Dataset accession	Repository	PMID	Publication title	Publication date	Species	UniProt Taxonomy ID	Sample category	MS acquisition workflow	MS platform	Quantification strategy	Number of raw files processed	Raw files name	Reidentified Kla sites	Reidentified Kla proteins	MaxQuant parameter files	Tissue / cell type	Experimental condition / comparison	Kla enrichment method / reagent	Enrichment reagent supplier	Enrichment reagent catalogue no.	Metadata sources	Sample condition
OEP0002852	OEP	36593272	Lactylome analysis suggests lactylation-dependent mechanisms of metabolic adaptation in hepatocellular carcinoma	2023/01	Homo sapiens	9606	Disease tissue	TIMS-DDA	Bruker TIMS	Label-free	110	WA141LPLa_P_102_Slot2-36_1_411.d;WA141LPLa_P_103_Slot2-34_1_407.d;WA141LPLa_P_106_Slot2-29_1_397.d;WA141LPLa_P_107_Slot2-27_1_393.d;WA141LPLa_P_108_Slot2-25_1_389.d;WA141LPLa_P_110_Slot2-24_1_580.d;WA141LPLa_P_111_Slot2-22_1_576.d;WA141LPLa_P_112_Slot2-20_1_572.d;WA141LPLa_P_113_Slot2-18_1_568.d;WA141LPLa_P_114_Slot2-16_1_564.d;WA141LPLa_P_116_Slot2-14_1_560.d;WA141LPLa_P_118_Slot2-10_1_552.d;WA141LPLa_P_119_Slot2-8_1_542.d;WA141LPLa_P_120_Slot2-6_1_538.d;WA141LPLa_P_121_Slot2-4_1_534.d;WA141LPLa_P_122_Slot2-2_1_530.d;WA141LPLa_P_124_Slot2-37_1_526.d;WA141LPLa_P_125_Slot2-35_1_522.d;WA141LPLa_P_126_Slot2-33_1_518.d;WA141LPLa_P_127_Slot2-21_1_488.d;WA141LPLa_P_128_Slot2-12_1_556.d;WA141LPLa_P_12_Slot2-31_1_510.d;WA141LPLa_P_130_Slot2-32_1_403.d;WA141LPLa_P_36_Slot2-29_1_506.d;WA141LPLa_P_38_Slot2-27_1_502.d;WA141LPLa_P_42_Slot2-25_1_498.d;WA141LPLa_P_43_Slot2-23_1_494.d;WA141LPLa_P_70_Slot2-19_1_484.d;WA141LPLa_P_72_Slot2-17_1_480.d;WA141LPLa_P_73_Slot2-15_1_476.d;WA141LPLa_P_77_Slot2-13_1_472.d;WA141LPLa_P_78_Slot2-11_1_468.d;WA141LPLa_P_79_Slot2-9_1_457.d;WA141LPLa_P_80_Slot2-7_1_453.d;WA141LPLa_P_81_Slot2-5_1_449.d;WA141LPLa_P_84_Slot2-3_1_445.d;WA141LPLa_P_85_Slot2-49_1_437.d;WA141LPLa_P_86_Slot2-46_1_431.d;WA141LPLa_P_87_Slot2-43_1_425.d;WA141LPLa_P_88_Slot2-41_1_421.d;WA141LPLa_P_89_Slot2-39_1_417.d;WA141LPLa_P_90_Slot2-23_1_385.d;WA141LPLa_P_91_Slot2-21_1_381.d;WA141LPLa_P_92_Slot2-19_1_377.d;WA141LPLa_P_93_Slot2-17_1_373.d;WA141LPLa_P_94_Slot2-15_1_369.d;WA141LPLa_P_95_Slot2-13_1_365.d;WA141LPLa_P_96_Slot2-10_1_359.d;WA141LPLa_P_97_Slot2-8_1_355.d;WA141LPLa_P_98_Slot2-6_1_351.d;WA141LPLa_P_99_Slot2-4_1_347.d;WA141LPLa_P_9_Slot2-2_1_343.d;WA141LPLa_T1_130_Slot2-30_1_399.d;WA141LPLa_T1_84_Slot2-2_1_443.d;WA141LPLa_T1_85_Slot2-48_1_435.d;WA141LPLa_T1_86_Slot2-44_1_427.d;WA141LPLa_T1_89_Slot2-38_1_415.d;WA141LPLa_T1_95_Slot2-11_1_361.d;WA141LPLa_T2_130_Slot2-31_1_401.d;WA141LPLa_T2_84_Slot2-1_1_441.d;WA141LPLa_T2_85_Slot2-47_1_433.d;WA141LPLa_T2_86_Slot2-45_1_429.d;WA141LPLa_T2_89_Slot2-37_1_413.d;WA141LPLa_T2_95_Slot2-12_1_363.d;WA141LPLa_T_102_Slot2-35_1_409.d;WA141LPLa_T_103_Slot2-33_1_405.d;WA141LPLa_T_106_Slot2-28_1_395.d;WA141LPLa_T_107_Slot2-26_1_391.d;WA141LPLa_T_108_Slot2-24_1_387.d;WA141LPLa_T_110_Slot2-23_1_578.d;WA141LPLa_T_111_Slot2-21_1_574.d;WA141LPLa_T_112_Slot2-19_1_570.d;WA141LPLa_T_113_Slot2-17_1_566.d;WA141LPLa_T_114_Slot2-15_1_562.d;WA141LPLa_T_116_Slot2-13_1_558.d;WA141LPLa_T_118_Slot2-9_1_550.d;WA141LPLa_T_119_Slot2-7_1_540.d;WA141LPLa_T_120_Slot2-5_1_536.d;WA141LPLa_T_121_Slot2-3_1_532.d;WA141LPLa_T_122_Slot2-1_1_528.d;WA141LPLa_T_124_Slot2-36_1_524.d;WA141LPLa_T_125_Slot2-34_1_520.d;WA141LPLa_T_126_Slot2-32_1_512.d;WA141LPLa_T_127_Slot2-20_1_486.d;WA141LPLa_T_128_Slot2-11_1_554.d;WA141LPLa_T_12_Slot2-30_1_508.d;WA141LPLa_T_36_Slot2-28_1_504.d;WA141LPLa_T_38_Slot2-26_1_500.d;WA141LPLa_T_42_Slot2-24_1_496.d;WA141LPLa_T_43_Slot2-22_1_492.d;WA141LPLa_T_70_Slot2-18_1_482.d;WA141LPLa_T_72_Slot2-16_1_478.d;WA141LPLa_T_73_Slot2-14_1_474.d;WA141LPLa_T_77_Slot2-12_1_470.d;WA141LPLa_T_78_Slot2-10_1_459.d;WA141LPLa_T_79_Slot2-8_1_455.d;WA141LPLa_T_80_Slot2-6_1_451.d;WA141LPLa_T_81_Slot2-4_1_447.d;WA141LPLa_T_87_Slot2-42_1_423.d;WA141LPLa_T_88_Slot2-40_1_419.d;WA141LPLa_T_90_Slot2-22_1_383.d;WA141LPLa_T_91_Slot2-20_1_379.d;WA141LPLa_T_92_Slot2-18_1_375.d;WA141LPLa_T_93_Slot2-16_1_371.d;WA141LPLa_T_94_Slot2-14_1_367.d;WA141LPLa_T_96_Slot2-9_1_357.d;WA141LPLa_T_97_Slot2-7_1_353.d;WA141LPLa_T_98_Slot2-5_1_349.d;WA141LPLa_T_99_Slot2-3_1_345.d;WA141LPLa_T_9_Slot2-1_1_341.d	10049	2647	OEP0002852_mqpar.xml	Human HBV-related hepatocellular carcinoma (HCC) tumors and matched adjacent non-tumor liver tissue	HBV-related HCC tumor versus matched adjacent liver: 58 tumor specimens and 52 adjacent liver specimens from 52 patients. Six patients contributed two separate tumor foci.	PTM-1404 antibody beads; peptide immunoaffinity enrichment	PTM Bio	PTM-1404	"https://doi.org/10.1038/s42255-022-00710-w
Abstract; Extended Data Figs. 1-2; Reporting Summary (including supplementary information)"	110 biological tissue specimens from 52 patients, with one selected raw acquisition per specimen: 52 adjacent liver, 46 single tumor, and 12 tumor specimens from six multifocal cases. T1/T2 denote distinct tumor foci from the same patient, not technical replicates or peptide fractions.
