. 2020 Aug 31;15(8):e0237883. doi: 10.1371/journal.pone.0237883

Table 3. Summary of the protein candidates crosslinked to PamA in N. meningitidis identified by mass spectrometry.

1. Protein identified from the photocrosslinking products for a molecular weight around 150kDa
Accession number	Protein name	*N. meningitidis* strain**	Estimated Molecular weight	Number of matched peptides	MASCOT score	Sequence coverage
gi\|325136153	hypothetical protein NMBM0579_0886	NMBM0579_0886	57kDa	102	1843	25%
gi\|325144519	hypothetical protein	NMBM01240013_0931	57kDa	99	1758	24%
gi\|325140435	hypothetical protein	CU385	57kDa	93	1718	24%
gi\|488174415	hypothetical protein		57kDa	93	1920	22%
gi\|485353984	DNA-directed RNA polymerase, β subunit	73696	150kDa	24	1436	22%
gi\|488170470	hypothetical protein		57kDa	71	1394	20%
gi\|6977941	App protein		160kDa	7	425	7%
gi\|915797040	adhesin		160kDa	6	390	6%
gi\|83270238	AusI		158kDa	4	288	4%
gi\|389605917	NAD(P) transhydrogenase subunit alpha	α522	54kDa	2	162	2%
gi\|488141712	carbon starvation protein A		75kDa	3	146	3%
gi\|896381024	hypothetical protein		57kDa	8	119	2%
gi\|488158877	hypothetical protein		147kDa	2	109	2%
gi\|254672742	alanine or glycine: cation symporter, AGCS family	α275	45kDa	2	109	1%
2. Protein identified from the photocrosslinking products for a molecular weight around 140kDa.
Accession number	Protein name	*N. meningitidis* strain**	Estimated Molecular weight	Number of matched peptides	MASCOT score	Sequence coverage
gi\|325136153	hypothetical protein NMBM0579_0886	NMBM0579_0886	57kDa	80	1852	25%
gi\|120866758	hypothetical protein NMC1281	FAM18	56kDa	69	1863	23%
gi\|501178984	DNA-directed RNA polymerase β subunit		154kDa	28	1808	27%
gi\|325140435	hypothetical protein NMBCU385_0826	CU385	57kDa	72	1803	22%
gi\|325144519	hypothetical protein	NMBM01240013_0931	57kDa	78	1782	24%
gi\|488171514	hypothetical protein		57kDa	70	1656	23%
gi\|488170470	hypothetical protein		57kDa	54	1267	18%
gi\|488186495	hypothetical protein		147kDa	12	800	12%
gi\|488186095	immunoglobulin A1 protease		121kDa	9	653	9%
gi\|488151215	peptidylprolyl isomerase		56kDa	8	500	8%
gi\|316985319	filamentous hemagglutinin family N-terminal domain protein	H44/76	261kDa	8	496	8%
gi\|488154218	heme biosynthesis operon protein HemX		48kDa	7	490	7%
gi\|488151215	peptidylprolyl isomerase		56kDa	8	465	8%
gi\|488146114	D-lactate dehydrogenase		64kDa	5	363	5%
gi\|389605276	UPF0141 inner membrane protein yhjW		62kDa	6	351	5%
gi\|488170091	peptidase		200kDa	3	202	3%
gi\|120866107	putative protein-export membrane protein	FAM18	66kDa	3	176	3%
gi\|732853	IgA1 protease		54kDa	3	168	3%
gi\|488141712	carbon starvation protein A		74kDa	3	165	3%
gi\|316985875	4Fe-4S binding domain protein		146kDa	3	150	3%
gi\|389605917	NAD(P) transhydrogenase subunit α		54kDa	2	140	2%
gi\|488141355	arginine decarboxylase		71kDa	2	129	2%
gi\|349520	pilus structural subunit, partial		17kDa	2	128	2%
gi\|488143525	protein translocase component YidC		60kDa	2	125	2%
gi\|254670993	1-deoxy-D-xylulose 5-phosphate synthase		69kDa	2	114	2%
gi\|304337210	methionine-R-sulfoxide reductase		59kDa	2	112	2%
gi\|4838369	NatD		52kDa	2	109	2%
3. Protein identified from the photocrosslinking products for a molecular weight around 85kDa.
Accession number	Protein name	*N. meningitidis* strain**	Estimated Molecular weight	Number of matched peptides	MASCOT score	Sequence coverage
gi\|2460281	outer membrane protein Omp85		88kDa	63	2799	41%
gi\|488170971	membrane protein		88kDa	58	2599	38%
gi\|325136153	hypothetical protein NMBM0579_0886		57kDa	63	1774	24%
gi\|325144519	hypothetical protein NMBM01240013_0931		57kDa	60	1692	23%
gi\|488171514	hypothetical protein		57kDa	56	1619	22%
gi\|488174415	hypothetical protein		57kDa	56	1577	22%
gi\|325141117	LPS-assembly protein LptD	CU385	87kDa	21	1440	19%
gi\|488147360	elongation factor G		77kDa	27	1398	20%
gi\|325141117	putative organic solvent tolerance protein	CU385	87kDa	20	1149	18%
gi\|409107079	type IV pilus biogenesis and competence protein PilQ		80kDa	17	973	15%
gi\|209363328	hemoglobin receptor, partial		87kDa	16	909	14%
gi\|488154195	ATP-dependent Clp protease ATP-binding subunit ClpA		85kDa	21	905	16%
gi\|30017077	TonB-dependent siderophore receptor FetA		73kDa	14	793	13%
gi\|120866913	RNA polymerase sigma factor		75kDa	11	616	10%
gi\|325142240	2-oxoglutarate dehydrogenase E1 component		102kDa	10	496	8%
gi\|488150134	GNAT family N-acetyltransferase		89kDa	7	421	7%
gi\|496712676	fimbrial protein		18kDa	9	307	4%
gi\|645213765	peptidase		88kDa	5	295	5%
gi\|402319479	hypothetical protein NMEN93004_1215		18kDa	6	294	5%
gi\|488144915	phosphoenolpyruvate synthase		87kDa	5	293	5%
gi\|254673965	putative efflux system transmembrane protein		113kDa	5	249	4%
gi\|496706569	transferrin-binding protein 2		74kDa	5	239	4%
gi\|896272027	pilus assembly protein PilQ		75kDa	5	222	4%
gi\|45245	periplasmic iron-binding protein		34kDa	4	204	4%
gi\|121052755	GTP pyrophosphokinase		86kDa	3	199	3%

Proteins shown in italics corresponds to the PamA protein itself.

Proteins shown in bold indicates the candidates examined for crosslinking to PamA K278(pBPa) in N. meningitidis by constructing the FLAG-tagged candidate mutants, but the crosslinking could not be detected.

The protein shown underlined is PilE crosslinked to PamA K278(pBPa) in N. meningitidis, which was confirmed in this study.