General proteomics

80 workflows · 2000–2026

General proteomics: Ordinary discovery proteomics, where de novo sequencing fills in what the database search could not explain. 80 catalogued workflows and 81 papers.

Ordinary discovery proteomics, where de novo sequencing fills in what the database search could not explain.

Workflows	80
Papers	81
Authors	507
Active	2000-10-01 to 2026-06-13

Workflows (80)

Mitochondrial small subunit ribosome proteomics (2000): Bovine mitochondrial small subunit ribosomal proteins resolved by two-dimensional PAGE, in-gel tryptic digestion, capillary LC and electrospray MS/MS, with the resulting peptide sequences used as virtual probes to screen the human EST database by tBLASTN and assemble consensus cDNAs in silico. Spectra without an exact match in either the protein or EST databases were sequenced de novo, manually or with PepSeq. Seven proteins are reported in Table I, and the two de novo-derived peptides are the sole identifying evidence for two of them, MRP-S26 and MRP-S14; MRP-S14 is also one of only two proteins in the study with significant prokaryotic homology, to Escherichia coli S14. Five of the seven belong to a new class of ribosomal proteins with no prokaryotic counterpart.
Bacillus pumilus novel protein sequencing (2001): Determined the sequence of an unknown environmental-pollutant-adsorbing protein from Bacillus pumilus PH-01 using de novo MS/MS peptide sequencing on a QTOF together with N-terminal sequencing.
Atlantic salmon vitellogenin sequencing (2004): Characterised salmon vitellogenin by MALDI and Q-ToF MS/MS, de novo sequencing 14 tryptic peptides with Lutefisk, three of them from a portion of the protein not yet in databases.
Mycobacterium PAH response proteome (2004): Compares protein profiles of Mycobacterium vanbaalenii PYR-1 grown on high-molecular-weight polycyclic aromatic hydrocarbons by two-dimensional gel electrophoresis, identifying induced proteins partly by de novo sequencing.
Holm oak leaf proteome by de novo sequencing (2005): Established a 2-DE reference map of the holm oak leaf proteome and identified its major proteins through de novo MS/MS sequencing and homology searching, as the species lacked a sequenced genome.
Pleurotus ostreatus proteins by de novo sequencing (2005): 18O-type isotopic labeling and ESI-MS/MS de novo sequencing with homology searching identified fungal proteins, including a candidate steroid-transforming enzyme.
Human skin elastin pepsin/thermitase peptides (2005): Maps peptides from pepsin and thermitase digests of human skin elastin by combined database and de novo sequencing, locating proline hydroxylation and exon usage.
Atlantic cod vitellogenin de novo sequencing (2005): Determined partial sequence of Atlantic cod vitellogenin, a protein with no sequence in databases, by de novo sequencing of tryptic peptides, and compared it with haddock vitellogenin.
Human skin elastin elastase peptides (2005): Identifies peptides from elastase digests of human skin elastin by database search and de novo sequencing, mapping cleavage sites and proline hydroxylation.
Barley thylakoid membrane proteome (2006): Mapped transmembrane proteins of barley thylakoid membranes by de novo sequencing of their hydrophilic intermembrane peptide domains.
Banana proteome by de novo of derivatized peptides (2007): Chemical derivatization and MALDI-TOF/TOF de novo sequencing with homology search (MS-BLAST etc.) identified more than 40 proteins and isoforms in banana, a non-model plant.
Rhesus macaque proteome annotation (2007): Applies de novo sequencing at proteomic scale to Macaca mulatta, whose roughly 42,000 protein annotations against a human 330,000 make database search unreliable, so that a primate disease model can be studied proteomically at all.
Medaka brain hypoxia proteome (2007): Identified hypoxia-responsive proteins in medaka brain by difference gel electrophoresis and de novo sequencing of SPITC-derivatized peptides by MALDI-TOF/TOF.
Nosema bombycis structural proteins (2007): Identifies spore wall and polar tube proteins of the silkworm microsporidian Nosema bombycis from de novo sequence tags evaluated by database search.
Cytochrome c4 bottom-up sequencing (2007): Determines the primary structure of the 21 kDa cytochrome c4 of Thiocapsa roseopersicina de novo, bottom-up, from three separate digests (trypsin, Lys-C, Glu-C) read by ion-trap and FTICR mass spectrometry.
Nepenthes pitcher fluid proteome (2008): Identifies the digestive enzymes in carnivorous Nepenthes alata pitcher fluid by de novo sequencing of in-gel tryptic peptides followed by homology search.
Loquat polyphenol oxidase isoforms (2008): De novo sequencing of polyphenol oxidases from loquat, a database-underrepresented species, aligned to homologues to infer the minimal number of encoding genes.
Alkalimonas amylolytica pH proteomics (2009): A combined de novo sequencing strategy identified most pH-responsive proteins of an alkaliphilic bacterium without a genome.
Aphanizomenon phycocyanin isoform sequencing (2009): SPITC-derivatized tryptic peptides were de novo sequenced by MALDI-TOF/TOF to partially determine the primary structure of phycocyanin subunits from the cyanobacterium Aphanizomenon flos-aquae and reveal subunit isoforms.
Senegalese sole testis proteome (2009): 2-D DIGE of Solea senegalensis testis from wild and F1 males, with differential proteins identified by de novo MS/MS sequencing.
Yeast PSA1 interactome by database plus de novo (2009): Identifies interaction partners of yeast mannose-1-phosphate guanyltransferase PSA1 across batch cultivation phases, combining database search with de novo identification to add observations.
Pseudomonas aeruginosa phage diversity (2009): Used de novo peptide sequencing of structural proteins to group 15 newly isolated Pseudomonas aeruginosa phages from 14 countries and assess their relatedness.
