Introduction

These data represent the proteome and phosphoproteome of de novo, Acute Myeloid Leukemia (AML) as well as matching mRNA data from the same patients. Please click the links above to explore these datasets.

Sample information

Bone marrow samples were collected at presentation from 44 adult patients with de novo AML. All 44 patients included in this study were also part of the Cancer Genome Atlas (TCGA) LAML study (NEJM 2013, DOI: 10.1056/NEJMoa1301689 ). The 44 patients were selected to represent major cytogenetic and mutational landscapes amongst the 200 TCGA LAML patients with adequate remaining diagnosis cryovials. Cryovials were thawed in the presence of the cell-permeable, irreversible serine protease inhibitor diisopropyl fluorophosphate (DFP) to inactivate neutrophil serine proteases. Healthy control bone marrow samples were lineage-depleted (3 samples) or CD34-selected (3 samples) using autoMACS prior to analysis. Samples were analyzed using tandem-mass-tag (TMT) or label-free-quantification (LFQ) mass spectrometry to obtain protein abundance. A fraction of each sample was IMAC enriched for phosphopeptide analysis also using TMT mass spectrometry. Each of these datasets (TMT, LFQ and phosphopeptides) along with matching RNA-seq from the same patients (previously published by the TCGA LAML study) are made available here for public analysis and download. These data are from Kramer et. al, Proteomic and Phosphoproteomic Landscapes of Acute Myeloid Leukemia, Blood, 2022 (DOI: 10.1182/blood.2022016033 ). Please cite this paper for any uses of these data.

Data download

Data are available freely for download and use. These data represent the proteomic, phosphoproteomic and mRNA measurements from 44 adult patients with de novo Acute Myeloid Leukemia. Each row in the spreadsheet represents one protein, gene, or phosphosite as indicated. Each column represents one sample identified by the UPN (patients) or an appropriate identifier (healthy controls). Please refer to the following paper for further information and please cite this paper for any use of these data: Kramer et. al, Proteomic and Phosphoproteomic Landscapes of Acute Myeloid Leukemia, Blood, 2022 (DOI: 10.1182/blood.2022016033 ).
Datasets included:
  • Tandem-mass-tag (TMT) mass spectrometry-based protein abundance measurements from the bone marrow of 44 patients and 3 healthy, lineage-depleted controls. Values are log2 transformed and median centered at 0.
  • Label-free quantification (LFQ) mass spectrometry protein abundance measurements from the bone marrow of 44 patients, 3 healthy, lineage-depleted controls and 3 healthy, CD34-selected controls.
  • Phosphosite abundance measurements after IMAC enrichment and aggregation of phosphopeptide abundances as measured by tandem-mass-tage (TMT) mass spectrometry from the bone marrow of 44 patients and 3 healthy, lineage-depleted controls. Values are log2 transformed and median centered at 0.
  • mRNA sequencing for the 44 patients included in this study as initially measured by the TCGA LAML study. Also included are data from healthy control marrows which were CD19 selected (B-cells), CD3 selected (T-cells), CD34-selected (enriched for hematopoietic stem and progenitor cells), as well as monocytes, neutrophils and promyelocytes. Values represent TPMs for each gene.
  • Clinical annotations and information for each included patient including mutational status, survival data, treatment information and demographics.
  • Spearman correlation of protein abundance vs. mRNA abundance for 10,125 genes/proteins detected in at least 20% of the 44 AML samples. Protein abundance is measured by tandem-mass-tag (TMT) mass spectrometry and mRNA sequencing is performed on matched cryovials from the same patients.

Download the TMT, LFQ, and mRNA abundance data
Download the phosphosite abundance data
Download the clinical patient data
Download protein abundance vs. mRNA abundance correlations

See also: NPMc Turbo ID dataset also from this publication