PXD014870	PRIDE	31645732	Metabolic regulation of gene expression by histone lactylation	2019/10	Homo sapiens	9606	Cell line	Standard	Orbitrap	SILAC	3	MCF7_DCA_SILAC_Kla_IP.raw;MCF7_Hypoxia_SILAC_Kla_IP.raw;MCF7_Rotenone_SILAC_Kla_IP.raw	340	128	PXD014870_mqpar.xml	Human MCF-7 breast cancer cells; acid-extracted histones	Three separate SILAC comparisons: DCA (10 mM, 24 h) versus PBS; rotenone (10 nM, 24 h) versus DMSO; hypoxia (1% O2, 24 h) versus normoxia.	Pan anti-Kla antibody conjugated to nProtein A Sepharose; histone-peptide immunoprecipitation	PTM Bio Inc. (pan anti-Kla antibody); GE Healthcare BioSciences (nProtein A Sepharose)	PTM-1401 (pan anti-Kla antibody); nProtein A Sepharose catalogue no. not specified	"https://doi.org/10.1038/s41586-019-1678-1
https://www.ebi.ac.uk/pride/archive/projects/PXD014870
Methods: Reagents, histone peptide enrichment and SILAC; Extended Data Figs. 2-3"	Three different SILAC treatment/control comparisons, one raw acquisition per comparison. Heavy- and light-labeled cells were mixed 1:1 before histone extraction. These are not biological triplicates; independent biological n per comparison is not specified. H/L orientation for the current k_site_positive-derived ratios was not independently recovered, so the follow-up output retains unoriented H/L values.
PXD019323	PRIDE	39113798	Astrocyte-derived lactate aggravates brain injury of ischemic stroke in mice by promoting the formation of protein lactylation	2024/07	Mus musculus	10090	Animal model	Standard	Orbitrap	Label-free	12	S9755LPLA_B1_1.raw;S9755LPLA_B1_2.raw;S9755LPLA_B1_3.raw;S9755LPLA_B3_1.raw;S9755LPLA_B3_2.raw;S9755LPLA_B3_3.raw;S9755LPLA_B4_1.raw;S9755LPLA_B4_2.raw;S9755LPLA_B4_3.raw;S9755LPLA_B7_1.raw;S9755LPLA_B7_2.raw;S9755LPLA_B7_3.raw	550	303	PXD019323_mqpar.xml	Mouse ischemic/reperfused brain cortex tissue	B4/B1: 6 h ischemia vs sham; B7/B1: 1.5 h ischemia + 24 h reperfusion vs sham. B3 remains unmapped.	Pan anti-lactyllysine antibody conjugated to Protein A Sepharose beads; peptide immunoaffinity enrichment	PTM Bio (anti-lactyllysine antibody)	PTM-1401	"DOI: 10.7150/thno.96375
PRIDE PXD019323
Evidence E01-E04"	Three sample-level quantitative observations in each published B1, B4 and B7 group. B3 has three submitted raw files but no published condition key. Independent animal counts and pooling are not explicitly documented for each MS sample.
PXD020746	PRIDE	33193272	Systematic Analysis of Lysine Lactylation in the Plant Fungal Pathogen Botrytis cinerea	2020/10	Botryotinia fuckeliana	332648	Fungi	Standard	Orbitrap	Label-free	8	BC-1.raw;BC-2.raw;BC-3.raw;BC-4.raw;BC-5.raw;BC-6.raw;BC-7.raw;BC-8.raw	17	10	PXD020746_mqpar.xml	Botrytis cinerea strain B05.10 mycelia	Baseline B. cinerea B05.10 lactylome, YEPD culture; no treatment/control MS comparison. Published extraction protocol: 150 rpm, 12 h (repository differs: 180 rpm, 14 h). Lactate-treatment Western blots are separate assays.	Pan anti-Kla antibody-conjugated agarose beads; peptide immunoaffinity enrichment	Not specified in accessible enrichment protocol	Not specified in accessible enrichment protocol	"https://doi.org/10.3389/fmicb.2020.594743
https://www.ebi.ac.uk/pride/archive/projects/PXD020746
Methods: fungal cultivation and affinity enrichment; PRIDE sample protocol"	Protein from four independent biological preparations was pooled. The pooled digest was separated into 80 HPLC fractions and combined into eight fractions. BC-1 to BC-8 are the eight peptide-fraction acquisitions, not eight independent biological replicates.
PXD022700	PRIDE	36216028	Protein Lactylation and Metabolic Regulation of the Zoonotic Parasite Toxoplasma gondii	2022/10	Toxoplasma gondii	5811	Parasite	Standard	Orbitrap	Label-free	12	K9184PILa01_1.raw;K9184PILa01_2.raw;K9184PILa01_3.raw;K9184PILa01_4.raw;K9184PILa02_1.raw;K9184PILa02_2.raw;K9184PILa02_3.raw;K9184PILa02_4.raw;K9184PILa03_1.raw;K9184PILa03_2.raw;K9184PILa03_3.raw;K9184PILa03_4.raw	109	45	PXD022700_mqpar.xml	Toxoplasma gondii RH-strain tachyzoites purified from the peritoneal fluid of infected mice	Baseline global tachyzoite lactylome; no selected treatment/control MS comparison. Vero-cell culture and high/low glucose experiments described elsewhere in the article are separate functional assays.	Pan anti-lactyllysine antibody-conjugated beads; peptide immunoaffinity enrichment	PTM BIO, Hangzhou, China	PTM-1401	"https://doi.org/10.1016/j.gpb.2022.09.010
https://www.ebi.ac.uk/pride/archive/projects/PXD022700
Methods: protein extraction and lactylated peptide enrichment"	Three biological replicates, each analyzed as four combined peptide fractions: 3 x 4 = 12 raw files. The 01/02/03 component identifies biological replicate and the final _1 to _4 identifies peptide fraction; these are not 12 biological replicates.
