J. Proteome Res.

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.

Bouyssié D, Altıner P, Capella-Gutierrez S, ..., Winkelhardt D, Schwämmle V

J. Proteome Res. 23 (1) 418-429 [2024-01-05; online 2023-12-01]

Bioinformatics Support, Infrastructure and Training [Technology development]

Year 2022

Well-Plate μFASP for Proteomic Analysis of Single Pancreatic Islets.

Sandbaumhüter FA, Nezhyva M, Eriksson O, ..., Andrén PE, Jansson ET

J. Proteome Res. 21 (4) 1167-1174 [2022-04-01; online 2022-03-16]

Spatial Mass Spectrometry [Collaborative]

Year 2021

Multiomics Profiling of Alzheimer's Disease Serum for the Identification of Autoantibody Biomarkers.

San Segundo-Acosta P, Montero-Calle A, Jernbom-Falk A, ..., Nilsson P, Barderas R

J. Proteome Res. 20 (11) 5115-5130 [2021-11-05; online 2021-10-10]

Autoimmunity and Serology Profiling [Collaborative]

Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma.

Cao X, Sandberg A, Araújo JE, ..., Eriksson LE, Pernemalm M

J. Proteome Res. 20 (9) 4610-4620 [2021-09-03; online 2021-07-28]

Global Proteomics and Proteogenomics [Technology development]

High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins.

Niksirat H, Siino V, Steinbach C, Levander F

J. Proteome Res. 20 (8) 4075-4088 [2021-08-06; online 2021-06-29]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.

Morgell A, Reisz JA, Ateeb Z, ..., Chen MS, D'Alessandro A

J. Proteome Res. 20 (5) 2725-2738 [2021-05-07; online 2021-03-15]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Year 2020

Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum.

Khoomrung S, Nookaew I, Sen P, ..., Harandi AM, Nielsen J

J. Proteome Res. 19 (1) 269-278 [2020-01-03; online 2019-11-01]

Swedish Metabolomics Centre (SMC) [Service]

Year 2019

Mining the Proteome Associated with Rheumatic and Autoimmune Diseases.

Ruiz-Romero C, Lam MPY, Nilsson P, ..., Watt FE, Blanco FJ

J. Proteome Res. 18 (12) 4231-4239 [2019-12-06; online 2019-10-23]

Autoimmunity and Serology Profiling [Technology development]

Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.

Pineau C, Hikmet F, Zhang C, ..., Uhlén M, Lindskog C

J. Proteome Res. 18 (12) 4215-4230 [2019-12-06; online 2019-08-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.

Ignjatovic V, Geyer PE, Palaniappan KK, ..., Deutsch EW, Schwenk JM

J. Proteome Res. 18 (12) 4085-4097 [2019-12-06; online 2019-10-11]

Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.

Gaetani M, Sabatier P, Saei AA, ..., Lundström SL, Zubarev RA

J. Proteome Res. 18 (11) 4027-4037 [2019-11-01; online 2019-10-14]

Chemical Proteomics [Technology development]

Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.

Edfors F, Forsström B, Vunk H, ..., Schwenk JM, Uhlen M

J. Proteome Res. 18 (7) 2706-2718 [2019-07-05; online 2019-06-07]

Affinity Proteomics Stockholm [Technology development]

Exploring the Arctic Charr Intestinal Glycome: Evidence of Increased N-Glycolylneuraminic Acid Levels and Changed Host-Pathogen Interactions in Response to Inflammation.

Venkatakrishnan V, Padra JT, Sundh H, ..., Karlsson NG, Lindén SK

J. Proteome Res. 18 (4) 1760-1773 [2019-04-05; online 2019-03-19]

Glycoproteomics and MS Proteomics [Service]

GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical.

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

J. Proteome Res. 18 (2) 664-677 [2019-02-01; online 2019-01-15]

Glycoproteomics and MS Proteomics [Collaborative]

Year 2018

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project.

Omenn GS, Lane L, Overall CM, ..., Baker MS, Deutsch EW

J. Proteome Res. 17 (12) 4031-4041 [2018-12-07; online 2018-08-23]

NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.

Willforss J, Chawade A, Levander F

J. Proteome Res. - (-) - [2018-10-02; online 2018-10-02]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Higher Energy Collisional Dissociation Mass Spectrometry of Sulfated O-Linked Oligosaccharides.

Issa SMA, Vitiazeva V, Hayes CA, Karlsson NG

J. Proteome Res. 17 (9) 3259-3267 [2018-09-07; online 2018-08-13]

Glycoproteomics and MS Proteomics [Technology development]

Impact in Plasma Metabolome as Effect of Lifestyle Intervention for Weight-Loss Reveals Metabolic Benefits in Metabolically Healthy Obese Women.

