMETADAPTER } from '../modules/local/openms_cometadapter' include { OPENMS_PEPTIDEINDEXER } from '../modules/local/openms_peptideindexer' include { DATAMASH_HISTOGRAM } from '../modules/local/datamash_histogram' +include { EASYPQP_CONVERT } from '../modules/local/easypqp/convert' +include { EASYPQP_LIBRARY } from '../modules/local/easypqp/library' include { PYOPENMS_IONANNOTATOR } from '../modules/local/pyopenms_ionannotator' include { OPENMS_TEXTEXPORTER } from '../modules/local/openms_textexporter' include { OPENMS_MZTABEXPORTER } from '../modules/local/openms_mztabexporter' @@ -33,14 +35,15 @@ include { QUANT } from '../subworkflows/local/quant' // // MODULE: Installed directly from nf-core/modules // -include { OPENMS_DECOYDATABASE } from '../modules/nf-core/openms/decoydatabase/main' -include { OPENMS_IDMASSACCURACY } from '../modules/nf-core/openms/idmassaccuracy/main' -include { OPENMS_IDMERGER } from '../modules/nf-core/openms/idmerger/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_mhcquant_pipeline' +include { OPENMS_DECOYDATABASE } from '../modules/nf-core/openms/decoydatabase/main' +include { OPENMS_IDMASSACCURACY } from '../modules/nf-core/openms/idmassaccuracy/main' +include { OPENMS_IDMERGER } from '../modules/nf-core/openms/idmerger/main' +include { OPENMS_IDFILTER as OPENMS_IDFILTER_FOR_SPECLIB } from '../modules/nf-core/openms/idfilter/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_mhcquant_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -131,6 +134,34 @@ workflow MHCQUANT { // RESCORE( ch_rescore_in ) ch_versions = ch_versions.mix(RESCORE.out.versions) + + // + // GENERATE SPECTRUM LIBRARY + // + RESCORE.out.fdr_filtered.join(ch_clean_mzml_file).view() + OPENMS_COMETADAPTER.out.idxml + .map { meta, idxml -> [ [id: "${meta.sample}_${meta.condition}"], meta, idxml] } + .combine(RESCORE.out.fdr_filtered, by:0) + .map { groupKey, meta, comet_idxml, fdr_filtered_idxml -> [meta, comet_idxml, fdr_filtered_idxml] } + .set { ch_fdrfilter_comet_idxml } + + OPENMS_IDFILTER_FOR_SPECLIB(ch_fdrfilter_comet_idxml) + + unimod = file("$projectDir/assets/250120_unimod_tables.xml", checkIfExists: true) + EASYPQP_CONVERT(OPENMS_IDFILTER_FOR_SPECLIB.out.filtered.join(ch_clean_mzml_file), unimod) + ch_versions = ch_versions.mix(EASYPQP_CONVERT.out.versions) + + EASYPQP_CONVERT.out.psmpkl + .map { meta, psmpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), psmpkl] } + .groupTuple() + .set { ch_psmpkl } + EASYPQP_CONVERT.out.peakpkl + .map { meta, peakpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), peakpkl] } + .groupTuple() + .set { ch_peakpkl } + + EASYPQP_LIBRARY(ch_psmpkl.join(ch_peakpkl)) + // // SUBWORKFLOW: QUANT // From d934dae7d556b5096169e6c7c50642b5f9327379 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 08:35:09 +0000 Subject: [PATCH 02/13] add support for global fdr-filtered spectrum library --- modules/local/easypqp/library.nf | 8 ++++++++ workflows/mhcquant.nf | 34 ++++++++++++++++++++++---------- 2 files changed, 32 insertions(+), 10 deletions(-) diff --git a/modules/local/easypqp/library.nf b/modules/local/easypqp/library.nf index 3a10a360..2abacf59 100644 --- a/modules/local/easypqp/library.nf +++ b/modules/local/easypqp/library.nf @@ -22,6 +22,10 @@ process EASYPQP_LIBRARY { def prefix = task.ext.prefix ?: "${meta.id}" """ + export MPLCONFIGDIR=/tmp/matplotlib + export XDG_CACHE_HOME=/tmp/fontconfig-cache + mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME + easypqp library \ --out ${prefix}_speclib.tsv \ $args \ @@ -38,6 +42,10 @@ process EASYPQP_LIBRARY { def prefix = task.ext.prefix ?: "${meta.id}" """ + export