Snow crab allergen de novo sequencing (2010): Profiled snow crab muscle allergens and de novo sequenced the newly recognised 40 kDa allergen, arginine kinase, by MALDI and ESI tandem mass spectrometry; the group also de novo sequenced its tropomyosin.
Thielaviopsis basicola plant-extract proteome (2010): Identifies proteome changes of the black root rot fungus Thielaviopsis basicola grown with plant root extracts, using cross-species similarity search and de novo sequencing.
Phanerochaete carnosa secretome (2010): Proteomics of lignocellulose-degrading enzymes secreted by an unsequenced white-rot fungus, annotating 665 and 365 de novo peptides by MS BLAST homology search.
Pomacea embryo proteome (2010): Proteins changing during embryonic development of the apple snail Pomacea canaliculata were identified by de novo sequencing and MS-BLAST cross-species search.
Brassica aquaporin PTM analysis (2010): Characterises root plasma membrane aquaporins of Brassica oleracea by LC-MS/MS, using de novo sequencing to resolve post-translational modifications and to tell isoforms apart.
Cynara cardunculus etiolation proteome (2010): 2-DE MALDI-TOF proteomics of cardoon stalks identified etiolation-related proteins by de novo sequencing and similarity search.
Aspergillus ochraceus proteome (2010): 2-DE MALDI-TOF/TOF proteome of an unsequenced fungus where over half the identified spots relied on de novo sequencing.
Alexandrium catenella cell wall proteome (2011): 2D DIGE separated cell wall proteins of the toxic dinoflagellate Alexandrium catenella were identified by MALDI TOF-TOF de novo sequencing followed by homology search, giving 120 proteins.
Dinoflagellate homology-driven proteomics (2011): Layered MALDI-TOF/TOF identification of dinoflagellate proteins in which de novo sequences searched with MS-BLAST identified proteins missed by database search.
Banana cultivar protein polymorphisms by de novo sequencing (2011): Combined 2-DE and DIGE with de novo MS/MS sequencing of derivatized peptides to characterize protein isoforms and possible gene silencing across triploid banana cultivars.
Banana plasma membrane proteome workflow (2011): A shotgun membrane proteomics workflow for the poorly sequenced banana, using de novo sequencing for sequence homology search and Cytoscape to remove redundant or wrong assignments.
PrISM actinobacteria NRPS/PKS proteomics (2012): Screens 26 unsequenced actinomycetes for expressed NRPS and PKS enzymes by protein-first proteomics with improved de novo sequencing, linking products to gene clusters.
Alligator serum lectin sequencing (2012): Multi-enzyme digestion and de novo sequencing determined 98% of the 313-residue sequence of a mannose-binding lectin from alligator serum.
Aureoumbra lagunensis nutrient-limitation proteome (2012): Proteomic profiles of the brown tide alga under phosphate and nitrogen limitation, with proteins identified by de novo sequencing and cross-species search, including a phosphate-limitation alkaline phosphatase.
Dreissena polymorpha triclosan gill proteome (2012): Ecotoxicoproteomics of zebra mussel gills exposed to triclosan; altered proteins in this poorly sequenced organism were identified by 2-DE and de novo sequencing.
Mangifera indica leaf proteome (2012): First high-throughput proteome of mango leaf, an unsequenced plant, combining EST and cross-species database search with de novo sequencing and homology-based identification (1001 peptides, 538 proteins).
Pseudoalteromonas biofilm outer-membrane proteins (2012): Identifies biofilm-induced outer membrane proteins of the marine bacterium Pseudoalteromonas sp. D41 by MS/MS de novo sequencing.
Pine processionary moth setae allergens (2012): Allergens in the urticating setae of Thaumetopoea pityocampa were characterized, and MALDI-MS de novo sequencing gave a partial sequence of a new major allergen named Tha p 2.
Brevibacterium linens proteome map (2013): Cellular and extracellular proteome map of Brevibacterium linens DSM 20158, an unsequenced strain, built by Mascot homology search extended with de novo sequencing and MS BLAST.
Vel blood group antigen identification (SMIM1) (2013): De novo peptide sequencing of the protein purified from red blood cell membranes identified the long-sought Vel blood group antigen carrier as SMIM1, later confirmed genetically.
Lactobacillus brevis starvation proteome by CAF-/CAF+ de novo (2013): Uses negative- and positive-mode chemically activated fragmentation of derivatized peptides to de novo sequence proteins of Lactobacillus brevis, revealing 36 proteins changed after long-term starvation.
Intestinal epithelial chemokine peptidomics (2013): A non-targeted differential peptidomic comparison of intestinal epithelial cells with and without LPS stimulation, where high-resolution MS and partial de novo sequencing name the secreted chemokines.
Citrus thermally tolerant PME (2013): Purifies thermally tolerant pectin methylesterase from orange and uses MALDI-TOF/TOF de novo sequences to match ESTs and clone its gene.
De novo SAV discovery (2014): Discovers single amino-acid variants without SNP databases by pairing de novo sequencing candidates against theoretical proteins, then re-searching to control FDR; applied to human brain tissue.
Honeybee drone accessory gland peptides (2015): Combined SEQUEST with manual de novo sequencing of all unassigned spectra to characterise the proteins and peptides of honeybee drone reproductive glands.
High-throughput de novo for crop proteomics (2016): A proteomic workflow built on high-throughput de novo sequencing for non-model crop plants, where the genome information needed for a database search is missing and cultivars have to be compared anyway.
Mycoplasma pneumoniae discarded-spectra rescue (2016): Reanalysed the unassigned spectra of a minimal bacterial proteome with de novo sequencing, attributing them to modifications, sequence variants and mistranslation.
