Recent advances in mass spectrometry-based proteomics of gastric cancer

Table 1 Summary of recent proteomic analyses of gastric cancer

Sample	Measurand	Mass spectrometry	Identification/quantification	Ref.
Tissue samples
GC tissue	Global proteome	MALDI TOF/TOF, LTQ Orbitrap XL	Label-free, Mascot	Balluff et al[16], 2011
GC tissue	Global proteome	Q-TOF	O18/O16, MassLynx (v4.0)	Zhang et al[73], 2013
GC tissue	Global proteome	LTQ Orbitrap	Label-free, ProLuCID (v1.3)	Aquino et al[74], 2014
GC tissue	Global proteome	MALDI TOF/TOF	Label-free, Mascot (v2.2)	Wu et al[75], 2014
GC tissue	Global proteome	LTQ Orbitrap XL	Label-free, Mascot (v2.2)	Ichikawa et al[38], 2015
GC tissue	Global proteome	LTQ Orbitrap XL	Label-free, Bioworks Browser (v3.3.1), Trans-Proteomic Pipeline (v4.0)	Shen et al[76], 2015
GC tissue	Membrane proteome	LTQ Orbitrap Velos	TMT, MaxQuant (v1.2.2.5)	Gao et al[31], 2015
Gastroesophageal malignancy	Global proteome	MALDI TOF/TOF	iTRAQ, Mascot	Singhal et al[14], 2013
Serum samples
Sera from GC patients	Serum proteome	MALDI-TOF LTQ Orbitrap XL MS/MS	Label-free, Autoflex, Peptide mass fingerprinting	Fan et al[37], 2013
Sera from GC patients	Serum proteome	Triple TOF 5600	Multiple reaction monitoring	Humphries et al[59], 2014
Sera from GC patients	Serum proteome	MALDI-TOF Orbitrap Q-Exactive	Label-free, MaxQuant (v1.4.1.1)	Abramowicz et al[50], 2015
Sera from GC patients	Serum proteome	LTQ Orbitrap Velos	iTRAQ, SEQUSET HT, Mascot (v2.2)	Subbannayya et al[29], 2015
Sera from GC patients	Serum proteome	SELDI TOF MS MALDI TOF/TOF	Label-free, Mascot	Song et al[17], 2016
Cell lines
BGC823, MKN45, SCG7901	Global proteome	MALDI TOF/TOF	Label-free, Mascot	Cai et al[71], 2013
AGS, AZ521, FU97, MKN7, MKN74, NCI-N87, SNU16, YCC1, YCC2, YCC3, YCC9	Global proteome	MALDI TOF/TOF	iTRAQ, ProteinPilot	Hou et al[69], 2013
AGS	Global proteome	Q-TOF	iTRAQ, Mascot (v2.1.1)	Hu et al[72], 2013
MKN45	Global proteome	MALDI TOF/TOF	Label-free, Mascot	Hu et al[13], 2013
OCUM-2MD3, OCUM-12	Global proteome	Q-TOF	iTRAQ, ProteinPilot	Morisaki et al[28], 2014
AGS, BGC823, MKN45, SGC7901	Global proteome	MALDI TOF/TOF	Label-free, Peptide mass fingerprinting	Yang et al[67], 2014
HGC27, MGC803, SGC7901	Global proteome	LTQ Orbitrap	Label-free, Mascot (v2.3.2), Scaffold (v4.0.5), X! Tandem CYCLONE (v2010.12.01.1)	Qiao et al[62], 2015
AGS	Global proteome	Q-TOF	iTRAQ, Mascot (v2.3.2)	Lin et al[61], 2015
HGC27	Global proteome	Triple TOF 5600	iTRAQ, Mascot (v2.3.2)	Chen et al[77], 2016
AGS, MKN7	Secretome	MALDI TOF/TOF	iTRAQ, ProteinPilot	Loei et al[51], 2011
AGS, KATO III, NCI-N87, SNU1, SNU5, SNU16	Secretome	LTQ Orbitrap Velos	SILAC, Proteome Discoverer (v1.3.0.339), Mascot, SEQUEST	Marimuthu et al[33], 2013
AGS, KATO III, SNU1, SNU5, MKN7, IM95	Membrane proteome	LTQ-FT Ultra	Label-free, Trans-Proteomic Pipeline, Mascot (v2.2.07)	Guo et al[68], 2012
AGS, IM95, KATO3, MKN7, MKN28, MKN45, NUGC3, NUGC4, SCH, SNU1, SNU5, SNU16	Membrane proteome	Q-TOF	iTRAQ, ProteinPilot	Yang et al[70], 2012
AGS, HGC27, KATO III, MKN45, NUGC3, SCH, SGC7901, SNU5, SNU484, TSK1	Membrane proteome	Q-TOF	iTRAQ, ProteinPilot	Goh et al[60], 2015
Multidrug-resistant GC cell lines: GC7901/VCR, SGC7902/ADR	Surface glycoproteome	LTQ Orbitrap XL	Triplex stable isotope dimethyl labeling, Mascot, MSQuant (v2.0a81)	Li et al[47], 2013
AGS	Interactome	LTQ Orbitrap Velos	Label-free, Mascot (v2.2.2)	Yu et al[57], 2013
AGS	Phosphoproteome	MALDI TOF/TOF	SILAC, Mascot (v2.1)	Holland et al[43], 2011
AGS	Phosphoproteome	LTQ Orbitrap XL	SILAC, MaxQuant (v1.3.0.5)	Glowinski et al[42], 2014