PXD023011	PRIDE	34722503	Protein Lactylation Critically Regulates Energy Metabolism in the Protozoan Parasite Trypanosoma brucei	2021/10	Trypanosoma brucei	185431	Parasite	Standard	Orbitrap	Label-free	12	K9169PILa_Tb_1_1.raw;K9169PILa_Tb_1_2.raw;K9169PILa_Tb_1_3.raw;K9169PILa_Tb_1_4.raw;K9169PILa_Tb_2_1.raw;K9169PILa_Tb_2_2.raw;K9169PILa_Tb_2_3.raw;K9169PILa_Tb_2_4.raw;K9169PILa_Tb_3_1.raw;K9169PILa_Tb_3_2.raw;K9169PILa_Tb_3_3.raw;K9169PILa_Tb_3_4.raw	37	14	PXD023011_mqpar.xml	Bloodstream-form Trypanosoma brucei, experimental strain Lister 427, purified from infected BALB/c mouse blood	Baseline bloodstream-form parasite lactylome; no selected treatment/control MS comparison. Glucose, 2-deoxyglucose and oxamate interventions are separate functional assays. Strain 927/4 GUTat10.1 is the search reference database, not the stated experimental strain.	Antibody beads; peptide immunoaffinity enrichment	PTM Biolabs Inc., Chicago, IL, United States	Not specified in accessible enrichment protocol	"https://doi.org/10.3389/fcell.2021.719720
https://www.ebi.ac.uk/pride/archive/projects/PXD023011
Methods: parasite preparation and affinity enrichment"	Three biological replicates, each separated into four combined peptide fractions: 3 x 4 = 12 selected raw files. In K9169PILa_Tb_r_f, r=1-3 denotes replicate and f=1-4 denotes fraction.
PXD028488	iProX	35761067	Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome	2022/07	Homo sapiens;Mus musculus	9606;10090	Cell line	Standard	Orbitrap	Label-free	11	20211123-293T-lac-enrich-mix-HCD24.raw;20211123-293T-lac-enrich-mix-HCD28.raw;20211123-293T-lac-enrich-mix-HCD32.raw;20211123-293T-lac-enrich-mix-HCD36.raw;20211123-293T-lac-enrich-mix-HCD40.raw;20211127-HCT116-LAC-Enrichment-1.raw;TALL-NaLAC-enrichment-1.raw;TALL-NaLAC-enrichment-2.raw;TALL-NaLAC-enrichment-3.raw;20211215-BV2-Enrichment-HCD36.raw;20211215-RAW-Enrichment-HCD36.raw	335;119	223;95	PXD028488_human_mqpar.xml;PXD028488_mouse_mqpar.xml	Human HEK293T, HCT116 and TALL-104 cells; mouse BV2 microglial and RAW264.7 macrophage cells	Enriched cellular lactylproteomes after 25 mM lactate for 24 h; HEK293T measurements benchmark HCD collision energies 24/28/32/36/40. All 11 selected files are enriched lactylproteomes; no untreated-control acquisition is selected.	Anti-lactylation antibody conjugated to Protein A agarose; peptide affinity enrichment	Invitrogen (Protein A agarose); anti-lactylation antibody supplier not specified	15918014 (Protein A agarose); anti-lactylation antibody catalogue no. not specified	"https://doi.org/10.1038/s41592-022-01523-1
https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD028488
Supplementary Fig. 3; Supplementary Tables 2 and 4; Reporting Summary (including supplementary information)"	11 acquisitions: five HEK293T HCD collision-energy settings of an enriched mixture (24/28/32/36/40), one HCT116, three TALL-104, one BV2 and one RAW264.7. HEK293T settings are not biological replicates. Biological versus technical independence of TALL-104 files 1-3 is unspecified.
PXD028737	PRIDE	37085894	YY1 lactylation in microglia promotes angiogenesis through transcription activation-mediated upregulation of FGF2	2023/04	Homo sapiens	9606	Cell line	TIMS-DDA	Bruker TIMS	Label-free	4	H0_Slot1-35_1_10128.d;H0_Slot2-51_1_10185.d;H24_Slot1-34_1_10126.d;H24_Slot2-50_1_10183.d	2719	1178	PXD028737_mqpar.xml	Human HMC3 microglial cell line	Hypoxia (1% O2, 24 h) vs normoxia (24 h)	PTM Bio pre-washed pan-antibody beads; Kla-peptide immunoaffinity enrichment	PTM Bio	Not specified in accessible enrichment protocol	"DOI: 10.1186/s13059-023-02931-y
PRIDE PXD028737
Evidence E01-E04"	Selected four files comprise two assays: one lactylome acquisition per condition (Slot1) plus one total-proteome acquisition per condition (Slot2). These are not two Kla replicates per condition. Directional HMC3/ACHN cross-cell-line comparison is descriptive only: HMC3 has one selected Kla acquisition per group and ACHN biological independence is not established.
PXD030345	iProX	36333310	YiaC and CobB regulate lysine lactylation in Escherichia coli	2022/11	Escherichia coli	83333	Bacteria	FAIMS	Orbitrap	SILAC	3	20210626_LCC_DHY_La_FS-40.raw;20210626_LCC_DHY_La_FS-60.raw;20210626_LCC_DHY_La_FS-80.raw	1564	743	PXD030345_mqpar.xml	Escherichia coli K-12 MG1655 whole-cell lysate	delta cobB vs WT. Heavy=WT, light=delta cobB; original H/L=WT/KO. For KO/WT log2 response use -log2(H/L).	Anti-lactyllysine antibody-conjugated Protein A agarose beads; peptide immunoaffinity enrichment	PTM Biolabs	Not specified in accessible enrichment protocol	"DOI: 10.1038/s41467-022-34399-y
PRIDE PXD030345
Evidence E01-E04"	Metabolic SILAC WT/KO mixed 1:1; three selected RAW acquisitions. Published site table contains one aggregate H/L comparison and no independent replicate series. Biological n cannot be inferred from the three files or their 40/60/80 suffixes.
PXD030346	iProX	36333310	YiaC and CobB regulate lysine lactylation in Escherichia coli	2022/11	Escherichia coli	83333	Bacteria	FAIMS	Orbitrap	SILAC	3	20210425_LCC_ZK_Elute_40V.raw;20210425_LCC_ZK_Elute_60V.raw;20210425_LCC_ZK_Elute_80V.raw	955	528	PXD030346_mqpar.xml	Escherichia coli K-12 MG1655 whole-cell lysate	delta yiaC vs WT. Heavy=delta yiaC; light=yiaC WT. H/L=KO/WT. For KO/WT log2 response use log2(H/L).	Anti-lactyllysine antibody-conjugated Protein A agarose beads; peptide immunoaffinity enrichment	PTM Biolabs	Not specified in accessible enrichment protocol	"DOI: 10.1038/s41467-022-34399-y
PRIDE PXD030346
Evidence E01-E04"	Metabolic SILAC WT/KO mixed 1:1; three selected RAW acquisitions. Published site table contains one aggregate H/L comparison and no independent replicate series. Biological n cannot be inferred from the three files or their 40/60/80 suffixes.