Large-scale de novo application to complex proteomics (2016): Application of de novo sequencing to large-scale complex proteomics data sets.
FMO antenna cysteine quenching (2016): Pinpoints cysteines responsible for aerobic energy quenching in the FMO antenna protein of Chlorobaculum tepidum using de novo sequencing MS, chemical modification and mutagenesis.
Foraminifera thermal stress dual-compartment proteomics (2018): Label-free proteomics of the diatom-bearing foraminifer Amphistegina gibbosa and its symbionts under thermal stress, identifying proteins of a poorly sequenced host by de novo sequencing plus homology search.
Budding yeast CUG codon reassignment (2018): Determined the translation of the CUG codon in budding yeast species from de novo peptide sequences and proteome database matching, revealing three parallel genetic code changes.
Centroceras phycobiliprotein sequencing (2018): Purified R-phycocyanin and R-phycoerythrin from a red alga and derived near-complete subunit sequences from MS data using de novo tools, homology search and manual validation.
Tamarillo protease tamarillin (2018): Purification and characterization of a serine protease from tamarillo fruit, identified as subtilisin-like from de novo sequenced peptides.
Ole e 7 allergen de novo assembly (2018): Thirteen de novo sequenced peptides assembled the full sequence of the olive pollen allergen Ole e 7, which was then cloned and shown to retain allergenicity.
Encoded-sentence protein decoding (2019): Decodes an E. coli-expressed protein whose sequence spells two English sentences, by bottom-up proteomics, de novo sequencing and a dictionary search.
First YPIC challenge sentence decoding (infusion) (2019): De novo sequencing of 19 synthetic peptides from the first YPIC challenge recovered the hidden English sentence, later refined with a database approach.
YPIC book-preface de novo decoding (MaxQuant + Google) (2019): Decoded synthetic peptides encoding an English text by MaxQuant de novo sequencing, then identified the source book by web search and confirmed it by database search.
YPIC encoded-text de novo decoding (Thomson quote) (2019): De novo sequencing of synthetic peptides from the YPIC-EuPA challenge revealed a quotation from J.J. Thomson, later confirmed by database search.
Sordaria proteogenomics with de novo sequencing (2019): Combines proteogenomics with peptide de novo sequencing to refine the genome annotation of the fungus Sordaria macrospora, finding new genes and hidden post-transcriptional modifications.
2018 YPIC unknown protein characterization (2019): Spectral clustering and de novo identification decoded the unknown synthetic protein of the 2018 YPIC challenge and characterized its PTMs.
De novo database suitability assessment (2020): Uses automated de novo sequencing to test whether a set of spectra holds peptide spectra at all and whether a protein database suits it, for unsequenced species, metaproteomes and extinct organisms.
Spondylus gaederopus shell matrix proteomics (2020): Microstructural and proteomic study of the European thorny oyster shell matrix. In the absence of genomic data, de novo reconstructed peptides were reported, most of them matching no known shell protein.
Rubisco large subunit N-terminal determination (2020): De novo sequencing used to establish what the N terminus of a recombinant protein actually is, which the biological argument then rests on. Arabidopsis Rubisco large subunit variants expressed in E. coli are processed unpredictably by the host, so the construct sequence does not tell you which residues survive. Purified proteins were run on SDS gels, the RbcL band excised, and the N termini determined by de novo mass spectrometric sequencing in PEAKS Studio X+, alongside a semi-specific tryptic database search and peak-area quantification; the work was done as a service by the Bioprocessing Technology Institute, A*STAR. The result is Table 1 in full: the observed N termini for wild type and each truncation variant with their peak-area ratios, showing for instance that wild type is a mixture of MSPQTETKAS, SPQTETKAS and PQTETKAS at 36, 15 and 49 percent. Those assignments are what let the paper claim that large subunits lacking residues 1 to 4 are functional carboxylases that Rubisco activase cannot activate, and they drive a further inference about cooperativity, since some deltaN2 N termini proved identical to deltaN3 ones. A tryptic database search alone would not have found them, because host processing leaves ragged non-tryptic N termini.
3D OrbiSIMS in situ protein identification (2020): Gas cluster ion beam SIMS with Orbitrap analysis fragments surface proteins in situ, and de novo peptide sequencing annotates 16 proteins, enabling protein imaging and depth profiling in skin.
ProAlanase protease for proteomics and de novo sequencing (2020): Characterises the proline/alanine-specific protease ProAlanase and shows that combining its peptides with tryptic ones gives nearly complete de novo sequencing coverage of the proline-rich Notch3 intracellular domain with PEAKS.
Eucalyptus grandis novel protein-coding sequences (2021): Proteogenomic search for unannotated proteins in Eucalyptus grandis using a dedicated de novo peptide sequencing pipeline (PEAKS plus PatternLab), confirming 41 novel peptide forms, mostly from alternative reading frames, by PRM.
Snow alga Chlamydomonas nivalis salt-stress proteome (2021): iTRAQ comparison of salt stress in C. reinhardtii and the unsequenced snow alga C. nivalis, where de novo sequencing and homology matching in PEAKS identified the C. nivalis proteins.
sORF-encoded peptide discovery (2021): Combines top-down proteomics with de novo sequencing to identify peptides encoded by small open reading frames, 1682 of them mapping to human sORFs never characterised before.
Greenshell mussel protein identification strategies (2021): Compares Mascot, PEAKS DB and SPIDER homology search for identifying 2-DE spots of the unsequenced greenshell mussel, with de novo strategies adding proteins.
Modiolus kurilensis C1q-domain lectin (2021): A C1q domain-containing lectin from the mussel Modiolus kurilensis whose full sequence was assembled from de novo mass spectrometry peptide sequencing complemented by Edman degradation.
