Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics

Cited by (315)

Items 201–300 of 315

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2. Recognition of Ovarian Tumor-Derived Non-canonical Peptide Induces Memory-Like Features in Natural Killer Cells
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4. Tanycytic annexinA1-containing extracellular vesicles control thermogenesis by orchestrating microglial and neuronal functions
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5. MALDI-TOF mass spectrometry and proteomics as phenotypic screening tools for anti-inflammatory drugs
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6. ER-Lysosome Cholesterol Exchange Regulates Lysosomal Motility Through mTOR-Dependent LAMTOR1 Phosphorylation
   Pathma Muthukottiappan, Alireza Dehghani, Asisa Muchamedin, Michael Ebner, Mariana E. G. de Araújo, Cristina Coman, Sönke Rudnik, Milash Balachandran, Sofía Fajardo‐Callejón, Fatema Akter et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
7. A Bactericidal Phospholipase from Archaea
   Chahrazad Taissir, Romain Strock, Yi Wang, Charlotte Guffick, Pauline Misson, Valerie W. C. Soo, Antoine Hocher, Alex Montoya, Pavel V. Shliaha, Hanna M. Oksanen et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
8. Chromatin is dispensable for bacterial life
   Paul Villain, Antoine Hocher, Jacques Serizay, Chad Whilding, Alex Montoya, Pavel V. Shliaha, Romain Koszul, Tobias Warnecke · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
9. Extending the Range of SLIM-Labeling Applications: From Human Cell Lines in Culture to Caenorhabditis elegans Whole-Organism Labeling
   Laurent Lignières, Nicolas Sénécaut, Tien Dang, Laura Bellutti, Marion Hamon, Samuel Terrier, Véronique Legros, Guillaume Chevreux, Gaëlle Lelandais, René‐Marc Mège et al. · 2023 · Journal of Proteome Research
10. Automated multiplexed affinity‐based enrichment of peptides for LC‐MS/MS plasma proteomics
    Sergio Mosquim, Fredrik Levander · 2024 · PROTEOMICS
11. Associations between the mid-adolescent external exposome and proteomic biomarkers of mental health
    Zhiyang Wang, Gabin Drouard, Aleksei Afonin, Núria Botella, Carmen Peuters, Aino‐Kaisa Piironen, Alyce M. Whipp, Boris Cheval, Libor Šulc, Marja Heinonen-Guzejev et al. · 2024 · medRxiv
12. eLife Assessment: Maintenance of neuronal TDP-43 expression requires axonal lysosome transport
    Sofia Jorge Araújo · 2025 · eLife
13. Maintenance of neuronal TDP-43 expression requires axonal lysosome transport
    Veronica H. Ryan, Sydney Lawton, Joel F. Reyes, James Hawrot, Ashley M. Frankenfield, Sahba Seddighi, Daniel M. Ramos, Faraz Faghri, Nicholas L Johnson, Jizhong Zou et al. · 2025 · eLife
14. Mitochondrial dysfunction underlies monocyte immune deficiency in patients with severe alcohol-related hepatitis
    Paul K. Middleton, Ricardo J. Aramayo, Alex Montoya, Pavel V. Shliaha, Simon A. S. Pope, Louise Fets, Nikhil Vergis, Mark R. Thursz, Helena M. Cochemé · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
15. Characterization of mycobacteria isolated from the Brazilian Atlantic Forest: a public health and bioprospection perspective
    Leandro Santiago Emmerick, Marcos Gustavo Araujo Schwarz, Paloma Rezende Corrêa, Sindy Licette Pinero, Leonardo Henrique Ferreira Gomes, Ana Maria Lima Almeida, Richard Hemmi Valente, Wim Maurits Sylvain Degrave, Leila Mendonça-Lima · 2025 · Frontiers in Microbiology
16. LSD1 serine 166 is a phosphorylation switch for chromatin landscaping, gene activation, and tissue remodeling
    Mukund Sharma, Anna Aakula, Oxana V. Denisova, Elena Ceccacci, Kourosh Hayatigolkhatmi, Jonatan Caroli, Reetta Nätkin, Marie-Catherine Laisne, Riikka Huhtaniemi, Sujan Ghimire et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
17. Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using In Vitro Human Proteome