The studies are listed according to sample types (tissues, sera and cell lines) and measurands in the order of publication year and then in alphabetical order by the first author. GC: Gastric cancer; MALDI: Matrix-assisted laser desorption ionization; TOF: Time-of-flight.

Table 2 Cell line-based summary of recent proteomic analyses of gastric cancer

Cell line	Ref.	Aim of study	Proteins analyzed	Validation1
AGS	Holland et al[43], 2011	Phosphoproteome upon H. pylori infection	20 altered in abundance by H. pylori	No
	Loei et al[51], 2011	Secretome of AGS and MKN7	43 differed	IHC/WB
	Guo et al[68], 2012	Plasma membrane proteome	1473 identified	IHC
	Hou et al[69], 2013	Biomarkers for GC metastasis	19 increased and 34 decreased in metastasis	IHC/WB
	Hu et al[72], 2013	Global profile of miR-148a-regulated proteins	55 altered by miR-148a	WB
	Marimuthu et al[33], 2013	Secretome	263 increased and 45 decreased in GC	IHC
	Yu et al[57], 2013	Interactome of VCP	288 putative partners, including 18 PI3K/Akt proteins	WB
	Glowinski et al[42], 2014	Tyrosine signaling upon H. pylori transfection	85 altered by H. pylori	No
	Goh et al[60], 2015	Membrane proteome of 11 GC cell lines	882 altered, including 57 increased in ≥ 6 cell lines	WB
	Lin et al[61], 2015	Tanshinone IIA regulation	102 altered by tanshinone IIA treatment	WB
BGC-823	Cai et al[71], 2013	Effects of curcumin on viability and apoptosis	75 altered by curcumin treatment	No
HGC-27	Goh et al[60], 2015	Membrane proteome of 11 GC cell lines	882 altered, including 57 increased in ≥ 6 cell lines	WB
	Qiao et al[62], 2015	Proteomes of three GC cell lines	9 altered	IHC/WB
	Chen et al[77], 2016	Proteome with FAF1 or H. pylori	157 altered by FAF1, 500 by H. pylori and 246 by both	WB
MGC-803	Qiao et al[62], 2015	Proteomes of three GC cell lines	9 altered	IHC/WB
MKN7	Loei et al[51], 2011	Secretome of AGS and MKN7	43 differed	IHC/WB
	Guo et al[68], 2012	Plasma membrane proteome	1473 identified	IHC
	Yang et al[70], 2012	Membrane proteome	175 altered	IHC/WB
MKN45	Hu et al[13], 2013	Proteome changes following CXCR1 knockdown	16 increased and 13 decreased by CXCR1 knockdown	WB
	Yang et al[67], 2014	Proteome changes following NAIF1 overexpression	5 increased and 3 decreased by NAIF1 overexpression	WB
	Goh et al[60], 2015	Membrane proteome of 11 GC cell lines	882 altered, including 57 increased in ≥ 6 cell lines	WB
SGC-7901	Li et al[47], 2013	Cell surface glycoproteome of MDR	11 altered in MDR cell lines	WB
	Goh et al[60], 2015	Membrane proteome of 11 GC cell lines	882 altered, including 57 increased in ≥ 6 cell lines	WB
	Qiao et al[62], 2015	Proteomes of three GC cell lines	9 altered	IHC/WB

¹Validation indicates whether a selected set of altered proteins have been validated using immunohistochemistry (IHC) or Western blot (WB) or have not been (No). The cell line studies are listed in the order of publication year and then in alphabetical order by the first author. CXCR1: C-X-C chemokine receptor type 1; FAF1: Fas-associated factor 1; GC: Gastric cancer; H. pylori: Helicobacter pylori; MDR: Multidrug resistance; NAIF1: Nuclear apoptosis-inducing factor 1; VCP: Valosin-containing protein.