Drosophila developmental microproteins (2022): Microproteins across 11 Drosophila melanogaster developmental time points were identified, 44 of them by de novo sequencing validated with synthetic peptides.
Orchid tuber response to mycorrhizal fungus (2022): Proteome of Dactylorhiza tubers inoculated with a Tulasnella fungus, where de novo sequencing plus homology search covered the absence of an orchid genome.
Eucalyptus grandis seasonal dark proteome (2023): De novo sequencing with PEAKS identifies novel peptide forms in Eucalyptus grandis leaves that change with season and water restriction, from the part of the proteome a database search cannot see.
Sacha inchi seed protein proteome (2024): Characterises Sacha inchi press-cake proteins, using PEAKS de novo peptides to reach proteins the Euphorbiaceae database left unidentified.
Coagulation plasma peptidomics (2025): Peptidomics with de novo-assisted identification maps the limited proteolysis events of in vitro plasma coagulation.
Alzheimer amino acid substitution pipeline (2026): Bioinformatic pipeline that searches proteomic data for amino acid substitutions using a de novo sequencing assisted strategy, and identifies the substitutions specific to Alzheimer’s disease as candidate biomarkers or therapeutic targets.
De novo plus MS-BLAST for unsequenced organisms (thesis) (2026): A thesis developing and applying de novo sequencing followed by MS-BLAST to characterise proteins from plants, fungi and parasites without sequenced genomes.
Tintinnid ciliate shell proteins (Tintinnidorin) (2026): Combines Casanovo de novo sequencing of shell proteomes, Stitch assembly and single-cell transcriptomics to identify Tintinnidorin, a new family of self-assembling proteins forming the chemically resistant shells of tintinnid ciliates.

Papers (81)

A Proteomics Approach to the Identification of Mammalian Mitochondrial Small Subunit Ribosomal Proteins (2000, Journal of Biological Chemistry, peer-reviewed)
Sequencing of novel protein from Bacillus pumilus PH-01 using a high-resolution hybrid quadrupole-time-of-flight mass spectrometer (2001, International Journal of Mass Spectrometry, peer-reviewed)
Characterization and De Novo Sequencing of Atlantic Salmon Vitellogenin Protein by Electrospray Tandem and Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (2004, European Journal of Mass Spectrometry, peer-reviewed)
Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR‐1 using two‐dimensional polyacrylamide gel electrophoresis and de novo sequencing methods (2004, PROTEOMICS, peer-reviewed)
Mass spectrometry and database search in the analysis of proteins from the fungus Pleurotus ostreatus (2005, PROTEOMICS, peer-reviewed)
The Holm Oak leaf proteome: Analytical and biological variability in the protein expression level assessed by 2‐DE and protein identification tandem mass spectrometry de novo sequencing and sequence similarity searching (2005, PROTEOMICS, peer-reviewed)
Mass spectrometric characterization of human skin elastin peptides produced by proteolytic digestion with pepsin and thermitase (2005, Journal of Chromatography A, peer-reviewed)
‘ De novo ’ sequencing of Atlantic cod vitellogenin tryptic peptides by matrix‐assisted laser desorption/ionization quadrupole time‐of‐flight tandem mass spectrometry: similarities with haddock vitellogenin (2005, Rapid Communications in Mass Spectrometry, peer-reviewed)
Characterization of peptides resulting from digestion of human skin elastin with elastase (2005, Proteins: Structure, Function, and Bioinformatics, peer-reviewed)
Mapping the proteome of thylakoid membranes by de novo sequencing of intermembrane peptide domains (2006, PROTEOMICS, peer-reviewed)
De novo protein sequence analysis of Macaca mulatta (2007, BMC Genomics, peer-reviewed)
Functional Proteome Analysis of the Banana Plant (Musa spp.) Using de Novo Sequence Analysis of Derivatized Peptides (2007, Journal of Proteome Research, peer-reviewed)
Detection of hypoxia-related proteins in medaka (Oryzias latipes) brain tissue by difference gel electrophoresis and de novo sequencing of 4-sulfophenyl isothiocyanate-derivatized peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (2007, Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, peer-reviewed)
A proteomic‐based approach for the characterization of some major structural proteins involved in host–parasite relationships from the silkworm parasite Nosema bombycis (Microsporidia) (2007, PROTEOMICS, peer-reviewed)
De novo sequencing of a 21‐kDa cytochrome c₄ from Thiocapsa roseopersicina by nanoelectrospray ionization ion‐trap and Fourier‐transform ion‐cyclotron resonance mass spectrometry (2007, Journal of Mass Spectrometry, peer-reviewed)
Proteome Analysis of Pitcher Fluid of the Carnivorous Plant Nepenthes alata (2008, Journal of Proteome Research, peer-reviewed)
