Table 2.

Proteomics-based and proteomics-derived studies in breast cancer.

Proteomics-Based and Proteomics-Derived Investigation of BC	Samples	Omics-Based Techniques	Studies Relevance	References
proteomics	FFPE	SP3-CTP; LC-MS/MS	high sensitive MS-based methodology for capturing biological features in FFPE tumor samples; characterization of BC heterogeneity in a clinically-applicable manner, biomarkers and therapeutic targets discovery, clinical BC classification	[128]
	FF	SWATH-MS (LC-MS/MS)	highly multiplexed mode of targeted proteomics that generated large-scale quantitative proteomics profiles of BC tissues; BC classification into proteotype-based subtypes with different treatment strategies	[233]
	blood/serum/ plasma	LC-ESI-MS/MS	comparison between peptides and proteins specific to BC plasma and ovarian cancer and matched controls	[70]
	tumor interstitial fluid	LC-MS/MS	high-throughput proteomics for identification of tumor subtype-specific relevant biomarkers	[75]
	saliva and serum samples	iTRAQ LC-ToF-MS/MS	identification of protein biomarkers for early detection of BC; platform for investigating the responsive proteomic profile in benign and malignant breast tissue using saliva and serum from the same women	[227]
	urine	label free LC-MS/MS	identification of protein biomarkers for early screening detection and monitoring invasive BC progression	[90]
	colostrum and milk	nLC-MS/MS	BC biomarkers discovery	[234]
	NAF; NAF spots on Guthrie cards	SELDI-ToF-MS; 1D-LC-MS/MS	identification of differential proteomic profile between women with/without BC; BC biomarkers identification; identification of NAF proteome associated with BC development	[125,126,235]
salivaomics: transcriptomics and proteomics	saliva of BC patients vs. matched controls	proteomics: 2D-DIGE, MALDI-ToF MS; transcriptomics: Affymetrix HG-U133-Plus-2.0 Array, RT-qPCR	mRNA biomarkers and one protein biomarker were pre-validated on the preclinical validation sample set for BC detection	[123]
phosphoproteomics	FF	Fe-IMAC, iTRAQ SCX LC-ESI-MS/MS SID-SRM-MS for validation	large-scale phosphoproteome quantification in high- and low-risk recurrence groups as powerful tool for biomarker discovery using clinical samples	[215]
	FFPE, TNBC cell lines, mouse models (PDXs)	nano-LC-MS/MS	high-throughput phosphoproteomics for target-based clinical classification system for TNBC	[213]
kinomics, phosphoproteomics, proteomics, transcriptomics	PDX models of TNBC	RPPA, LC-MS/MS; MS-based kinome profiling	integrative phosphoproteogenomic analysis for identification of intrinsic resistance mechanisms of TNBC to PI3K inhibition	[217]
exosomics	plasma and total blood	MALDI-ToF/ToF MS	proteomic analysis of exosomes for BC diagnostic/prognostic biomarkers or novel therapeutic targets	[203]
	breast cell line derived exosomes	nanoLC-MS/MS	proteomic profile of cancerous and non-tumorigenic breast cell lines for BC diagnostic/prognostic biomarker discovery	[201]
secretomics, matrisomics	human breast samples (normal and IDC)	LC-SRM, LC-MS/MS, TPM, SHG, two-photon fluorescence imaging	targeted matrisome analysis for compositional change in matrisome proteins according to collagen re-organization during BC progression; candidate proteins involved in collagen alignment	[197]
		LC-MS/MS, MALDI-FT-ICR MS, MALDI-ToF MS, MALDI-MS/MS	proteomic remodeling of TME; review of significant dysregulated proteins involved in TME remodelling in IDC	[196]
phosphoproteomics and exosomics	plasma samples	LC-MS/MS	phosphoproteomic profile of EVs of patients and healthy controls for potential biomarkers to differentiate BC patients from healthy controls	[27]
interactomics	serum and saliva	network biology approach	PPI networks for proteins in serum and saliva for potential biomarkers in BC diagnosis and prognosis	[227]

Abbreviations: BC—breast cancer; Fe—IMAC-immobilized Fe (III) affinity chromatography; FF—fresh frozen; FFPE—formalin-fixed paraffin-embedded; IDC—invasive ductal carcinoma; iTRAQ—isobaric tag for relative quantification; LC-ESI-MS/MS—liquid chromatography electrospray ionisation tandem mass spectrometry; LC-SRM—liquid chromatography-selected reaction monitoring; NAF—nipple aspirate fluid; PDX—patient derived xenograft; RPPA—reverse-phase protein array; SCX—strong cation exchange chromatography; SID-SRM—stable isotope dilution-selected reaction monitoring; SHG—second-harmonic generation; SP3-CTP—Single-Pot, Solid-Phase-enhanced, Sample Preparation-Clinical Tissue Proteomics; SWATH-MS—sequential windowed acquisition of all theoretical fragment ion spectra-mass spectrometry; TNBC—triple-negative breast cancer; TME—tumor microenvironment; and TPM—two-photon microscopy.