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18. Multiomics profiling of zebrafish embryonic cell line PAC2 across growth phases to assess its relevance for toxicological studies
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19. Scheduled data-independent acquisition mass spectrometry for global proteomics and proximity labeling
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20. Analytical methods for in-depth characterisation of cell culture bioreactors: A case study
    J. Seidel, Clifford Young, Manuela Klingler‐Hoffmann, Mark R. Condina, Alok Kishorkumar Shah, Sri H. Ramarathinam, Woan Mei Kok, Craig T. Kyngdon, Peter Hoffmann · 2025 · Journal of Chromatography Open
21. Formation of non-enzymatic protein modifications (nePTMs) on caseins and whey proteins during dry heating and the impact on their in vitro infant digestion profile
    Yifan Liang, Hannah E. Zenker, Andreas Mauser, Monika Pischetsrieder, Josep Rubert, Kasper Arthur Hettinga · 2025 · Food Chemistry
22. From 2D Monolayer to 3D Spheroid: Matrigel’s Spatial and Chemical Cues Remodel the Calu-3 Proteome
    Ariel Moura Maia, Luiz Augusto Basso, Pablo Machado, Cristiano Valim Bizarro · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
23. Clozapine's Molecular Signature: Selective 5‐ HT2A Receptor Downregulation and Signalling in Rat Brain Cortical Regions
    Sylwia Kędracka–Krok, Jakub Nowak, Ewelina Fic, Joanna Solich, Piotr Rybczyński, Weronika Romanska, Patrycja Sarga, Katarzyna Pustelny, Marta Dziedzicka‐Wasylewska · 2025 · Journal of Neurochemistry
24. A procedure for controlling the false discovery rate of de novo peptide sequencing
    Justin A. Sanders, William Stafford Noble, Uri Keich · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
25. Multi-protein panel in pancreatic cyst fluid for improved risk stratification for pancreatic cancer
    Dimitrios Manolis, Darragh Patrick O'Brien, Benedikt Mathias Kessler, Eamon C. Faulkner, Pavlos Lykoudis, Farzana Haque, Sam Khulusi, Abdul Razack, Hemant Mahendrakumar Kocher, David Kuang-Fu Chang et al. · 2025 · medRxiv
26. Ribosomal frameshifting is a carefully tuned modifier of proteins
    Jonas Poehls, Cedric Landerer, Doris Richter, Maria Luisa Romero Romero, Anna Shevchenko, Andrej Shevchenko, Ágnes Tóth-Petróczy · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
27. Engineering Cortical Networks: An Open Platform for Controlled Human Circuit Formation and Synaptic Analysis In Vitro
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28. Identification Of Protein Cargo in Extracellular Vesicles from Macrophages in Progressing and Regressing Tumors
    Y. Zhu, Jiaxi Cai, Raymond T. Suhandynata, Jack D. Bui · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
29. A dimerization-activated proximity labeling system for direct characterization of cadherin cis interactions
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30. PBMC proteome is altered in children with high body fat percentage
    Maya Petek, Tjaša Hertiš Petek, Uroš Potočnik, Nataša Marčun Varda · 2025 · Scientific Reports
31. Sorghum bicolor membrane steroid binding protein 1 can bind heme and remodel ER membranes
    Khuanpiroon Ratanasopa, Rocio Ochoa‐Fernandez, Silas Busck Mellor, Valentina Travaglia, Kasper Hinz, Pernille Sønderby, Tomas Laursen · 2025 · Plant and Cell Physiology
32. TTLL6-mediated Polyglutamylation of PurA Maintains Colonic Crypt Integrity
    Vanessa Pires, Chloé Pangault, Conception Paul, Pascal Finetti, François Bertucci, Émilie Mamessier, Célia Jardin, Nuttanid Numnoi, Ilaria Cicalini, Damiana Pieragostino et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
33. Additional file 1 of Analyses of the brown stain on the Parthenon Centaur head in Denmark
    Rasmussen, Kaare Lund, Rasmussen, Bodil Bundgaard, Thomas Delbey, Ilaria Bonaduce, Kjeldsen, Frank, Vladimir Gorshkov · 2024 · Figshare
34. Additional file 2 of Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus
    Saleem, Waqar, Nathan Carpentier, Charlotte Hinnekens, Oh, Dayoung, Van Vlierberghe, Sandra, Kevin Braeckmans, Hans J. Nauwynck · 2024 · Figshare
35. Additional file 3 of Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization
    Alexandra Muntiu, Andrea Papait, Federica Vincenzoni, Alberto Vitali, Wanda Lattanzi, Pietro Romele, Anna Cargnoni, Antonietta Rosa Silini, Ornella Parolini, Claudia Desiderio · 2024 · Figshare
36. Additional file 4 of Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization
    Alexandra Muntiu, Andrea Papait, Federica Vincenzoni, Alberto Vitali, Wanda Lattanzi, Pietro Romele, Anna Cargnoni, Antonietta Rosa Silini, Ornella Parolini, Claudia Desiderio · 2024 · Figshare
37. Additional file 2 of Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization
    Alexandra Muntiu, Andrea Papait, Federica Vincenzoni, Alberto Vitali, Wanda Lattanzi, Pietro Romele, Anna Cargnoni, Antonietta Rosa Silini, Ornella Parolini, Claudia Desiderio · 2024 · Figshare
38. Additional file 2 of Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons
    Saadia Hasan, Michael S. Fernandopulle, Stewart W. Humble, Ashley M. Frankenfield, Li, Haorong, Ryan Prestil, Johnson, Kory R., Brent James Ryan, Richard Wade‐Martins, Ward, Michael E. et al. · 2024 · Figshare
39. Additional file 3 of Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons
    Saadia Hasan, Michael S. Fernandopulle, Stewart W. Humble, Ashley M. Frankenfield, Li, Haorong, Ryan Prestil, Johnson, Kory R., Brent James Ryan, Richard Wade‐Martins, Ward, Michael E. et al. · 2024 · Figshare
40. Additional file 2 of Analyses of the brown stain on the Parthenon Centaur head in Denmark
    Rasmussen, Kaare Lund, Rasmussen, Bodil Bundgaard, Thomas Delbey, Ilaria Bonaduce, Kjeldsen, Frank, Vladimir Gorshkov · 2024 · Figshare
41. Additional file 5 of Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization
    Alexandra Muntiu, Andrea Papait, Federica Vincenzoni, Alberto Vitali, Wanda Lattanzi, Pietro Romele, Anna Cargnoni, Antonietta Rosa Silini, Ornella Parolini, Claudia Desiderio · 2024 · Figshare
42. Additional file 4 of Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons
    Saadia Hasan, Michael S. Fernandopulle, Stewart W. Humble, Ashley M. Frankenfield, Li, Haorong, Ryan Prestil, Johnson, Kory R., Brent James Ryan, Richard Wade‐Martins, Ward, Michael E. et al. · 2024 · Figshare
43. Additional file 1 of Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization
    Alexandra Muntiu, Andrea Papait, Federica Vincenzoni, Alberto Vitali, Wanda Lattanzi, Pietro Romele, Anna Cargnoni, Antonietta Rosa Silini, Ornella Parolini, Claudia Desiderio · 2024 · Figshare
44. Additional file 1 of Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons
    Saadia Hasan, Michael S. Fernandopulle, Stewart W. Humble, Ashley M. Frankenfield, Li, Haorong, Ryan Prestil, Johnson, Kory R., Brent James Ryan, Richard Wade‐Martins, Ward, Michael E. et al. · 2023 · Figshare
45. Additional file 1 of Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus
    Saleem, Waqar, Nathan Carpentier, Charlotte Hinnekens, Oh, Dayoung, Van Vlierberghe, Sandra, Kevin Braeckmans, Hans J. Nauwynck · 2024 · Figshare
46. Acute IFN-γ elicits long-term proteomic IFN-γ signature in melanoma cells
    Agnete W.P. Jensen, Anne-Christine Kiel Rasmussen, Ilaria Piga, Anne Weiß, Marta Sanchez Sanchez, Marco Donia, Giulia Franciosa, Jesper Velgaard Olsen · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
47. The opposite effects of stringent response on phage infection of Pseudomonas putida
    Alicja Cecylia Lewańczyk, Mariliis Hinnu, Elise Mägi, Roger Rikberg, Age Brauer, Hedvig Tamman · 2026 · microLife
48. YAP/TEAD drives treatment-induced adaptive immunosuppression in EGFR-mutant lung cancer