Proteomics of Multigenic Families from Species Underrepresented in Databases: The Case of Loquat (Eriobotrya japonica Lindl.) Polyphenol Oxidases (2008, Journal of Proteome Research, peer-reviewed)
Exploring membrane and cytoplasm proteomic responses of Alkalimonas amylolytica N10 to different external pHs with combination strategy of de novo peptide sequencing (2009, PROTEOMICS, peer-reviewed)
A combined database related and de novo MS-identification of yeast mannose-1-phosphate guanyltransferase PSA1 interaction partners at different phases of batch cultivation (2009, International Journal of Mass Spectrometry, peer-reviewed)
2‐D DIGE analysis of Senegalese sole (Solea senegalensis) testis proteome in wild‐caught and hormone‐treated F1 fish (2009, PROTEOMICS, peer-reviewed)
De novo sequence analysis and intact mass measurements for characterization of phycocyanin subunit isoforms from the blue‐green alga Aphanizomenon flos‐aquae (2009, Journal of Mass Spectrometry, peer-reviewed)
Survey of Pseudomonas aeruginosa and its phages: de novo peptide sequencing as a novel tool to assess the diversity of worldwide collected viruses (2009, Environmental Microbiology, peer-reviewed)
Plant‐extract‐induced changes in the proteome of the soil‐borne pathogenic fungus Thielaviopsis basicola (2010, PROTEOMICS, peer-reviewed)
Characterization and de novo sequencing of snow crab tropomyosin enzymatic peptides by both electrospary ionization and matrix‐assisted laser desorption ionization QqToF tandem mass spectrometry (2010, Journal of Mass Spectrometry, peer-reviewed)
Proteomic characterization of lignocellulose-degrading enzymes secreted by Phanerochaete carnosa grown on spruce and microcrystalline cellulose (2010, Applied Microbiology and Biotechnology, peer-reviewed)
Protein expression during the embryonic development of a gastropod (2010, PROTEOMICS, peer-reviewed)
Analysis of Root Plasma Membrane Aquaporins from Brassica oleracea: Post-Translational Modifications, de novo Sequencing and Detection of Isoforms by High Resolution Mass Spectrometry (2010, Journal of Proteome Research, peer-reviewed)
The Proteomic Changes in Cynara Cardunculus L. var. altilis DC Following the Etiolation Phenomena Using De Novo Sequence Analysis (2010, Journal of Botany, peer-reviewed)
Proteome analysis of Aspergillus ochraceus (2010, Mycotoxin Research, peer-reviewed)
Homology‐Driven Proteomics of Dinoflagellates with Unsequenced Genomes Using MALDI‐TOF/TOF and Automated De Novo Sequencing (2011, Evidence-Based Complementary and Alternative Medicine, peer-reviewed)
Identification and Characterization of Cell Wall Proteins of a Toxic Dinoflagellate Alexandrium catenella Using 2‐D DIGE and MALDI TOF‐TOF Mass Spectrometry (2011, Evidence-Based Complementary and Alternative Medicine, peer-reviewed)
Biomolecular characterization of allergenic proteins in snow crab (Chionoecetes opilio) and de novo sequencing of the second allergen arginine kinase using tandem mass spectrometry (2011, Journal of Proteomics, peer-reviewed)
The use of 2D-electrophoresis and de novo sequencing to characterize inter- and intra-cultivar protein polymorphisms in an allopolyploid crop (2011, Phytochemistry, peer-reviewed)
A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana (2011, Journal of Proteomics, peer-reviewed)
A Proteomic Survey of Nonribosomal Peptide and Polyketide Biosynthesis in Actinobacteria (2012, Journal of Proteome Research, peer-reviewed)
Isolation and determination of the primary structure of a lectin protein from the serum of the American alligator (Alligator mississippiensis) (2012, Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, peer-reviewed)
Characterization of the Proteomic Profiles of the Brown Tide Alga Aureoumbra lagunensis under Phosphate- and Nitrogen-Limiting Conditions and of Its Phosphate Limitation-Specific Protein with Alkaline Phosphatase Activity (2012, Applied and Environmental Microbiology, peer-reviewed)
Effects of triclosan in the freshwater mussel Dreissena polymorpha: A proteomic investigation (2012, Aquatic Toxicology, peer-reviewed)
Proteomic analysis of an unsequenced plant — Mangifera indica (2012, Journal of Proteomics, peer-reviewed)
Proteomic studies highlight outer‐membrane proteins related to biofilm development in the marine bacterium Pseudoalteromonas sp. D41 (2012, PROTEOMICS, peer-reviewed)
Setae from the pine processionary moth ( Thaumetopoea pityocampa ) contain several relevant allergens (2012, Contact Dermatitis, peer-reviewed)
Disruption of SMIM1 causes the Vel− blood type (2013, EMBO Molecular Medicine, peer-reviewed)
Charting the cellular and extracellular proteome analysis of Brevibacterium linens DSM 20158 with unsequenced genome by mass spectrometry-driven sequence similarity searches (2013, Journal of Proteomics, peer-reviewed)