PXD031526	PRIDE	35610722	Systematic identification of the lysine lactylation in the protozoan parasite Toxoplasma gondii	2022/05	Toxoplasma gondii	5811	Parasite	TIMS-DDA	Bruker TIMS	Label-free	1	lactylation_in_Toxoplasma.d	98	39	PXD031526_mqpar.xml	Intracellular Toxoplasma gondii RH delta ku80 delta hx tachyzoites grown in human foreskin fibroblasts (HFFs) and purified from host cells	Baseline intracellular tachyzoite lactylome; parasites harvested at approximately 64-128 parasites per vacuole. No selected treatment/control MS comparison. Sodium-lactate treatments (1, 5 and 25 mM) were separate Western-blot experiments.	Anti-L-lactyllysine antibody-conjugated agarose beads; peptide immunoaffinity enrichment	PTM Bio, Hangzhou, China	PTM-1404	"https://doi.org/10.1186/s13071-022-05315-6
https://www.ebi.ac.uk/pride/archive/projects/PXD031526
Methods: parasite culture, protein preparation and affinity enrichment"	Protein from at least four independent biological preparations was pooled to obtain approximately 2 mg total parasite protein. One selected raw acquisition (lactylation_in_Toxoplasma.d) represents the pooled sample; there are no independently acquired biological replicates in this selected file set.
PXD033146	PRIDE	37159428	Multi-Proteomic Analysis Reveals the Effect of Protein Lactylation on Matrix and Cholesterol Metabolism in Tendinopathy	2023/05	Homo sapiens	9606	Disease tissue	Reporter MS2	Orbitrap	TMT	4	HA119TPLa_Fr1.raw;HA119TPLa_Fr2.raw;HA119TPLa_Fr3.raw;HA119TPLa_Fr4.raw	1624	537	PXD033146_mqpar.xml	Human rotator cuff tendinopathy lesion tendon and adjacent unaffected tendon from nine patients (paired tissue collection)	RCT lesion group pool versus adjacent unaffected tendon group pool	Anti-L-lactyllysine antibody-conjugated agarose beads; peptide immunoaffinity enrichment	PTM Bio	PTM-1404	"DOI: 10.1021/acs.jproteome.2c00756
PRIDE PXD033146
Evidence E01-E05"	Nine paired patients were pooled by group; each pool analyzed three times. Table S3 has RCT1-3 and NC1-3, representing repeated analyses of pooled material, not independent patient replicates. Four RAW files are fractions of one TMT-6plex multiplex. Reporter-mass-to-RCT/NC mapping remains unresolved; the pooled analyses do not provide patient-level biological variance.
PXD033454	PRIDE	35685793	A bioorthogonal chemical reporter for the detection and identification of protein lactylation	2022/04	Homo sapiens	9606	Cell line	Standard	Orbitrap	Label-free	16	NonNucLB1.raw;NonNucLB2.raw;NonNucLB3.raw;NonNucLB4.raw;NonNucPB1.raw;NonNucPB2.raw;NonNucPB3.raw;NonNucPB4.raw;NucLB1.raw;NucLB2.raw;NucLB3.raw;NucLB4.raw;NucPB1.raw;NucPB2.raw;NucPB3.raw;NucPB4.raw	215	125	PXD033454_mqpar.xml	Human HEK293T cells, separately analysed nuclear and nonnuclear/cytoplasmic fractions.	YnLac metabolic-probe labelling versus L-lactate-treated control in both nuclear and nonnuclear fractions. LB files are YnLac-labelled; PB files are L-lactate controls (as explicitly defined in Supplementary Tables S2/S4).	YnLac chemical-reporter labeling, CuAAC with acid-cleavable azido-DADPS-biotin, then streptavidin-agarose affinity capture	Click Chemistry Tools (azido-DADPS-biotin); ThermoFisher (streptavidin agarose)	1330 (acid-cleavable azido-DADPS-biotin); streptavidin agarose catalogue no. not specified	"https://doi.org/10.1039/d2sc00918h
https://www.ebi.ac.uk/pride/archive/projects/PXD033454
Results: Chemical proteomic profiling of lactylation using YnLac; Fig. 3"	Four biological replicates per treatment, with separate nuclear and nonnuclear fractions: 2 treatments x 4 biological replicates x 2 subcellular fractions = 16 selected raw files. Subcellular fractions are not additional independent biological replicates.
PXD033991	PRIDE	35800753	Identification of lysine-lactylated substrates in gastric cancer cells	2022/07	Homo sapiens	9606	Cell line	Standard	Orbitrap	Label-free	1	QE_HFX_20210524_50cm_60min_IP.raw	2952	1228	PXD033991_mqpar.xml	Human AGS gastric adenocarcinoma cells.	Baseline global lysine-lactylome profiling of AGS cells; the selected MS file does not encode a lactate-versus-vehicle comparison. The paper's lactate treatment comparisons belong to separate RNA-seq and validation experiments.	Anti-L-lactyllysine antibody-conjugated agarose beads; peptide immunoaffinity enrichment	Micron Biotechnology Company	WM102	"https://doi.org/10.1016/j.isci.2022.104630
https://www.ebi.ac.uk/pride/archive/projects/PXD033991
STAR Methods: key resources table and LC-MS/MS analysis"	One selected LC-MS/MS acquisition from three independently cultured AGS replicates harvested and mixed before MS sample preparation; pooled biological material, not three independently quantified MS replicates.
PXD036307	iProX	37170646	Global profiling of lysine lactylation in human lungs	2025/05	Homo sapiens	9606	Tissue	Standard	Orbitrap	Label-free	12	HD145LPLa_PTB340_FS_40.raw;HD145LPLa_PTB340_FS_55.raw;HD145LPLa_PTB342_FS_40.raw;HD145LPLa_PTB342_FS_55.raw;HD145LPLa_PTB344_FS_40.raw;HD145LPLa_PTB344_FS_55.raw;HD145LPLa_PTB346_FS_40.raw;HD145LPLa_PTB346_FS_55.raw;HD145LPLa_PTB364_FS_40.raw;HD145LPLa_PTB364_FS_55.raw;HD145LPLa_PTB372_FS_40.raw;HD145LPLa_PTB372_FS_55.raw	839	428	PXD036307_mqpar.xml	Healthy elderly human lung tissue from six donors	Female vs male, three donors each; donor-ID-to-sex key remains unavailable. No disease/treatment comparison.	Prewashed antibody beads; lactylated-peptide enrichment	Not specified in accessible article or supplementary-material link record	Not specified in accessible article or supplementary-material link record	"DOI: 10.1002/pmic.202200437
iProX IPX0004918001
Evidence E01-E04"	Six biological donor samples (three female and three male). Selected dataset contains two RAW acquisitions per donor; retain PTB IDs as biological units. Original repository has another six non-FS RAWs outside the selected set.