    Meija Honkanen, Jonas Baumgarten, Nikol Dibus, Jenna H. Rannikko, Miloš Gojković, Paloma Cejas, Yingtian Xie, Zsuzsanna Ortutay, Johannes A. M. Merilahti, Mari Tienhaara et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
49. Comparative profiling of SARS-CoV-2 variant infections reveals diverse impacts on host cell RNA and RNA binding protein distribution and regulation
    Grégoire De Bisschop, Tram N. Q. Pham, Nicolas Jacques-De Vries, Monford Paul Abishek Nelson Vimalanathan, Jonathan Boulais, Gabrielle Deschamps-Francoeur, Eunjeong Kwon, Éric A. Cohen, Éric Lécuyer · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
50. Kv11.1 (hERG) Protein Interaction Networks Connect Endocytic Trafficking to Polygenic Influences on Cardiac Repolarization
    Christian L. Egly, Lea A. Barny, Suah Woo, Devyn Mitchell, Matthew Ku, Björn C. Knollmann, Lars Plate, Brett M. Kroncke · 2026 · Molecular & Cellular Proteomics
51. Meloidogyne graminicola hijacks host metabolism and suppresses immunity: insights from DIA-based proteomics in rice
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52. Interactome Analysis of the CC2D1A Scaffold Reveals Novel Neuronal Interactions and a Postsynaptic Role
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53. From Variability to Consensus: Rescoring Harmonizes Peptide Identification across Diverse Search Engines and Data Sets
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54. Proteomic Signatures of Conversion Risk and Disease Severity in Multiple Sclerosis
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55. SPROUTS_DB: An Implemented Database of Contaminants for Extracellular Vesicle Proteomics Studies
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56. Altered Sphingolipid Metabolism is Associated with Osimertinib Resistance in Nonsmall-Cell Lung Cancer
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57. Keratin 7 protein presence in stool is indicative of active pediatric-onset inflammatory bowel disease
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58. A posttranslational proteomic survey of a single anatomically preserved human 20‐week postconception brain
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59. Effects of triethylene glycol dimethacrylate and bisphenol A‐glycidyl methacrylate on annexin A proteins in human mesangial cells
    Ayşe Nur Doğan, Niharika Bala, Zenab Shahzad, Erika S. Galban, Abdel A. Alli · 2026 · European Journal Of Oral Sciences
60. Opsonization Improves Dual Proteomic Analysis of Burkholderia cenocepacia Infections
    Michael G. Bacus, Leila Jebeli, Jessica M. Lewis, Nancy Wang, Hayley J. Newton, Nichollas E. Scott · 2026 · Journal of Proteome Research
61. Reelin level in serum-derived extracellular vesicles predicts regression of M2BPGi-defined liver fibrosis following hepatitis C virus eradication by direct-acting antiviral agents
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62. Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity
    Lael Werner, T Nissenbaum, Morine Fibelman, Haim Leibovitzh, Nathaniel A. Cohen, Moran Brenner, Lior Lobel, Nitsan Maharshak · 2026 · Cell Reports
63. Protein Sequence and Structural Diversity in Plodia interpunctella Silk Governs Microparticle Function and Macrophage Response
    Lauren E. Eccles, Rebecca K. Liwang, Andrea A. Orozco, Elizabeth L. Aikman, Whitney L. Stoppel · 2026 · Biomacromolecules
64. Endocytic turnover of endothelial cell-membrane proteins as a driver of rat blood-brain barrier specialization and dysfunction
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65. Comparative Evaluation of DDA- and DIA-Based Proteomic Workflows in Beryllium-Related Lung Disease
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66. APOE interacts with COX-2 on lipid droplets to modulate inflammatory lipid signaling
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67. Development of a Xylene-Free Sample Preparation Protocol for Quantitative Proteomics of Clinically Relevant Formaldehyde-Fixed Paraffin-Embedded Needle Biopsy Samples