The effect of starvation stress on Lactobacillus brevis L62 protein profile determined by de novo sequencing in positive and negative mass spectrometry ion mode (2013, Rapid Communications in Mass Spectrometry, peer-reviewed)
High‐resolution mass spectrometry and partial de novo sequencing constitute a useful approach for determining the profile of chemokine secretion following the stimulation of human intestinal epithelial cells (2013, Rapid Communications in Mass Spectrometry, peer-reviewed)
Structural Characterization of the Thermally Tolerant Pectin Methylesterase Purified from Citrus sinensis Fruit and Its Gene Sequence (2013, Journal of Agricultural and Food Chemistry, peer-reviewed)
De novo identification and quantification of single amino-acid variants in human brain (2014, Journal of Molecular Cell Biology, peer-reviewed)
Protein and Peptide Composition of Male Accessory Glands of Apis mellifera Drones Investigated by Mass Spectrometry (2015, PLOS ONE, peer-reviewed)
A Proteomic Workflow Using High-Throughput De Novo Sequencing Towards Complementation of Genome Information for Improved Comparative Crop Science (2016, Methods in Molecular Biology, peer-reviewed)
Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome (2016, PROTEOMICS, peer-reviewed)
Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets (2016, Journal of Proteome Research, peer-reviewed)
Evidence for a cysteine-mediated mechanism of excitation energy regulation in a photosynthetic antenna complex (2016, Proceedings of the National Academy of Sciences, peer-reviewed)
Disentangling thermal stress responses in a reef-calcifier and its photosymbionts by shotgun proteomics (2018, Scientific Reports, peer-reviewed)
Evolutionary instability of CUG-Leu in the genetic code of budding yeasts (2018, Nature Communications, peer-reviewed)
Identification, purification, biochemical and mass spectrometric characterization of novel phycobiliproteins from a marine red alga, Centroceras clavulatum (2018, International Journal of Biological Macromolecules, peer-reviewed)
Purification and characterisation of a protease (tamarillin) from tamarillo fruit (2018, Food Chemistry, peer-reviewed)
A recombinant isoform of the Ole e 7 olive pollen allergen assembled by de novo mass spectrometry retains the allergenic ability of the natural allergen (2018, Journal of Proteomics, peer-reviewed)
Quick and clean: Cracking sentences encoded in E. coli by LC–MS/MS, de novo sequencing, and dictionary search (2019, EuPA Open Proteomics, peer-reviewed)
Math, science, history, unraveling the mystery—That all started with de novo! (2019, EuPA Open Proteomics, peer-reviewed)
Let me infuse this for you – A way to solve the first YPIC challenge (2019, EuPA Open Proteomics, peer-reviewed)
Sweet google O’ mine—The importance of online search engines for MS-facilitated, database-independent identification of peptide-encoded book prefaces (2019, EuPA Open Proteomics, peer-reviewed)
Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications (2019, mBio, peer-reviewed)
2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample (2019, Journal of Proteome Research, peer-reviewed)
Assessing Protein Sequence Database Suitability Using De Novo Sequencing (2020, Molecular & Cellular Proteomics, peer-reviewed)
The shell matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization (2020, Journal of Structural Biology, peer-reviewed)
Rubisco activase requires residues in the large subunit N terminus to remodel inhibited plant Rubisco (2020, Journal of Biological Chemistry, peer-reviewed)
Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling (2020, Nature Communications, peer-reviewed)
ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping (2020, Molecular & Cellular Proteomics, peer-reviewed)
Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry (2021, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, peer-reviewed)
Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing (2021, International Journal of Molecular Sciences, peer-reviewed)
Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources (2021, Biotechnology for Biofuels, peer-reviewed)
Protein Identification Strategies for the Greenshell Mussel Perna canaliculus (2021, thesis)
A Novel C1q Domain-Containing Protein Isolated from the Mollusk Modiolus kurilensis Recognizing Glycans Enriched with Acidic Galactans and Mannans (2021, Marine Drugs, peer-reviewed)
Systematic Identification of Microproteins during the Development of Drosophila melanogaster (2022, Journal of Proteome Research, peer-reviewed)
Interaction With Fungi Promotes the Accumulation of Specific Defense Molecules in Orchid Tubers and May Increase the Value of Tubers for Biotechnological and Medicinal Applications: The Case Study of Interaction Between Dactylorhiza sp. and Tulasnella calospora (2022, Frontiers in Plant Science, peer-reviewed)