Almanza-Aguilera E, Brunius C, Bernal-Lopez MR, ..., Landberg R, Andres-Lacueva C

J. Proteome Res. 17 (8) 2600-2610 [2018-08-03; online 2018-06-28]

Swedish NMR Centre (SNC) [Service]

Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice.

Torell F, Bennett K, Cereghini S, ..., Trygg J, Lundstedt T

J. Proteome Res. 17 (7) 2293-2306 [2018-07-06; online 2018-06-15]

Swedish Metabolomics Centre (SMC) [Service]

Comprehensive Mass Spectrometric Survey of Streptococcus pyogenes Subcellular Proteomes.

Wilk L, Happonen L, Malmström J, Herwald H

J. Proteome Res. 17 (1) 600-617 [2018-01-05; online 2017-12-04]

Structural Proteomics [Service]

Year 2017

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM, Omenn GS, Sun Z, ..., Moritz RL, Deutsch EW

J. Proteome Res. 16 (12) 4299-4310 [2017-12-01; online 2017-10-10]

Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods.

Carapito C, Duek P, Macron C, ..., Lane L, Pineau C

J. Proteome Res. - (-) - [2017-09-26; online 2017-09-26]

Tissue Profiling [Collaborative]

Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.

Sierra-Sánchez Á, Garrido-Martín D, Lourido L, ..., Blanco F, Fuentes M

J. Proteome Res. 16 (5) 1890-1899 [2017-05-05; online 2017-04-17]

Autoimmunity and Serology Profiling [Collaborative]

Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy.

Zandian A, Forsström B, Häggmark-Månberg A, ..., Nilsson P, Ayoglu B

J. Proteome Res. 16 (3) 1300-1314 [2017-03-03; online 2017-02-09]

Autoimmunity and Serology Profiling [Technology development]

Posttranscriptional Regulation in Adenovirus Infected Cells.

Zhao H, Konzer A, Mi J, ..., Pettersson U, Lind SB

J. Proteome Res. 16 (2) 872-888 [2017-02-03; online 2016-12-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.

Pin E, Henjes F, Hong MG, ..., Nilsson P, Schwenk JM

J. Proteome Res. 16 (1) 204-216 [2017-01-06; online 2016-10-05]

Autoimmunity and Serology Profiling [Collaborative]

Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.

Skogs M, Stadler C, Schutten R, ..., Uhlén M, Lundberg E

J. Proteome Res. 16 (1) 147-155 [2017-01-06; online 2016-10-12]

Spatial Proteomics [Technology development]

Year 2016

Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update.

Vandenbrouck Y, Lane L, Carapito C, ..., Garin J, Pineau C

J. Proteome Res. 15 (11) 3998-4019 [2016-11-04; online 2016-08-23]

Tissue Profiling [Collaborative]

Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

Hong MG, Lee W, Nilsson P, Pawitan Y, Schwenk JM

J. Proteome Res. 15 (10) 3473-3480 [2016-10-07; online 2016-08-30]

Affinity Proteomics Stockholm [Technology development]

Establishing a Proteomics-Based Monocyte Assay To Assess Differential Innate Immune Activation Responses.

Tarasova NK, Ytterberg AJ, Lundberg K, ..., Harris RA, Zubarev RA

J. Proteome Res. 15 (7) 2337-2345 [2016-07-01; online 2016-06-03]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Technology development]

Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

Teleman J, Chawade A, Sandin M, Levander F, Malmström J

J. Proteome Res. 15 (7) 2143-2151 [2016-07-01; online 2016-05-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Targeted Proteomics Approach for Precision Plant Breeding.

Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F

J. Proteome Res. 15 (2) 638-646 [2016-02-05; online 2015-12-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Systems Proteomics View of the Endogenous Human Claudin Protein Family.

Liu F, Koval M, Ranganathan S, ..., Kelleher NL, Baker MS

J. Proteome Res. 15 (2) 339-359 [2016-02-05; online 2016-01-12]

Spatial Proteomics [Service]

Elucidating the Molecular Composition of Cartilage by Proteomics.

Hsueh MF, Khabut A, Kjellström S, Önnerfjord P, Kraus VB

J. Proteome Res. 15 (2) 374-388 [2016-02-05; online 2016-01-15]

Structural Proteomics [Service]

Year 2015

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, ..., Nesvizhskii AI, Deutsch EW

J. Proteome Res. 14 (9) 3452-3460 [2015-09-04; online 2015-07-15]

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Horvatovich P, Lundberg EK, Chen YJ, ..., Paik YK, Hancock WS

J. Proteome Res. 14 (9) 3415-3431 [2015-09-04; online 2015-07-23]

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

Chawade A, Sandin M, Teleman J, Malmström J, Levander F

J. Proteome Res. 14 (2) 676-687 [2015-02-06; online 2014-11-20]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Year 2014

Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.

Mardinoglu A, Kampf C, Asplund A, ..., Uhlen M, Nielsen J

J. Proteome Res. 13 (11) 5106-5119 [2014-11-07; online 2014-09-16]

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

Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.