MPLCONFIGDIR=/tmp/matplotlib + export XDG_CACHE_HOME=/tmp/fontconfig-cache + mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME + touch "${prefix}_speclib.tsv" cat <<-END_VERSIONS > versions.yml diff --git a/workflows/mhcquant.nf b/workflows/mhcquant.nf index b7e5a3ae..14e67a49 100644 --- a/workflows/mhcquant.nf +++ b/workflows/mhcquant.nf @@ -8,16 +8,17 @@ // MODULE: Loaded from modules/local/ // -include { OPENMS_FILEFILTER } from '../modules/local/openms_filefilter' -include { PYOPENMS_CHROMATOGRAMEXTRACTOR } from '../modules/local/pyopenms_chromatogramextractor' -include { OPENMS_COMETADAPTER } from '../modules/local/openms_cometadapter' -include { OPENMS_PEPTIDEINDEXER } from '../modules/local/openms_peptideindexer' -include { DATAMASH_HISTOGRAM } from '../modules/local/datamash_histogram' -include { EASYPQP_CONVERT } from '../modules/local/easypqp/convert' -include { EASYPQP_LIBRARY } from '../modules/local/easypqp/library' -include { PYOPENMS_IONANNOTATOR } from '../modules/local/pyopenms_ionannotator' -include { OPENMS_TEXTEXPORTER } from '../modules/local/openms_textexporter' -include { OPENMS_MZTABEXPORTER } from '../modules/local/openms_mztabexporter' +include { OPENMS_FILEFILTER } from '../modules/local/openms_filefilter' +include { PYOPENMS_CHROMATOGRAMEXTRACTOR } from '../modules/local/pyopenms_chromatogramextractor' +include { OPENMS_COMETADAPTER } from '../modules/local/openms_cometadapter' +include { OPENMS_PEPTIDEINDEXER } from '../modules/local/openms_peptideindexer' +include { DATAMASH_HISTOGRAM } from '../modules/local/datamash_histogram' +include { EASYPQP_CONVERT } from '../modules/local/easypqp/convert' +include { EASYPQP_LIBRARY; + EASYPQP_LIBRARY as EASYPQP_LIBRARY_GLOBAL } from '../modules/local/easypqp/library' +include { PYOPENMS_IONANNOTATOR } from '../modules/local/pyopenms_ionannotator' +include { OPENMS_TEXTEXPORTER } from '../modules/local/openms_textexporter' +include { OPENMS_MZTABEXPORTER } from '../modules/local/openms_mztabexporter' // // SUBWORKFLOW: Loaded from subworkflows/local/ @@ -161,6 +162,19 @@ workflow MHCQUANT { .set { ch_peakpkl } EASYPQP_LIBRARY(ch_psmpkl.join(ch_peakpkl)) + ch_versions = ch_versions.mix(EASYPQP_LIBRARY.out.versions) + + if (params.global_fdr) { + EASYPQP_CONVERT.out.psmpkl + .map { meta, psmpkl -> [[id: "global"], psmpkl] } + .groupTuple() + .set { ch_global_psmpkl } + EASYPQP_CONVERT.out.peakpkl + .map { meta, peakpkl -> [[id: "global"], peakpkl] } + .groupTuple() + .set { ch_global_peakpkl } + EASYPQP_LIBRARY_GLOBAL(ch_global_psmpkl.join(ch_global_peakpkl)) + } // // SUBWORKFLOW: QUANT From c2369e7cd7016f90043cc5b4074ff4d5b1ece273 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 08:39:56 +0000 Subject: [PATCH 03/13] add tests for speclib generation --- .github/workflows/ci.yml | 2 +- conf/test_speclib.config | 30 ++++++++++++++++++++++++++++++ nextflow.config | 2 ++ nextflow_schema.json | 6 ++++++ 4 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 conf/test_speclib.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2b55a60b..e7a070b6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -101,7 +101,7 @@ jobs: # Test latest edge release of Nextflow - NXF_VER: "" NXF_EDGE: "1" - tests: ["test_mokapot", "test_percolator", "test_ionannotator"] + tests: ["test_mokapot", "test_percolator", "test_ionannotator", "test_speclib"] steps: - name: Check out pipeline code uses: actions/checkout@v2 diff --git a/conf/test_speclib.config b/conf/test_speclib.config new file mode 100644 index 00000000..c37601b7 --- /dev/null +++ b/conf/test_speclib.config @@ -0,0 +1,30 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/mhcquant -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 2, + memory: '6.GB', + time: '2.h' + ] +} + +params { + config_profile_name = 'Test profile' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = params.pipelines_testdata_base_path + 'mhcquant/testdata/HepG2_sample_sheet.tsv' + fasta = params.pipelines_testdata_base_path + 'mhcquant/testdata/UP000005640_9606.fasta' + generate_speclib = true + +} diff --git a/nextflow.config b/nextflow.config index bc61b1f4..f004ec97 100644 --- a/nextflow.config +++ b/nextflow.config @@ -17,6 +17,7 @@ params { skip_decoy_generation = false run_centroidisation = false filter_mzml = false + generate_speclib = false quantify = false annotate_ions = false @@ -219,6 +220,7 @@ profiles { test_mokapot { includeConfig 'conf/test_mokapot.config' } test_percolator { includeConfig 'conf/test_percolator.config' } test_ionannotator { includeConfig 'conf/test_ionannotator.config' } + test_speclib { includeConfig 'conf/test_speclib.config' } test_timstof { includeConfig 'conf/test_timstof.config' } test_full { includeConfig 'conf/test_full.config' } } diff --git a/nextflow_schema.json b/nextflow_schema.json index 9f8ada9e..7b826b3f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -414,6 +414,12 @@ "default": 12, "description": "Specify the maximum length of peptides to be considered after processing" }, + "generate_speclib": { + "type": "boolean", + "default": false, + "fa_icon": "fas fa-database", + "description": "Generate a spectral library from the search results. If `global_fdr` is specified, an additional global FDR-filtered library is generated from all MSruns in the samplesheet." + }, "annotate_ions": { "type": "boolean", "default": false, From 3e006e9249cbada756947429d76ef9cce5eb090f Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 09:13:00 +0000 Subject: [PATCH 04/13] create subworkflow for speclib generation --- conf/modules.config | 6 ++++ subworkflows/local/speclib.nf | 61 +++++++++++++++++++++++++++++++++++ workflows/mhcquant.nf | 40 +++++------------------ 3 files changed, 75 insertions(+), 32 deletions(-) create mode 100644 subworkflows/local/speclib.nf diff --git a/conf/modules.config b/conf/modules.config index ce8c56d6..65b58351 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -146,6 +146,12 @@ process { ] } + withName: 'OPENMS_IDFILTER_FOR_SPECLIB' { + publishDir = [ + enabled: false + ] + } + withName: 'EASYPQP_CONVERT' { publishDir = [ enabled: false diff --git a/subworkflows/local/speclib.nf b/subworkflows/local/speclib.nf new file mode 100644 index 00000000..50e5978d --- /dev/null +++ b/subworkflows/local/speclib.nf @@ -0,0 +1,61 @@ +/* + * Generates spectrum library for DIA-based searches + */ + +// +// MODULE: Loaded from modules/local/ +// + +include { EASYPQP_CONVERT } from '../../modules/local/easypqp/convert' +include { EASYPQP_LIBRARY; + EASYPQP_LIBRARY as EASYPQP_LIBRARY_GLOBAL } from '../../modules/local/easypqp/library' + +// +// MODULE: Installed directly from nf-core/modules +// + +workflow SPECLIB { + + take: + fdrfiltered_comet_idxml + mzml + + main: + ch_versions = Channel.empty() + + // Load unimod tables (Future:) + unimod = file("$projectDir/assets/250120_unimod_tables.xml", checkIfExists: true) + + // Convert psms and spectra to pickle files + EASYPQP_CONVERT(fdrfiltered_comet_idxml.join(mzml), unimod) + ch_versions = ch_versions.mix(EASYPQP_CONVERT.out.versions) + + EASYPQP_CONVERT.out.psmpkl + .map { meta, psmpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), psmpkl] } + .groupTuple() + .set { ch_psmpkl } + EASYPQP_CONVERT.out.peakpkl + .map { meta, peakpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), peakpkl] } + .groupTuple() + .set { ch_peakpkl } + + // Generate spectrum library for each sample-condition pair + EASYPQP_LIBRARY(ch_psmpkl.join(ch_peakpkl)) + ch_versions = ch_versions.mix(EASYPQP_LIBRARY.out.versions) + + // Generate spectrum library for all MSruns in the samplesheet + if (params.global_fdr) { + EASYPQP_CONVERT.out.psmpkl + .map { meta, psmpkl -> [[id: "global"], psmpkl] } + .groupTuple() + .set { ch_global_psmpkl } + EASYPQP_CONVERT.out.peakpkl + .map { meta, peakpkl -> [[id: "global"], peakpkl] } + .groupTuple() + .set { ch_global_peakpkl } + EASYPQP_LIBRARY_GLOBAL(ch_global_psmpkl.join(ch_global_peakpkl)) + } + + emit: + versions = ch_versions +} diff --git a/workflows/mhcquant.nf b/workflows/mhcquant.nf index 14e67a49..d9ee1de7 100644 --- a/workflows/mhcquant.nf +++ b/workflows/mhcquant.nf @@ -13,9 +13,6 @@ include { PYOPENMS_CHROMATOGRAMEXTRACTOR } from '../modules/local/pyope include { OPENMS_COMETADAPTER } from '../modules/local/openms_cometadapter' include { OPENMS_PEPTIDEINDEXER } from '../modules/local/openms_peptideindexer' include { DATAMASH_HISTOGRAM } from '../modules/local/datamash_histogram' -include { EASYPQP_CONVERT } from '../modules/local/easypqp/convert' -include { EASYPQP_LIBRARY; - EASYPQP_LIBRARY as EASYPQP_LIBRARY_GLOBAL } from '../modules/local/easypqp/library' include { PYOPENMS_IONANNOTATOR } from '../modules/local/pyopenms_ionannotator' include { OPENMS_TEXTEXPORTER } from '../modules/local/openms_textexporter' include { OPENMS_MZTABEXPORTER } from '../modules/local/openms_mztabexporter' @@ -25,6 +22,7 @@ include { OPENMS_MZTABEXPORTER } from '../modules/local/openm // include { PREPARE_SPECTRA } from '../subworkflows/local/prepare_spectra' include { RESCORE } from '../subworkflows/local/rescore' +include { SPECLIB } from '../subworkflows/local/speclib' include { QUANT } from '../subworkflows/local/quant' /* @@ -136,44 +134,22 @@ workflow MHCQUANT { RESCORE( ch_rescore_in ) ch_versions = ch_versions.mix(RESCORE.out.versions) - // // GENERATE SPECTRUM LIBRARY - // - RESCORE.out.fdr_filtered.join(ch_clean_mzml_file).view() + if (params.generate_speclib) { OPENMS_COMETADAPTER.out.idxml .map { meta, idxml -> [ [id: "${meta.sample}_${meta.condition}"], meta, idxml] } .combine(RESCORE.out.fdr_filtered, by:0) .map { groupKey, meta, comet_idxml, fdr_filtered_idxml -> [meta, comet_idxml, fdr_filtered_idxml] } .set { ch_fdrfilter_comet_idxml } + // Backfilter Comet identifications with FDR threshold OPENMS_IDFILTER_FOR_SPECLIB(ch_fdrfilter_comet_idxml) - unimod = file("$projectDir/assets/250120_unimod_tables.xml", checkIfExists: true) - EASYPQP_CONVERT(OPENMS_IDFILTER_FOR_SPECLIB.out.filtered.join(ch_clean_mzml_file), unimod) - ch_versions = ch_versions.mix(EASYPQP_CONVERT.out.versions) - - EASYPQP_CONVERT.out.psmpkl - .map { meta, psmpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), psmpkl] } - .groupTuple() - .set { ch_psmpkl } - EASYPQP_CONVERT.out.peakpkl - .map { meta, peakpkl -> [groupKey([id: "${meta.sample}_${meta.condition}"], meta.group_count), peakpkl] } - .groupTuple() - .set { ch_peakpkl } - - EASYPQP_LIBRARY(ch_psmpkl.join(ch_peakpkl)) - ch_versions = ch_versions.mix(EASYPQP_LIBRARY.out.versions) - - if (params.global_fdr) { - EASYPQP_CONVERT.out.psmpkl - .map { meta, psmpkl -> [[id: "global"], psmpkl] } - .groupTuple() - .set { ch_global_psmpkl } - EASYPQP_CONVERT.out.peakpkl - .map { meta, peakpkl -> [[id: "global"], peakpkl] } - .groupTuple() - .set { ch_global_peakpkl } - EASYPQP_LIBRARY_GLOBAL(ch_global_psmpkl.join(ch_global_peakpkl)) + // + // SUBWORKFLOW: SPECLIB + // + SPECLIB(OPENMS_IDFILTER_FOR_SPECLIB.out.filtered, ch_clean_mzml_file) + ch_versions = ch_versions.mix(SPECLIB.out.versions) } // From f67284ac1e0ca48fee555d5715bded7a6ea394cf Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 09:17:09 +0000 Subject: [PATCH 05/13] update docs --- CHANGELOG.md | 1 + docs/output.md | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73beaedc..93f5bf0b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added `PYOPENMS_CHROMATOGRAMEXTRACTOR` extracting MS1 Chromatograms and visualize them in multiQC report [#329](https://github.com/nf-core/mhcquant/pull/329) - Added `OPENMS_IDMASSACCURACY` and `DATAMASH_HISTOGRAM` to compute fragment mass errors and visualizte them in multiQC report [#332](https://github.com/nf-core/mhcquant/pull/332) - Added global fdr evaluation in new local subworkflow `RESCORE` [#338](https://github.com/nf-core/mhcquant/pull/338) +- Added flag `generate_speclib` that will generate a spectrum library for DIA searches with EasyPQP [#349](https://github.com/nf-core/mhcquant/pull/349) ### `Fixed` diff --git a/docs/output.md b/docs/output.md index 52bc75cb..f27ee5e7 100644 --- a/docs/output.md +++ b/docs/output.md @@ -90,6 +90,11 @@ This folder contains the intermediate results from various steps of the MHCquant - `features`: Holds information of quantified features in `featureXML` files as a result of the [FeatureFinderIdentification](https://openms.de/doxygen/release/3.0.0/html/TOPP_FeatureFinderIdentification.html) in the quantification mode. +- `spectrum_library` + + - `{Sample}_{Condition}_speclib.tsv`: FDR-filtered spectrum library for sample-condition pair + - `global_speclib.tsv`: Global FDR-filtered spectrum library for all MS runs in samplesheet. This file is only written if `--global_fdr` is specified + - `ion_annotations` - `{Sample}_{Condition}_all_peaks.tsv`: Contains metadata of all measured ions of peptides reported after peptide identification. From 7e91d122ce9bdd74cd5c7505af2920b1653f1426 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 09:22:01 +0000 Subject: [PATCH 06/13] fix indents --- workflows/mhcquant.nf | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/mhcquant.nf b/workflows/mhcquant.nf index d9ee1de7..93bc15eb 100644 --- a/workflows/mhcquant.nf +++ b/workflows/mhcquant.nf @@ -8,14 +8,14 @@ // MODULE: Loaded from modules/local/ // -include { OPENMS_FILEFILTER } from '../modules/local/openms_filefilter' -include { PYOPENMS_CHROMATOGRAMEXTRACTOR } from '../modules/local/pyopenms_chromatogramextractor' -include { OPENMS_COMETADAPTER } from '../modules/local/openms_cometadapter' -include { OPENMS_PEPTIDEINDEXER } from '../modules/local/openms_peptideindexer' -include { DATAMASH_HISTOGRAM } from '../modules/local/datamash_histogram' -include { PYOPENMS_IONANNOTATOR } from '../modules/local/pyopenms_ionannotator' -include { OPENMS_TEXTEXPORTER } from '../modules/local/openms_textexporter' -include { OPENMS_MZTABEXPORTER } from '../modules/local/openms_mztabexporter' +include { OPENMS_FILEFILTER } from '../modules/local/openms_filefilter' +include { PYOPENMS_CHROMATOGRAMEXTRACTOR } from '../modules/local/pyopenms_chromatogramextractor' +include { OPENMS_COMETADAPTER } from '../modules/local/openms_cometadapter' +include { OPENMS_PEPTIDEINDEXER } from '../modules/local/openms_peptideindexer' +include { DATAMASH_HISTOGRAM } from '../modules/local/datamash_histogram' +include { PYOPENMS_IONANNOTATOR } from '../modules/local/pyopenms_ionannotator' +include { OPENMS_TEXTEXPORTER } from '../modules/local/openms_textexporter' +include { OPENMS_MZTABEXPORTER } from '../modules/local/openms_mztabexporter' // // SUBWORKFLOW: Loaded from subworkflows/local/ From 1e92238c52d8fe7a28e64f6ad7db49e22ec9fd6e Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 09:37:32 +0000 Subject: [PATCH 07/13] nf-core lint ignore unimod_tables.xml --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index 137301a6..aa35bf62 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,6 +1,7 @@ lint: files_unchanged: - .github/CONTRIBUTING.md + - assets/250120_unimod_tables.xml nf_core_version: 3.1.1 repository_type: pipeline template: From 7297cb0d7ada6db1885ef7df6099431003f5bdfc Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 09:57:47 +0000 Subject: [PATCH 08/13] ignore editorconfig-checker for unimod_tables.xml --- .editorconfig | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.editorconfig b/.editorconfig index 6d9b74cc..fc24b506 100644 --- a/.editorconfig +++ b/.editorconfig @@ -28,6 +28,9 @@ indent_style = unset [/assets/email*] indent_size = unset +[/assets/250120_unimod_tables.xml] +indent_size = unset + # ignore python and markdown [*.{py,md}] indent_style = unset From d6142fc26f61e93bdaa67a5ca291e8c50d85e8fc Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 09:59:42 +0000 Subject: [PATCH 09/13] ignore indent_style editorconfig-checker for unimod_tables.xml --- .editorconfig | 1 + 1 file changed, 1 insertion(+) diff --git a/.editorconfig b/.editorconfig index fc24b506..09af0716 100644 --- a/.editorconfig +++ b/.editorconfig @@ -29,6 +29,7 @@ indent_style = unset indent_size = unset [/assets/250120_unimod_tables.xml] +indent_style = unset indent_size = unset # ignore python and markdown From f8fc69ede8d7fdde05ae061d1f4274c3533e6f05 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 10:04:21 +0000 Subject: [PATCH 10/13] ignore end_of_line style editorconfig-checker for unimod_tables.xml --- .editorconfig | 1 + 1 file changed, 1 insertion(+) diff --git a/.editorconfig b/.editorconfig index 09af0716..4795d8c3 100644 --- a/.editorconfig +++ b/.editorconfig @@ -31,6 +31,7 @@ indent_size = unset [/assets/250120_unimod_tables.xml] indent_style = unset indent_size = unset +end_of_line = unset # ignore python and markdown [*.{py,md}] From d26a98b11fdbfde781eccfb2756bf2e924988ee2 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 10:05:45 +0000 Subject: [PATCH 11/13] ignore trim_trailing_whitespace editorconfig-checker for unimod_tables.xml --- .editorconfig | 1 + 1 file changed, 1 insertion(+) diff --git a/.editorconfig b/.editorconfig index 4795d8c3..20500856 100644 --- a/.editorconfig +++ b/.editorconfig @@ -32,6 +32,7 @@ indent_size = unset indent_style = unset indent_size = unset end_of_line = unset +trim_trailing_whitespace = unset # ignore python and markdown [*.{py,md}] From 31b9b5251cf520d68e3abbacfd5dc0bbc9246256 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 11:14:35 +0000 Subject: [PATCH 12/13] change prefix in idfilter for speclib --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index e958c618..0d28aaff 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -147,6 +147,7 @@ process { } withName: 'OPENMS_IDFILTER_FOR_SPECLIB' { + ext.prefix = {"${meta.id}_comet_fdr_filtered"} publishDir = [ enabled: false ] From c40fcb7398d6e5e73e99092f5db383a0c32119b4 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Tue, 21 Jan 2025 14:26:13 +0000 Subject: [PATCH 13/13] manually add template fix with latest nextflow version --- nextflow.config | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/nextflow.config b/nextflow.config index f004ec97..a7f72aae 100644 --- a/nextflow.config +++ b/nextflow.config @@ -252,14 +252,13 @@ env { } // Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false