Mol. Cell Proteomics

Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model.

Enström A, Carlsson R, Buizza C, Lewi M, Paul G

Mol. Cell Proteomics 23 (6) 100782 [2024-06-00; online 2024-05-04]

Affinity Proteomics Stockholm [Service]

Year 2023

Glycan Complexity and Heterogeneity of Glycoproteins in Somatic Extracts and Secretome of the Infective Stage of the Helminth Fasciola hepatica.

De Marco Verissimo C, Cwiklinski K, Nilsson J, ..., Karlsson NG, Dalton JP

Mol. Cell Proteomics 22 (12) 100684 [2023-12-00; online 2023-11-21]

Breast Milk Oligosaccharides Contain Immunomodulatory Glucuronic Acid and LacdiNAc.

Jin C, Lundstrøm J, Korhonen E, Luis AS, Bojar D

Mol. Cell Proteomics 22 (9) 100635 [2023-09-00; online 2023-08-18]

Mapping the Human Chondroitin Sulfate Glycoproteome Reveals an Unexpected Correlation Between Glycan Sulfation and Attachment Site Characteristics.

Noborn F, Nilsson J, Sihlbom C, ..., Kjellén L, Larson G

Mol. Cell Proteomics 22 (8) 100617 [2023-08-00; online 2023-07-14]

Increasing Complexity of the N-Glycome During Caenorhabditis Development.

Wilson IBH, Yan S, Jin C, ..., Schnabel R, Paschinger K

Mol. Cell Proteomics 22 (3) 100505 [2023-03-00; online 2023-01-28]

Year 2022

A Complex Connection Between the Diversity of Human Gastric Mucin O-Glycans, Helicobacter pylori Binding, Helicobacter Infection and Fucosylation.

Chahal G, Padra M, Erhardsson M, ..., Karlsson NG, Lindén SK

Mol. Cell Proteomics 21 (11) 100421 [2022-11-00; online 2022-09-29]

Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles.

Lischnig A, Bergqvist M, Ochiya T, Lässer C

Mol. Cell Proteomics 21 (9) 100273 [2022-09-00; online 2022-07-30]

Glycoproteomics and MS Proteomics [Service]

Year 2021

Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication.

Krishnan S, Nordqvist H, Ambikan AT, ..., Treutiger CJ, Neogi U

Mol. Cell Proteomics 20 (-) 100159 [2021-10-05; online 2021-10-05]

Affinity Proteomics Uppsala [Service]

Sulfation of O-glycans on Mucin-type Proteins From Serous Ovarian Epithelial Tumors.

Thomsson KA, Vitiazeva V, Mateoiu C, ..., Sundfeldt K, Karlsson NG

Mol. Cell Proteomics 20 (-) 100150 [2021-09-21; online 2021-09-21]

Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans.

Persson A, Nikpour M, Vorontsov E, Nilsson J, Larson G

Mol. Cell Proteomics 20 (-) 100074 [2021-03-20; online 2021-03-20]

Year 2020

Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy.

van Westering TLE, Johansson HJ, Hanson B, ..., Aoki Y, Roberts TC

Mol. Cell Proteomics 19 (12) 2047-2068 [2020-12-00; online 2020-09-29]

Global Proteomics and Proteogenomics [Service]

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.

Zhu Y, Orre LM, Zhou Tran Y, ..., Anders S, Lehtiö J

Mol. Cell Proteomics 19 (6) 1047-1057 [2020-06-00; online 2020-03-23]

Global Proteomics and Proteogenomics [Technology development]

Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics.

Herr P, Boström J, Rullman E, ..., Maddalo G, Altun M

Mol. Cell Proteomics 19 (4) 608-623 [2020-04-00; online 2020-02-12]

Global Proteomics and Proteogenomics [Collaborative]

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping.

Karlsson R, Thorsell A, Gomila M, ..., Kristiansson E, Moore ERB

Mol. Cell Proteomics 19 (3) 518-528 [2020-03-00; online 2020-01-15]

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.

Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S

Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]

Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative]

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods.

De Leoz MLA, Duewer DL, Fung A, ..., Yuan H, Stein SE

Mol. Cell Proteomics 19 (1) 11-30 [2020-01-00; online 2019-10-07]

Year 2019

A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection.

Månberg A, Bradley F, Qundos U, ..., Nilsson P, Broliden K

Mol. Cell Proteomics 18 (3) 461-476 [2019-03-00; online 2018-11-30]

Affinity Proteomics Stockholm [Collaborative]

Year 2018

Glycomics@ExPASy: Bridging the Gap.

Mariethoz J, Alocci D, Gastaldello A, ..., Packer NH, Lisacek F

Mol. Cell Proteomics 17 (11) 2164-2176 [2018-11-00; online 2018-08-10]

Isomeric Separation and Recognition of Anionic and Zwitterionic N-glycans from Royal Jelly Glycoproteins.

Hykollari A, Malzl D, Eckmair B, ..., Wilson IBH, Paschinger K

Mol. Cell Proteomics 17 (11) 2177-2196 [2018-11-00; online 2018-08-13]

Glycoproteomics and MS Proteomics [Service]

Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS.

Karlsson CAQ, Järnum S, Winstedt L, ..., Linder A, Malmström JA

Mol. Cell Proteomics 17 (6) 1097-1111 [2018-06-00; online 2018-03-06]

Structural Proteomics [Technology development]

Year 2017

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics.

Boulund F, Karlsson R, Gonzales-Siles L, ..., Moore ERB, Kristiansson E

Mol. Cell Proteomics 16 (6) 1052-1063 [2017-06-00; online 2017-04-18]

Glycoproteomics and MS Proteomics [Service]

Structural Diversity of Human Gastric Mucin Glycans.