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69. Plasma proteomics analysis of vitamin C supplementation in people with type 2 diabetes
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70. AURORA A interacts with DICER and SETD2 to promote S-phase progression
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71. Pre-existing levels of pro-survival proteins and induction of BCL-XL dictate cell fate after p53 activation
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72. Integrated multi-omics profiling of gut bacterial extracellular vesicles links cargo composition to host transcriptional responses
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73. Exoproteome Remodeling by the BraI/R Quorum Sensing Circuit and Interspecies Competition in Paraburkholderia
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74. Aggrecan and polymeric immunoglobulin receptor in extracellular vesicles of patients with seropositive rheumatoid arthritis
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75. Untargeted plasma proteomics and clinical phenotypes in adolescent depression
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76. Quantitative Proteomic Profiling of Plasma Alterations Associated with Thrombotic Risk and Insulin Resistance in Type 1 Diabetes
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77. AKAP2/PKA complex coordinates primary ciliogenesis, ciliary trafficking and Shh signaling
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78. TRMT10A Deficiency and tRNA Fragmentation Disrupt Human Pancreatic β-Cell Identity and Insulin Maturation
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79. Human Tear Corona Insights of PEG-Mimetic Sustainable Oligopeptylated Ultra-Stable AuNPs vs PEGylated-AuNPs
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80. Compromised extracellular vesicle-mediated communication impairs bull spermatozoa function
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81. Avidin is evolutionarily conserved in fish but dispensable for development and resistance against Streptococcus agalactiae in zebrafish
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82. Brain metastasis‐associated fibroblasts shape the tumour microenvironment to enhance cancer cell invasion
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83. Size-exclusion chromatography as a clinically applicable method for extracellular vesicles collection as liquid biopsies shows potential diagnostic relevance and correlation with poorer outcome in common cancer types
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84. LCM-Enriched Proteomic Characterization of Antibody-Mediated Glomerular Damage and Complement Activation in Pre-Clinical Models
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85. Endogenous lipid droplets exhibit profound proteomic and lipidomic differences across neural stem cell states
    Diana Panfilova, Mergim Ramosaj, Manfredo Quadroni, Marlen Knobloch · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
86. Role of valve endothelial cells and extracellular vesicles in aortic valve calcification in vitro
    Daria Evensen, Arkady Rutkovskiy, Krizia Sagini, Hanne Haslene‐Hox, Arsenii Zabirnyk, Maria Bogdanova, John‐Peder Escobar Kvitting, Mari‐Liis Kaljusto, Alicia Llorente, Kåre‐Olav Stensløkken et al. · 2026 · Scientific Reports
87. Identification of circulating parasite and host biomarkers in the serum proteome of Trypanosoma vivax-infected sheep under immunosuppression
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88. Advances in Mass Spectrometry‐Based Proteomics for Kidney Disease Biomarker Discovery and Clinical Translation
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89. A porcine spectral assay library to quantify brain proteome by DIA-MS
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