PXD037027	PRIDE	37669396	Lysine lactylation regulates metabolic pathways and biofilm formation in Streptococcus mutans	2023/09	Streptococcus mutans	210007	Bacteria	TIMS-DDA	Bruker TIMS	Label-free	2	HA155LPLa_HIB_Slot1-28_1_11494.d;HA155LPLa_HIBS_Slot1-29_1_11496.d	1176	245	PXD037027_mqpar.xml	Streptococcus mutans UA159 whole bacterial cells	HIB planktonic group versus HIBS biofilm-associated group; conditions verified from article and submitter original summary.	Anti-Kla antibody resin; peptide immunoaffinity enrichment	PTM BioLab Inc.	PTM-1401	"DOI: 10.1126/scisignal.adg1849
PRIDE PXD037027
Evidence E01-E03"	Two selected acquisitions, one HIB and one HIBS. Independent biological replicate number and pooling are unreported for these MS samples. Current local mqpar experiment names are reversed relative to the original submitted summary.
PXD037371	PRIDE	36625413	Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	2023/01	Homo sapiens	9606	Disease tissue	Reporter MS2	Orbitrap	TMT	10	QE_HFX_20211228_50cm_60min_01.raw;QE_HFX_20211228_50cm_60min_02.raw;QE_HFX_20211228_50cm_60min_03.raw;QE_HFX_20211228_50cm_60min_04.raw;QE_HFX_20211228_50cm_60min_05.raw;QE_HFX_20211228_50cm_60min_06.raw;QE_HFX_20211228_50cm_60min_07.raw;QE_HFX_20211228_50cm_60min_08.raw;QE_HFX_20211228_50cm_60min_09.raw;QE_HFX_20211228_50cm_60min_10.raw	2565	1156	PXD037371_mqpar.xml	Human normal liver, primary hepatocellular carcinoma without metastasis during 3-year follow-up, and lung metastases from hepatocellular carcinoma.	Three tissue groups: normal liver versus nonmetastatic primary HCC versus HCC lung metastases; TMT-labelled comparative lactylome. Separate exploratory comparison: lung metastasis versus primary HCC; do not pool this effect with tumor-versus-normal comparisons.	Pan anti-Kla antibody-conjugated agarose beads; peptide immunoaffinity enrichment	Not specified in accessible enrichment protocol	Not specified in accessible enrichment protocol	"https://doi.org/10.1002/pmic.202200432
https://www.ebi.ac.uk/pride/archive/projects/PXD037371
Abstract; PRIDE project description and affinity enrichment protocol
User-shared working sample map (conditional; not independently confirmed in primary archive): https://chatgpt.com/share/6adee875-f0e4-83e9-9d7e-5d6a2c369442"	Article reports nine tissue samples, three per group. Ten selected RAWs are HPLC peptide fractions of one TMT experiment. The working reporter map used for conditional analysis is user-shared and not independently confirmed in PRIDE: 126C/127N/127C=normal liver; 128N=reference/QC and excluded; 128C/129N/129C=lung metastasis; 130N/130C/131N=primary HCC. Ten fractions were summed within each Site ID and channel; fractions are not biological replicates. The three mapped reporter channels per tissue group are conditional sample units pending the primary reporter-to-sample key.
PXD037530	PRIDE	37886975	Protein Lactylation Modification and Proteomics Features in Cirrhosis Patients after UC-MSC Treatment	2023/10	Homo sapiens	9606	Disease tissue	Reporter MS2	Orbitrap	TMT	6	MD218TPLa_01_IP_1.raw;MD218TPLa_01_IP_2.raw;MD218TPLa_01_IP_3.raw;MD218TPLa_02_IP_1.raw;MD218TPLa_02_IP_2.raw;MD218TPLa_02_IP_3.raw	2183	758	PXD037530_mqpar.xml	Human paired liver biopsy tissue from patients with decompensated HBV-related cirrhosis	Baseline versus one month after UC-MSC treatment; clinical study design is paired, but selected RAW/TMT-channel-to-patient mapping is unresolved.	Lactic acid resin; peptide immunoaffinity enrichment	Hangzhou Jingjie Biotechnology Co., Ltd.	PTM-1404	"DOI: 10.3390/cimb45100532
PRIDE PXD037530
Evidence E01-E03"	Clinical cohort contains 11 patients with before/after tissue sampling. Six selected TMT acquisitions are named 01_IP_1-3 and 02_IP_1-3. Supplement describes 60 peptide fractions combined into two fractions; the relation of 01/02 and IP1-3 to fractions, repeated analyses and sample channels remains unconfirmed.
PXD039257	PRIDE	38479452	The characterization of protein lactylation in relation to cardiac metabolic reprogramming in neonatal mouse hearts	2024/07	Mus musculus	10090	Tissue	TIMS-DDA	Bruker TIMS	Label-free	3	ED204LPLa_WT1_Slot2-19_1_16420.d;ED204LPLa_WT2_Slot2-21_1_16424.d;ED204LPLa_WT3_Slot2-23_1_16428.d	3562	1097	PXD039257_mqpar.xml	Neonatal C57BL/6J mouse whole-heart tissue; WT1-WT3 ages unresolved	Study profiles postnatal P1, P5 and P7 hearts. The selected WT1/WT2/WT3 files cannot be assigned to these ages from the accessible annotation.	Pan-antibody-based PTM peptide enrichment with pre-washed antibody beads	PTM Bio	Not specified in accessible enrichment protocol	"DOI: 10.1016/j.jgg.2024.02.009
PRIDE PXD039257
Evidence E01-E03"	Three selected WT1-WT3 acquisitions. Accessible preprint states each sample pooled 16 P1 hearts, 8 P5 hearts or 6 P7 hearts. Whether WT1-WT3 denote ages or independent pools is not documented in a verified RAW key; pooled hearts do not each constitute independent MS replicates.
PXD040514	PRIDE	37851814	Global lactylome reveals lactylation-dependent mechanisms underlying TH17 differentiation in experimental autoimmune uveitis	2023/10	Mus musculus	10090	Primary cell	TIMS-DDA	Bruker TIMS	Label-free	2	EE369LPLaB1_Control_Slot1-52_1_21416.d;EE369LPLaB1_EAU_Slot1-53_1_21418.d	3682	1271	PXD040514_mqpar.xml	Primary splenic CD4+ T cells from normal control and EAU mice	EAU versus normal control mouse CD4+ T-cell lactylome; two selected files explicitly named Control and EAU.	Pan-Kla antibody with pre-washed beads; peptide immunoaffinity enrichment	PTM Bio	PTM-1404	"DOI: 10.1126/sciadv.adh4655
PRIDE PXD040514
Evidence E01-E03"	Two selected group-level acquisitions. Article reports 1 x 10^8 primary CD4+ T cells isolated from more than 10 mice in each group for profiling. The number of independent pools/preparations and exact pool-to-RAW assignment are not specified.