Jin C, Kenny DT, Skoog EC, ..., Lindén SK, Karlsson NG

Mol. Cell Proteomics 16 (5) 743-758 [2017-05-00; online 2017-05-04]

Affinity Proteomics Uppsala [Service] Glycoproteomics and MS Proteomics [Service] PLA and Single Cell Proteomics [Service]

Year 2016

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples.

Heyder T, Kohler M, Tarasova NK, ..., Grunewald J, Ytterberg AJ

Mol. Cell Proteomics 15 (9) 3017-3029 [2016-09-00; online 2016-07-24]

Advanced Mass Spectrometry Proteomics [Collaborative]

Single Chain Antibodies as Tools to Study transforming growth factor-β-Regulated SMAD Proteins in Proximity Ligation-Based Pharmacological Screens.

Blokzijl A, Zieba A, Hust M, ..., Dübel S, Landegren U

Mol. Cell Proteomics 15 (6) 1848-1856 [2016-06-00; online 2016-03-02]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

DeMix-Q: Quantification-Centered Data Processing Workflow.

Zhang B, Käll L, Zubarev RA

Mol. Cell Proteomics 15 (4) 1467-1478 [2016-04-00; online 2016-01-04]

Chemical Proteomics [Technology development]

Year 2014

Numerical compression schemes for proteomics mass spectrometry data.

Teleman J, Dowsey AW, Gonzalez-Galarza FF, ..., Deutsch EW, Levander F

Mol. Cell Proteomics 13 (6) 1537-1542 [2014-06-00; online 2014-03-29]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.

Edfors F, Boström T, Forsström B, ..., Mann M, Uhlen M

Mol. Cell Proteomics 13 (6) 1611-1624 [2014-06-00; online 2014-04-12]

SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Zhu Y, Hultin-Rosenberg L, Forshed J, ..., Orre LM, Lehtiö J

Mol. Cell Proteomics 13 (6) 1552-1562 [2014-06-00; online 2014-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.

Forsström B, Axnäs BB, Stengele K, ..., Rockberg J, Uhlen M

Mol. Cell Proteomics 13 (6) 1585-1597 [2014-06-00; online 2014-04-08]

Autoimmunity and Serology Profiling [Technology development]

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.

Fagerberg L, Hallström BM, Oksvold P, ..., Ponten F, Uhlén M

Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Year 2013

Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.

Ayoglu B, Häggmark A, Khademi M, ..., Schwenk JM, Nilsson P

Mol. Cell Proteomics 12 (9) 2657-2672 [2013-09-00; online 2013-06-05]

Autoimmunity and Serology Profiling [Technology development]

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

Lyutvinskiy Y, Yang H, Rutishauser D, Zubarev RA

Mol. Cell Proteomics 12 (8) 2324-2331 [2013-08-00; online 2013-04-17]

Advanced Mass Spectrometry Proteomics

Parallel visualization of multiple protein complexes in individual cells in tumor tissue.

Leuchowius KJ, Clausson CM, Grannas K, ..., Landegren U, Söderberg O

Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]

Affinity Proteomics Uppsala [Technology development] NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure PLA and Single Cell Proteomics

Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.

Geiger T, Velic A, Macek B, ..., Cox J, Mann M

Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]

Spatial Proteomics Tissue Profiling

An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F

Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Year 2012

High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays.

Buus S, Rockberg J, Forsström B, ..., Uhlen M, Schafer-Nielsen C

Mol. Cell Proteomics 11 (12) 1790-1800 [2012-12-00; online 2012-09-18]

Autoimmunity and Serology Profiling [Service]

Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry.

Olsson N, James P, Borrebaeck CA, Wingren C

Mol. Cell Proteomics 11 (8) 342-354 [2012-08-00; online 2012-05-01]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Intercellular variation in signaling through the TGF-β pathway and its relation to cell density and cell cycle phase.

Zieba A, Pardali K, Söderberg O, ..., Heldin CH, Landegren U

Mol. Cell Proteomics 11 (7) M111.013482 [2012-07-00; online 2012-03-24]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens.

Dengjel J, Høyer-Hansen M, Nielsen MO, ..., Jäättelä M, Andersen JS

Mol. Cell Proteomics 11 (3) M111.014035 [2012-03-00; online 2012-02-06]

Antibody-based protein profiling of the human chromosome 21.

Uhlén M, Oksvold P, Älgenäs C, ..., Kondo T, Sivertsson Å

Mol. Cell Proteomics 11 (3) M111.013458 [2012-03-00; online 2011-11-02]

Spatial Proteomics Tissue Profiling

A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.

Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M

Mol. Cell Proteomics 11 (3) O111.009613 [2012-03-00; online 2011-10-04]

Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.

Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI

Mol. Cell Proteomics 11 (3) M111.013680 [2012-03-00; online 2011-10-18]

Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.

Larance M, Kirkwood KJ, Xirodimas DP, ..., Uhlen M, Lamond AI

Mol. Cell Proteomics 11 (3) M111.014407 [2012-03-00; online 2011-10-29]

Year 2011

Western blotting via proximity ligation for high performance protein analysis.

Liu Y, Gu J, Hagner-McWhirter Å, ..., Ivansson D, Landegren U

Mol. Cell Proteomics 10 (11) O111.011031 [2011-11-00; online 2011-08-02]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Year 2010

Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.

Schwenk JM, Igel U, Neiman M, ..., Nilsson P, Uhlen M

Mol. Cell Proteomics 9 (11) 2497-2507 [2010-11-00; online 2010-08-05]

Affinity Proteomics Stockholm [Technology development]