Byström S, Ayoglu B, Häggmark A, ..., Nilsson P, Schwenk JM

J. Proteome Res. 13 (11) 4607-4619 [2014-11-07; online 2014-09-19]

Affinity Proteomics Stockholm [Collaborative] Fluorescence Tissue Profiling

Analysis of autoantibody profiles in osteoarthritis using comprehensive protein array concepts.

Henjes F, Lourido L, Ruiz-Romero C, ..., Nilsson P, Fuentes M

J. Proteome Res. 13 (11) 5218-5229 [2014-11-07; online 2014-10-09]

Autoimmunity and Serology Profiling [Collaborative]

Analysis of candidate genes for lineage-specific expression changes in humans and primates.

Lindskog C, Kuhlwilm M, Davierwala A, ..., Pääbo S, Pontén F

J. Proteome Res. 13 (8) 3596-3606 [2014-08-01; online 2014-07-15]

Tissue Profiling

Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.

Chawade A, Alexandersson E, Levander F

J. Proteome Res. 13 (6) 3114-3120 [2014-06-06; online 2014-04-29]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.

Stadler C, Fagerberg L, Sivertsson Å, ..., Lundberg E, Uhlén M

J. Proteome Res. 13 (4) 2019-2027 [2014-04-04; online 2014-03-04]

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

Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.

Resjö S, Ali A, Meijer HJ, ..., Govers F, Andreasson E

J. Proteome Res. 13 (4) 1848-1859 [2014-04-04; online 2014-03-05]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.

Alm T, von Feilitzen K, Lundberg E, Sivertsson Å, Uhlén M

J. Proteome Res. 13 (3) 1669-1676 [2014-03-07; online 2014-02-19]

Identification of novel downstream molecules of tissue factor activation by comparative proteomic analysis.

Kask L, Jorsback A, Winkvist M, ..., Bergquist J, Siegbahn A

J. Proteome Res. 13 (2) 477-488 [2014-02-07; online 2013-12-11]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.

Lane L, Bairoch A, Beavis RC, ..., Lundberg E, Omenn GS

J. Proteome Res. 13 (1) 15-20 [2014-01-03; online 2013-12-25]

Year 2013

Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice.

Yang H, Lowenson JD, Clarke S, Zubarev RA

J. Proteome Res. 12 (10) 4566-4576 [2013-10-04; online 2013-08-21]

Advanced Mass Spectrometry Proteomics

Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).

Fagerberg L, Oksvold P, Skogs M, ..., von Feilitzen K, Uhlén M

J. Proteome Res. 12 (6) 2439-2448 [2013-06-07; online 2013-01-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

Liu S, Im H, Bairoch A, ..., Beavis RC, Hancock WS

J. Proteome Res. 12 (1) 45-57 [2013-01-04; online 2012-12-25]

RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.

Danielsson F, Wiking M, Mahdessian D, ..., Uhlén M, Lundberg E

J. Proteome Res. 12 (1) 299-307 [2013-01-04; online 2012-12-12]

Year 2012

Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.

Bock T, Moest H, Omasits U, ..., Frei K, Wollscheid B

J. Proteome Res. 11 (10) 4885-4893 [2012-10-05; online 2012-08-23]

Automated selected reaction monitoring software for accurate label-free protein quantification.

Teleman J, Karlsson C, Waldemarson S, ..., Malmström J, Levander F

J. Proteome Res. 11 (7) 3766-3773 [2012-07-06; online 2012-06-05]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Multimodel pathway enrichment methods for functional evaluation of expression regulation.

Kirik U, Cifani P, Albrekt AS, ..., Heyden A, Levander F

J. Proteome Res. 11 (5) 2955-2967 [2012-05-04; online 2012-04-05]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Characterization of the lipid droplet proteome of a clonal insulin-producing β-cell line (INS-1 832/13).

Larsson S, Resjö S, Gomez MF, James P, Holm C

J. Proteome Res. 11 (2) 1264-1273 [2012-02-03; online 2012-01-25]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Year 2011

Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.

Neiman M, Hedberg JJ, Dönnes PR, ..., Schwenk JM, Nilsson P

J. Proteome Res. 10 (11) 4925-4934 [2011-11-04; online 2011-09-29]

Large-scale protein profiling in human cell lines using antibody-based proteomics.

Fagerberg L, Strömberg S, El-Obeid A, ..., Ponten F, Asplund A

J. Proteome Res. 10 (9) 4066-4075 [2011-09-02; online 2011-07-06]

Tissue Profiling

Mapping the subcellular protein distribution in three human cell lines.

Fagerberg L, Stadler C, Skogs M, ..., Uhlén M, Lundberg E

J. Proteome Res. 10 (8) 3766-3777 [2011-08-05; online 2011-06-17]