PXD040840	iProX	39030363	Lysine L-lactylation is the dominant lactylation isomer induced by glycolysis	2025/01	Homo sapiens	9606	Cell line	Standard	Orbitrap	Label-free;SILAC	10	Kce_IP_R1.raw;Kce_IP_R2.raw;Kce_IP_R3.raw;KD-la_IP_R1.raw;KD-la_IP_R2.raw;KD-la_IP_R3.raw;KL-la_IP_R1.raw;KL-la_IP_R2.raw;KL-la_IP_R3.raw;KL-la_IP_SILAC_high_low_glucose.raw	187	68	PXD040840_label-free_mqpar.xml;PXD040840_silac_mqpar.xml	Human MCF-7 breast cancer cells; selected SILAC quantification is acid-extracted histones	Selected histone SILAC: 25 mM versus 0 mM glucose for 24 h, heavy=25 mM and light=0 mM; high/no-glucose response=H/L. Nine other label-free files represent Kce, KD-la and KL-la enrichment classes, not glucose treatment groups. A separate whole-cell comparison used 0.1 versus 25 mM glucose.	nProtein A Sepharose antibody affinity enrichment of KL-la/KD-la/Kce peptides	Cytiva (nProtein A Sepharose); antibody supplier not specified in accessible peptide-enrichment protocol	Not specified for enrichment	"https://doi.org/10.1038/s41589-024-01680-8
Methods: Reagents and Peptide enrichment; Fig. 4; Extended Data Fig. 7"	One selected histone SILAC acquisition, H=25 mM glucose and L=0 mM glucose, mixed 1:1; independent biological n unspecified. Nine LFQ acquisitions are three enrichment classes with R1-R3 each, with biological/technical independence unspecified; they do not establish glucose-response replicates.
PXD041277	iProX	37847886	Global profiling of protein lactylation in Caenorhabditis elegans	2023/10	Caenorhabditis elegans	6239	Animal model	FAIMS	Orbitrap	Label-free	18	BE168PI_Lac09_Fr1_FS_-40v.raw;BE168PI_Lac09_Fr1_FS_-55v.raw;BE168PI_Lac09_Fr2_FS_-40v.raw;BE168PI_Lac09_Fr2_FS_-55v.raw;BE168PI_Lac09_Fr3_FS_-40v.raw;BE168PI_Lac09_Fr3_FS_-55v.raw;BE168PI_Lac13_Fr1_FS_-40v.raw;BE168PI_Lac13_Fr1_FS_-55v.raw;BE168PI_Lac13_Fr2_FS_-40v.raw;BE168PI_Lac13_Fr2_FS_-55v.raw;BE168PI_Lac13_Fr3_FS_-40v.raw;BE168PI_Lac13_Fr3_FS_-55v.raw;BE168PI_Lac17_Fr1_FS_-40v.raw;BE168PI_Lac17_Fr1_FS_-55v.raw;BE168PI_Lac17_Fr2_FS_-40v.raw;BE168PI_Lac17_Fr2_FS_-55v.raw;BE168PI_Lac17_Fr3_FS_-40v.raw;BE168PI_Lac17_Fr3_FS_-55v.raw	2434	609	PXD041277_mqpar.xml	Whole adult wild-type N2 Caenorhabditis elegans.	Baseline global lactylome under normal physiological conditions; no experimental treatment/control contrast.	Lactylated-peptide enrichment using lactylated resin (antibody resin)	PTM Bio / Hangzhou Jingjie Biotechnology Co., Ltd.	PTM-1404	"https://doi.org/10.1002/pmic.202300185
https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD041277
Abstract; ProteomeXchange dataset description"	Three biological replicates (Lac09, Lac13, Lac17). Each has three fractions (Fr1-Fr3) with two FS acquisition settings (-40v, -55v), yielding 18 selected files. Fractions and paired acquisition settings are not additional biological replicates.
PXD042171	PRIDE	39757301	Nonenzymatic lysine D-lactylation induced by glyoxalase II substrate SLG dampens inflammatory immune responses	2025/01	Mus musculus	10090	Primary cell	TIMS-DDA	Bruker TIMS	Label-free	6	FE139LPLaB1_C1_Slot2-5_1_21433.d;FE139LPLaB1_C2_Slot2-6_1_21435.d;FE139LPLaB1_C3_Slot2-7_1_21437.d;FE139LPLaB1_V1_Slot2-8_1_21439.d;FE139LPLaB1_V2_Slot2-9_1_21441.d;FE139LPLaB1_V3_Slot2-10_1_21443.d	2681	1077	PXD042171_mqpar.xml	Mouse macrophages; dedicated Table S1 identifies peritoneal macrophages, but Fig. 4i identifies BMDMs. Exact source of selected RAWs unresolved.	VSV-associated comparison group V versus medium-alone control C; C1-C3 and V1-V3 identify six quantitative samples.	Anti-lactyllysine antibody-conjugated agarose beads; peptide immunoaffinity enrichment	PTM Bio	PTM-1404	"https://doi.org/10.1038/s41422-024-01060-w
https://www.ebi.ac.uk/pride/archive/projects/PXD042171
Methods: lactylome sample preparation and affinity enrichment"	Downloaded dedicated lactylome Table S1 explicitly contains C1-C3 and V1-V3; relevant figure legends report n=3. Independent source animals, preparations and any pooling behind these numbered MS samples are not explicitly defined.
PXD045069	PRIDE	37919786	Herbal medicine formula Huazhuo Tiaozhi granule ameliorates dyslipidaemia via regulating histone lactylation and miR-155-5p biogenesis	2023/12	Homo sapiens	9606	Cell line	Reporter MS2	Orbitrap	TMT	2	XA01378LPLa_FFA_Slot2-1_1_25192.d;XA01378LPLa_HTG_Slot2-2_1_25194.d	1219	657	PXD045069_mqpar.xml	Human LO2 (L02) liver cell line	FFA model versus FFA model with Huazhuo Tiaozhi granule (HTG) comparison. No untreated-control RAW selected.	Pre-washed antibody-bead enrichment of modified peptides	Jingjie PTM BioLabs	Not specified in accessible enrichment protocol	"DOI: 10.1186/s13148-023-01573-y
PRIDE PXD045069
Evidence E01-E03"	Two selected acquisitions named FFA and HTG. Published Methods report TMT and Q Exactive HF-X, whereas selected RAWs are Bruker acquisitions. Reporter-channel sample key, pooling and independent preparations remain unresolved. Ordinary evidence-derived Intensity does not establish or disprove the original labeling method.
PXD046488	PRIDE	38003390	Global Analysis of Lysine Lactylation of Germinated Seeds in Wheat	2023/11	Triticum aestivum	4565	Plant	Reporter MS2	Orbitrap	TMT	10	1.raw;2.raw;3.raw;4.raw;5.raw;6.raw;7.raw;8.raw;9.raw;10.raw	188	80	PXD046488_mqpar.xml	Embryos of common wheat (Triticum aestivum L.), cultivar QiMin23	0 h versus 12 h after imbibition; seeds imbibed in darkness at 21 degrees C.	Pre-washed anti-lactyllysine antibody-conjugated agarose beads; peptide immunoaffinity enrichment	Micrometer Biotech	Not specified in accessible enrichment protocol	"https://doi.org/10.3390/ijms242216195
https://www.ebi.ac.uk/pride/archive/projects/PXD046488
Methods: plant materials and affinity enrichment"	Three biological replicates per time point (six samples total), TMT-labeled and pooled after labeling. The ten raws (1.raw-10.raw) are configured as peptide fractions 1-10 of experiment Ta in mqpar, not ten biological replicates.
