Table 1.

List of highlighted proteomics resources

Reference	Mass spec technique	Cell type/stimulation condition	Information available
Damasio [1]	TMT-labeled fractionated DDA	Mouse T cells, 3 biological replicates: —CD8 Naive —CD8 24 h peptide treatment —CD8 24 h peptide + Mek inhibitor treatment	Whole cell proteome
			Copies/cell
			Fold change, statistics
Howden* [2]	TMT-labeled fractionated DDA	Mouse T cells, 3 biological replicates: —CD8 Naive —CD4 Naive —CD8 treated for 24 h with peptide + IL2/IL12 —CD4 treated for 24 h with peptide/APC + IL2/IL12 —CTLs in vitro generated with IL2/12 —Th1 in vitro generated with IL2/12 —All activated T cell subsets treated for 24 h +/− rapamycin	Whole cell proteome
			Copies/cell
			Concentration (nM)
			Mass (pg)/cell
			Fold change, statistics
			website: immpres.co.uk
Hukelmann [33]	SILAC-labeled fractionated DDA	Mouse T cells, 3 biological replicates: —CTLs in vitro generated with IL2/IL12+/− rapamycin for the final 48 h	Whole cell proteome
			Copies/cell, fold change, statistics
Ma [36]	TMT-labeled fractionated DDA	Mouse T cells, 5 biological replicates: —Naive and activated OT1 CD8 T cells from day 2.5 of a Listeria-OVA infection	Whole cell proteome
			Summed peptide intensities
Marchingo [3]	Label-free fractionated DDA	Mouse T cells, 3 biological replicates: —CD8 Naive —CD8 WT treated for 24 h with αCD3/αCD28 —CD8 MycKO treated for 24 h with αCD3/αCD28 —CD4 Naive —CD4 WT treated for 24 h with αCD3/αCD28 —CD4 MycKO treated for 24 h with αCD3/αCD28 —CD4 WT treated for 24 h with αCD3/αCD28 + IL2/IL12 —CD4 Slc7a5KO treated for 24 h with αCD3/αCD28 + IL2/IL12	Whole cell proteome
			Copies/cell
			Mass (pg)/cell
			Fold change, statistics
			website: immpres.co.uk
Rieckmann [42]	Label-free single-shot DDA	Human T cells and other hematopoietic lineages, 4 biological replicates: —CD4/CD8 Naive, memory T cells, and effector memory T cells at steady state or activated for 48 h with αCD3/αCD28 and then cultured for 48 h with IL2 —CD4 Th1, Th2, and Th17 at steady state	Whole cell proteome
			Summed peptide intensities, LFQ, iBAQ, copies/cell
			website: immprot.org
Rollings [37]	Label-free fractionated DDA	Mouse T cells, 3 biological replicates: —In vitro IL2-expanded CTLs treated for 24 h +/− IL2 —In vitro IL2-expanded CTLs treated for 24 h +/− Jak1/3 inhibitor	Whole cell proteome
			Copies/cell
			Fold change, statistics
Ross [38]	SILAC-labeled Fractionated DDA	Mouse T cells, 3 biological replicates: —In vitro IL2-expanded CTLs treated overnight in IL12 only then +/− IL2 for 15 min —In vitro IL2-expanded CTLs treated for 30 min or 4 h with Jak1/3 inhibitor —In vitro IL2-expanded CTLs treated for 4 h with Src family inhibitor	Phosphoproteome
			SILAC ratio of summed peptides, stats
Tan* [6]	TMT-labeled fractionated DDA	Mouse T cells, 2 biological replicates —Naive CD4 T cells —αCD3/αCD28-activated WT CD4 T cells after 2, 8, or 16 h —αCD3/αCD28-activated Raptor KO CD4 T cells after 2 or 16 h	Whole cell proteome and phosphoproteome
			Summed peptide intensities, fold change, statistics
Wolf* [7]	SILAC-labeled Single-shot DDA	Human T cells, 3–7 biological replicates: —Naive/Memory CD4 T cell protein turnover (SILAC labeling time course) —Naive CD4 T cells treated for 24 h (control, + translation inhibitor, or + translation and proteasome inhibitor) —Naive or αCD3/αCD28-activated CD4 T cells at 6, 12, 24, 48, 72, 96, 120, and 144 h —RNAseq data for Naive and αCD3/αCD28-activated CD4 T cells at 6 and 24 h	Whole cell proteome
			Turnover kinetics (naive, memory), copies (CHX experiment)
			LFQ, copies (activation time course)
			Estimated transcript/cell
			website: immunomics.ch

Resource papers are studies of primary human or mouse T cells. For whole cell proteome studies, authors included intensity/copy number information as well as fold changes and statistics as Supplementary Tables or on Websites, therefore making data accessible for flexible interrogation by all readers without the need to reanalyze raw files.

An asterisk indicates studies that are particularly useful for understanding changes in protein expression over time.