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome (2023, Current Plant Biology, peer-reviewed)
Proteomic Analysis of the Major Alkali-Soluble Inca Peanut (Plukenetia volubilis) Proteins (2024, Foods, peer-reviewed)
Proteolytic signatures of coagulation identified by plasma peptidomics (2025, Journal of Thrombosis and Haemostasis, peer-reviewed)
Mapping protein variants associated with Alzheimer’s disease by mass-spectrometry based de novo sequencing assisted strategy (2026, Journal of Alzheimer’s Disease, peer-reviewed)
Un ensemble d’outils protéomiques pour la caractérisation de protéines d’organismes très divers : plantes, champignons et parasites (2026, thesis)
Self-assembling proteins compose the chemically resistant shell biomaterial of planktonic tintinnid ciliates (2026, Nature Communications, peer-reviewed)

Sequencing tools these papers used

Casanovo, Lutefisk, MS BLAST, Manual MS/MS de novo interpretation, PEAKS, PEAKS DB, PepExplorer, PepSeq, SPIDER, Stitch

Authors (507)

A. Vertommen, A.H.P. America, A.L.B. Møller, Ahmad Adnan, Aisling Y. Coughlan, Akhilesh Pandey, Alain Dufour, Alain Roques, Albert Sickmann, Alberto Nuñez, Alejandro Cohen, Alette Kooiker, Alex von Kriegsheim, Alexander B. Meijer, Alexander G. Shard, Alexander Hogrebe, Alexander Janssen, Alexis Bazire, Amy N. Perez, Ana Butorac, Ana Isabel Rodriguez‐Mahillo, Anas M. Abdel Rahman, Andrea Battisti, Andrea Binelli, Andreas L. Lopata, Andreas Römpp, Andreas Vilcinskas, Andrei V. Grinchenko, Andrew Chibeu, Andrés Ritter, Andy Lin, Anna E. Egorova, Anna M. Kotowska, Anne Frary, Anne Poljak, Anne-Catherine Vanhove, Annelien Bredenoord, Annie Yart, Anske van der Bom, Antonis Rokas, Arthur Moseley, Arun Devabhaktuni, Arye Tishbee, Atef Mansour, Azeem Hasan, B. Muries, Bart Panis, Bart Samyn, Beatrice Demarchi, Bernhard Blank-Landeshammer, Bernhard Granvogl, Bernhard Spengler, Bing Wang, Bipin Gopalakrishnan Nair, Blanca Hernández-Ledesma, Bo Meng (Chinese Academy of Sciences), Brett J. Savary, Brian C. Searle, Brian Mooney, Britta Eggers, Brook L. Nunn, Bryan A. Ballif, Byung-Hoon Kim, Břetislav Brzobohatý, C. A. Evans, C. Finnie, Carin Uyl, Carl E. Cerniglia, Carlos Afonso, Carlos Porras, Carmen Oeo-Santos, Carmen van der Zwaan, Carmine Guarino, Carole Kerdelhué, Carole Saison, Caroline Mussert, Cassidy Moeke, Catherine Dreanno, Catherine H. Botting, Catherine Texier, Chang‐De Lu, Chang‐Jun Cha, Chantal Compère, Charles Pineau, Chelsea L. McIntosh, Cheng Li, Chris T. Amemiya, Chris Todd Hittinger, Christian D. Kelstrup, Christian E.H. Schmelzer, Christian N. Cramer, Christian P. Vivarès, Christof Lenz, Christof Regl, Christophe Chambon, Christopher M. Hosfield, Chuanqi Zhou, Claire E. Reymond, Cletus P. Kurtzman, Consuelo Riva, Cristobalina Mayorga, Csaba Bagyinka, Cuihong Wan, Cécile Menanteau, Cédric Broussard, D. James Gilmour, Da-Zhi Wang, Dana A. Opulente, Daniel De Vos, Daniel Zovi, Daria D. Emekeeva, Dariusz M. Niedzwiedzki, David Ariza, David J. Scurr, David Lyon, David P. Labeda, Denis C. Shields, Diana Samodova, Diana V. Ilyaskina, Diaz Prameyllawati, Divya Nair, Dominique Rainteau, Don Otter, E. Hounslow, Ebrahim Razzazi-Fazeli, Edoardo Petrucco Toffolo, Eduard Sabidó, Ekaterina Ilgisonis, Elise Huisman, Eliza Roest, Elodie Quévrain, Emile van den Akker, Emilio Camafeita, Emine Cavdar Koc, Emma R. Master, Emmanuelle Com, Enrico Cappellini, Erwin Torres-Sánchez, Esperanza Morato, Estelle Capton, Esther Asensio, F. Elortza, Fareeha Tasneem, Felix van der Meer, Floris P.J. van Alphen, Francesco Addeo, Francesco M. Mancuso, Frank Leebeek, Friederike von Rundstedt, Frédéric Jamme, Frédéric Marin, Fuli Peng, Gabriel L. Jorge, Gabriella Bodó, Gang Li, Gaël Le Pennec, Geertje Goedhart, Germain Trugnan, Getinet Desalegn, Ghantasala S. Sameer Kumar, Ginette Thomas, Giulia Franciosa, Gregory S. Orf, Griet Debyser, Gudrun Koeniger, Guido Volckaert, Gustavo F. Trindade, H.C. Harsha, Hannu Peltoniemi, Hans Kristian Ploos van Amstel, Hans-Peter Kaul, Hans‐W. Ackermann, Hao Chi, Hao Zhang, Hasan Koc, Heiko Vogel, Herm-Jan Brinkman, Hester Lingsma, Hildegard Westphal, Hong-Po Dong, Hongbin Liu, Hongmei Jing, Hua-Sheng Hong, Huan Zhang, Huiming Han, Huoming Zhang, Hyo-Bong Hong, Héctor Climente‐González, I. Iloro, I. Teichert, Ignacio Luque, Ignacio Moneo, Ignasi Forné, Igor V. Grigoriev, Ingrid Miller, Inmaculada Jorge, Ioanna Ntai, Irina A. Tarasova, Irina Y. Petrova, Iris van Moort, Ivana Dodig, Iñigo Saiz-Fernández, J. Casado-Vela, J. Pandhal, J.H.G. Cordewener, Jacek Kominek, James R. Doroghazi, Jan Hazelzet, Jan Verhaegen, Jan Voorberg, Jana Jersáková, Janko Diminić, Jaroslava Domkářová, Jasna Mrvčić, Jasna Peter‐Katalinić, Jason M. Gilmore, Jason W. Schultz, Jay J. Thelen, Jayashree Gopalakrishna Pai, Jean Pierre Grill, Jean‐Claude Tabet, Jean‐Paul Noben, Jean‐Paul Pirnay, Jean‐Pierre Cartron, Jediael