PXD046495	PRIDE	39246443	Lactylome analysis reveals potential target modified proteins in the retina of form-deprivation myopia	2024/09	Cavia porcellus	10141	Animal model	TIMS-DDA	Bruker TIMS	Label-free	6	GE039LPLaB2_Control_2W_1_Slot1-37_1_221.d;GE039LPLaB2_Control_2W_2_Slot1-37_1_223.d;GE039LPLaB2_OD_R_2W_1_Slot1-38_1_225.d;GE039LPLaB2_OD_R_2W_2_Slot1-38_1_227.d;GE039LPLaB2_OS_R_2W_1_Slot1-39_1_229.d;GE039LPLaB2_OS_R_2W_2_Slot1-39_1_231.d	78	33	PXD046495_mqpar.xml	Guinea pig (Cavia porcellus) neurosensory retina; male animals started at 2 weeks of age.	Two weeks of monocular form deprivation. NC: right eyes of untreated normal-control animals; FDM: covered right eyes in the form-deprivation group; CT: exposed left eyes of the same form-deprivation group.	Pre-washed antibody-bead enrichment of lysine-lactylation-modified peptides	Not specified in accessible enrichment protocol	Not specified in accessible enrichment protocol	"DOI: 10.1016/j.isci.2024.110606
PRIDE PXD046495
Evidence E01-E04"	6 TIMS-DDA acquisitions; NC=Control_2W_1/2, FDM=OD_R_2W_1/2, contralateral CT=OS_R_2W_1/2. Methods report 6 retinas extracted per group, but pooling and the relation to 2 quantitative columns/group are unreported; independent biological n remains unresolved. Not a fraction series.
PXD046631	PRIDE	39856050	Serpina3k lactylation protects from cardiac ischemia reperfusion injury	2025/01	Mus musculus	10090	Animal model	TIMS-DDA	Bruker TIMS	Label-free	9	KLa_MI30_1_Slot1-10_1_5761.d;KLa_MI30_2_Slot1-11_1_5763.d;KLa_MI30_3_Slot1-12_1_5765.d;KLa_MI_6h_1_Slot1-4_1_5749.d;KLa_MI_6h_2_Slot1-5_1_5751.d;KLa_MI_6h_3_Slot1-6_1_5753.d;KLa_SHAM_1_Slot1-7_1_5755.d;KLa_SHAM_2_Slot1-8_1_5757.d;KLa_SHAM_3_Slot1-9_1_5759.d	2313	492	PXD046631_mqpar.xml	Mouse left ventricular myocardium from the infarct area	Sham surgery (SHAM), 30 min myocardial ischemia (MI30), and 30 min ischemia followed by 6 h reperfusion (MI_6h).	Pre-washed pan-lactylation antibody beads; peptide immunoaffinity enrichment	PTM Bio	PTM-1404	"https://doi.org/10.1038/s41467-024-55589-w
https://www.ebi.ac.uk/pride/archive/projects/PXD046631
Methods: ischemia/reperfusion model and lactylome analysis"	Three pooled biological replicates per group, each formed by combining myocardium from three mice: nine mice per group and 27 mice total. One selected raw acquisition per pooled biological replicate; nine raws total.
PXD046800	iProX	39012622	Integrative Analysis of Lactylome and Proteome of Hypertrophic Scar To Identify Pathways or Proteins Associated with Disease Development	2024/07	Homo sapiens	9606	Disease tissue	Standard	Orbitrap	Label-free	8	HFX2_LFQ_QB001_HSP1_1.raw;HFX2_LFQ_QB001_HSP2_1.raw;HFX2_LFQ_QB001_HSP3_1.raw;HFX2_LFQ_QB001_HSP4_1.raw;HFX2_LFQ_QB001_NSP1_1.raw;HFX2_LFQ_QB001_NSP2_1.raw;HFX2_LFQ_QB001_NSP3_1.raw;HFX2_LFQ_QB001_NSP4_1.raw	1223	421	PXD046800_mqpar.xml	Human hypertrophic scar and patient-matched surrounding normal skin	Hypertrophic scar (HSP1-HSP4) versus paired surrounding normal skin (NSP1-NSP4), four patients; no experimental drug treatment.	Anti-L-lactyllysine antibody-conjugated agarose beads; peptide immunoaffinity enrichment	PTM BIO	PTM-1404	"https://doi.org/10.1021/acs.jproteome.3c00901
https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD046800
Abstract; ProteomeXchange dataset description"	Four paired patients, with one hypertrophic-scar and one normal-skin biological specimen per patient; four biological replicates per group, eight selected raw files. The matching number in HSP/NSP identifies the patient, not a peptide fraction.
PXD047535	PRIDE	39407253	Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma	2024/10	Homo sapiens	9606	Disease tissue	TIMS-DDA	Bruker TIMS	Label-free	12	XA00303B2LPLa_NAT16_E2_1_17773.d;XA00303B2LPLa_NAT3_C8_1_17753.d;XA00303B2LPLa_NAT4_D2_1_17757.d;XA00303B2LPLa_NAT5_D4_1_17761.d;XA00303B2LPLa_NAT7_D6_1_17765.d;XA00303B2LPLa_NAT9_D8_1_17769.d;XA00303B2LPLa_Tumor16_E3_1_17775.d;XA00303B2LPLa_Tumor3_D1_1_17755.d;XA00303B2LPLa_Tumor4_D3_1_17759.d;XA00303B2LPLa_Tumor5_D5_1_17763.d;XA00303B2LPLa_Tumor7_D7_1_17767.d;XA00303B2LPLa_Tumor9_E1_1_17771.d	3167	1189	PXD047535_mqpar.xml	Human oral squamous cell carcinoma (OSCC) and paired normal adjacent tissue (NAT)	OSCC tumor versus patient-matched normal adjacent tissue; selected patient IDs 3, 4, 5, 7, 9 and 16. The CAL27 lactate-treatment experiments elsewhere in the paper are not represented by these selected raws.	PTM-1404 resin; peptide immunoaffinity enrichment	PTM-Bio	PTM-1404	"https://doi.org/10.1186/s13059-024-03383-8
https://www.ebi.ac.uk/pride/archive/projects/PXD047535
Methods; Fig. 1; Additional files 1-2 (including supplementary information)"	Six paired biological tissue specimens per group from six patients, one selected acquisition per tissue: 12 raw files total. Numeric suffixes identify paired patients rather than fractions or technical repeats.
PXD048127	iProX	39779673	Genetic code expansion reveals site-specific lactylation in living cells reshapes protein functions	2025/01	Homo sapiens;Mus musculus	9606;10090	Cell line	Standard	Orbitrap	Label-free	7	A549-Enrichment.raw;H1299-Enrichment.raw;HepG2-Enrichment.raw;PC3-Enrichment.raw;THP1-Enrichment.raw;LLC-Enrichment.raw;MC38-Enrichment.raw	402;229	277;166	PXD048127_human_mqpar.xml;PXD048127_mouse_mqpar.xml	Seven selected tumor-derived cell lines: human A549, H1299, HepG2, PC3 and THP1; mouse LLC and MC38	Lactylproteome survey after 25 mM sodium lactate for 24 h; affinity-enriched lactylated peptides. No untreated-comparator raw file is selected.	Anti-lactylation antibody conjugated to Protein A agarose; peptide immunoprecipitation enrichment	Anti-lactylation antibody source not reported; Protein A agarose: Invitrogen	Antibody not reported; Protein A agarose: 15918014	"https://doi.org/10.1038/s41467-024-55165-2
Methods: Cell culture; Wet-lab strategy for lactylation mining; Fig. 1b (including supplementary information)"	One selected enriched-lactylome acquisition per cell line, seven raws total. Independent biological replicate count is unspecified for this survey. The other cell lines and later functional experiments in the article are outside the selected file set.