Ng, Jenny Renaut, Jeroen Eikenboom, Jesper V. Olsen, Jessica Del Castillo Alferez, Jesús Jorrín, Jia-Rui Wu, Jiahao Yan, Jian Wan, Jiangmei Huang, Jian‐Wen Qiu, Jian‐Yang Wang, Jin Sun, Jinfeng Chen, Jinghua Yang, Jissa Gopala Krishna, Joan Cerdà, Joaquín Abián, Joaquín Quiralte, Johan Boender, John J. Robinson, Jonathan Perrin, Jonathan W. Aylott, Joost C.M. Meijers, Jorune Sakalauskaite, Josef Böhm, Joseph Banoub, Joshua E. Elias, José Carlos Garcia Ortiz, José María Vega, Jozef Van Beeumen, Joëlle Masliah, Joëlle V. F. Coumans, Juan Antonio López, Julian Uszkoreit, Jyoti Sharma, Jérôme Thomas, Karin Fijnvandraat, Karina Meijer, Karlo Hock, Kathelijn Fischer, Katrin Marcus, Ken Scott, Kenneth H. Wolfe, Kermit K. Murray, Kevin Blackburn, Ke‐Wei Huang, Khadija Shabbiri, Kjell Sergeant, Kou-San Ju, Ksenia Kuznetsova, Lancia N.F. Darville, Laszlo Prokai, Laura A. Katz, Laura Bukkems, Laurent Plasseraud, Laxmikanth Kollipara, Lello Zolla, Leon P. Oehlers, Leonid Zamdborg, Lex Burdorf, Lieke Baas, Lili Niu, Lily Pereg, Lin Lin, Lina Chianese, Linda L. Spremulli, Lindsay Pino, Lionel Arnaud, Liviu M. Mirica, Lorenzo Romano, Lotte Haverman, Luciana De Simone, Ludovic Delage, Luis Serrano, Luis-Felipe Gutiérrez, Lutz Andreas Eichacker, M. Carvajal, M. Nowrousian, M.C. Martínez-Ballesta, Maartje van den Biggelaar, Maia Merabishvili, Maja Matis, Mamkoottathil Velayudhan Nataraja Panikkar, Manfred Gemeiner, Marcia I. Peña‐Paz, Maria Grazia Calabrese, Maria José Martínez-Esteso, Maria Lluch‐Senar, Maria V. Giuli, Marie Albéric, Marie Bachelet, Marieke Kruip, Marie‐Anne Maubert, Marija Žakelj‐Mavrič, Marina Dos Santos Goncalves, Mario Cindrić, Mario Vaneechoutte, Mariëtte Driessens, Marjon Cnossen, Mark E. Merchant, Mark J. Raftery, Markus Wiederstein, Marleen Stuhr, Martijn Brands, Martin Eisenacher, Martin Černý, María J. Agulleiro, María López-Lucendo, Masja de Haas, Mathieu Thoury, Matthew Fuszard, Matthias Mann, Maude Le Gall, Maximilian H. Ganser, Mayte Villalba, Melkamu Getie, Mettine Bos, Michael Cloesmeijer, Michael J. MacCoss, Michael M. Rosenblatt, Michal Kucera, Michelle Heck, Michelle Unger, Miguel Blanca, Miguel Gonzalez‐Muñoz, Mikhail V. Gorshkov, Ming-Ming Sun, Minka Zivkovic, Miroslav Berka, Molly Phillips, Moniek de Maat, Morgan R. Alexander, Muhammad Rizwan, N. Couto, Naoya Hatano, Nathalie Jansen, Neil L. Kelleher, Ni Pan, Nicole Lucien, Nikita A. Shved, Nikki van Leeuwen, Nikolay V. Goncharov, Nikunj Maheshwari, Nilesh S Tannu, Ning Fu, Ohgew Kweon, Olga Kiseleva, Oliver Mueller-Cajar, P. C. Wright, Paula M. Mendes, Pei‐Yuan Qian, Peter Roepstorff, Philip M. Williams, Philipp Khaitovich, Pierre D. J. Moens, Pierre Thibault, Pieter‐Jan Ceyssens, Pirkko Mattila, Pradip Kumar Acharya, Prasanna Vasu, Praveen Kumar, Qian Wang, Qing-Run Li, Quan-Hu Sheng, Quanhui Wang, R. Märker, Rafael G. Saer, Rafael M. Navarro, Rajesh Raju, Randall G. Cameron, Reinhard H.H. Neubert, Reinhard Turetschek, Renu Goel, Richard C. Jones, Richard S. Johnson, Ricky D. Edmondson, Rieke van der Graaf, Rinaldo C. de Paula, Risto Renkonen, Rob Lavigne, Robert E. Blankenship, Robert J. Helleur, Robert Riley, Robyn E. O’Hehir, Rodrigo Barderas, Roger Schutgens, Rolf Urbanus, Romana Hampejsová, Ron Mathôt, Ronald B. Walter, Rong Zeng, Rony Swennen, Roque Bru-Martínez, Rosa Rakownikow Jersie-Christensen, Ruben Bierings, Rui Miguel Mamede Branca, Ryanne Arisz, Sabine Agatha, Sakari Joenväärä, Salvador Mas, Samantha Gouw, Samiya Al‐Jaaidi, Sander Meijer, Sandip Kamath, Sandra Pacharra, Santosh Renuse, Sara Benedé, Sara Rinalducci, Sarah J. Robinson, Saskia Schols, Scott E Hemby, Sean de Jong, Sebastiaan Laan, Sebastien Carpentier, Seong‐Jae Kim, Sergio Lilla, Shannon van Hoorn, Si-Min He, Simona Santoro, Simone Cristoni, Simone Reitsma, Simonetta Caira, Siqi Liu, Sjoerd Koopman, Sonam Mahajan, Stefanie Wienkoop, Stephan Meijer, Steven C Hall, Sudarslal Sadasivan Nair, Susana Sellés-Marchart, Suzanne Polinder, Sébastien Bourgouin, T. Gregory McCollum, T. K. Pham, T. Sydney, T.S. Keshava Prasad, Tadeusz Krassowski, Tatiana D. Karp, Tatsuro Hamada, Tchilabalo Dilezitoko Alayi, Thierry Peyrard, Tiago S. Balbuena, Tina A Settineri, Tine Goedhart, Tirsa T. van Duijl, Tracey Slotta, U. Kück, Vadim V. Kumeiko, Vengatesen Thiyagarajan, Venkata Maccha, Veronika Berková, Veronika Reisinger, Ville Parviainen, Virginie Helias, Vivekananda Reddy Siddavarapu, Višnja Bačun‐Družina, Vladimir Gorshkov, Wala Al Arashi, Wei Tong, William Burkhart, William W. Metcalf, Wolfgang Blenau, Wout Bittremieux, Xi Jiang, Xiaofan Zhou, Xing-Xing Shen, Yacine Hemar, Yanfen Xue, Yang Yang, Yanhe Ma, Yonghao Guo, Yoon-Seok Chang, Yu Zhang, Yunqiu Chen, Zhang-Xian Xie, Zhao Li, Zheng Yan, Zhi-Duan Su, Zhijun Guo, Zhiwei Wang, Zhong Qian, Zhuowei Wang

Where the work happened

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