PXD048244	PRIDE	39524337	Systematic analysis of lysine lactylation in nucleus pulposus cells	2024/12	Rattus norvegicus	10116	Primary cell	TIMS-DDA	Bruker TIMS	Label-free	6	AE141LPLa_HY1_Slot2-17_1_10726.d;AE141LPLa_HY2_Slot2-18_1_10728.d;AE141LPLa_HY3_Slot2-19_1_10730.d;AE141LPLa_NC1_Slot2-14_1_10720.d;AE141LPLa_NC2_Slot2-15_1_10722.d;AE141LPLa_NC3_Slot2-16_1_10724.d	4363	1181	PXD048244_mqpar.xml	Primary rat nucleus pulposus cells isolated from central nucleus pulposus tissue of intervertebral discs from 8-week-old male Sprague-Dawley rats (~220 g).	NC: normoxia (21% O2), 24 h; HY: hypoxia (1% O2), 24 h. These cultured-cell oxygen treatments model different NP oxygen environments; the MS samples are not human IDD tissue.	Pre-washed antibody-bead immunoaffinity enrichment of Kla-modified peptides	PTM Bio Inc.	Not specified in accessible enrichment protocol	"DOI: 10.1016/j.isci.2024.111157
PRIDE PXD048244
Evidence E01-E04"	3 submitted cell samples/condition (HY1-3, NC1-3), one selected TIMS-DDA acquisition/sample, fraction=1. The MS method explicitly reports 3 samples/group; independent donor/isolation/culture replicates and pooling are not described. Do not transfer n=3 biological-replicate wording from Western-blot validation to the MS samples.
PXD050470	iProX	39610256	Global Profiling of Protein Lactylation in Human Hippocampi	2024/12	Homo sapiens	9606	Tissue	Standard	Orbitrap	Label-free	9	XA02614PILa_H187_Fr1.raw;XA02614PILa_H187_Fr2.raw;XA02614PILa_H187_Fr3.raw;XA02614PILaR1_H072_Fr1.raw;XA02614PILaR1_H072_Fr2.raw;XA02614PILaR1_H072_Fr3.raw;XA02614PILaR1_H081_Fr1.raw;XA02614PILaR1_H081_Fr2.raw;XA02614PILaR1_H081_Fr3.raw	3912	1219	PXD050470_mqpar.xml	Human hippocampal tissue from the National Developmental and Functional Human Brain Bank; three biological tissue samples under normal physiological conditions.	Baseline physiological hippocampus lactylome atlas; no disease/treatment comparison in the selected files.	Pre-washed antibody-bead enrichment of lactylated peptides	Not specified in accessible enrichment protocol	Not specified in accessible enrichment protocol	"https://doi.org/10.1002/prca.202400061
https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD050470
Abstract; ProteomeXchange dataset description"	3 biological human hippocampal tissue samples (H187, H072, H081), 3 fractions each (Fr1-3), total 9 RAWs. Baseline physiological atlas, no treatment comparison. WARNING: mqpar experiment labels are cyclically shifted relative to filename donor codes (H187->H072, H072->H081, H081->H187); preserve filename identities. Donor Table S1 unavailable.
PXD050752	PRIDE	38798264	Comparative Analysis of Post-Translational Modifications of Human Serum Albumin Derived from Human Plasma and Recombinant Sources in China	2024/05	Homo sapiens	9606	Body fluid	TIMS-DDA	Bruker TIMS	Label-free	2	XA00584LPLa_CZ_Slot1-50_1_24745.d;XA00584LPLa_RY_Slot1-51_1_24747.d	11	8	PXD050752_mqpar.xml	Commercial human serum albumin preparations: recombinant human serum albumin (rHSA) versus plasma-derived human serum albumin (pHSA). These are purified protein products, not tissue/cell samples.	CZ = rHSA; RY = pHSA. Product-source comparison. The full paper studies six plasma-derived manufacturer products plus yeast- and rice-derived recombinant products, but their contribution to the two selected MS preparations is unspecified.	Anti-lactyllysine antibody-resin enrichment of lactylated peptides in a multi-PTM workflow	PTM Bio, Hangzhou, China	PTM-1404	"https://doi.org/10.24976/discov.med.202436184.98
https://www.ebi.ac.uk/pride/archive/projects/PXD050752
PRIDE project description; sample protocol: Modification enrichment"	CZ=rHSA and RY=pHSA (explicit Figure 3 key); 1 selected TIMS-DDA lactylation acquisition/category, fraction=1. Commercial HSA preparations; exact product/lot composition, pooling and independent preparation n are unreported. Study-wide 6 pHSA + 2 rHSA products do not establish n for the selected 2 RAWs.
PXD050906	PRIDE	38961290	NBS1 lactylation is required for efficient DNA repair and chemotherapy resistance	2024/07	Homo sapiens	9606	Cell line	TIMS-DDA	Bruker TIMS	Label-free	6	KA460LPLa_Ctrl_1_Slot1-38_1_9994.d;KA460LPLa_Ctrl_2_Slot1-38_1_9996.d;KA460LPLa_Ctrl_3_Slot1-38_1_9998.d;KA460LPLa_Treat_1_Slot2-54_1_10072.d;KA460LPLa_Treat_2_Slot2-54_1_10074.d;KA460LPLa_Treat_3_Slot2-54_1_10076.d	4822	1902	PXD050906_mqpar.xml	Human AGS gastric cancer cells: parental AGS-P and acquired cisplatin-resistant AGS-R	Acquired cisplatin-resistant AGS-R (Treat_1-3) versus parental AGS-P (Ctrl_1-3); mapping confirmed by complete numerical matching to Supplementary Table 3.	Pre-washed antibody-bead affinity enrichment of lactyl-modified peptides	Not specified in accessible enrichment protocol	Not specified in accessible enrichment protocol	"https://doi.org/10.1038/s41586-024-07620-9
https://www.ebi.ac.uk/pride/archive/projects/PXD050906
Methods: cell models and lactylated peptide enrichment"	Six acquisitions, three per arm: Ctrl_1-3=parental AGS-P; Treat_1-3=cisplatin-resistant AGS-R. Independent cultures/preparations versus technical repeats remain unresolved. Matching numeric suffixes do not establish paired cultures. The AGS effect is therefore retained as descriptive until biological independence is confirmed.
PXD051415	PRIDE	38670996	HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription	2024/04	Homo sapiens	9606	Cell line	FAIMS	Orbitrap	SILAC	9	HeLa-Histone-La.raw;HeLa-Kla-1.raw;HeLa-Kla-2.raw;HeLa-Kla-3.raw;HeLa-Kla-4.raw;HeLa-Kla-5.raw;HeLa-Kla-6.raw;HeLa-Kla-7.raw;HeLa-Kla-8.raw	418	260	PXD051415_mqpar.xml	Human HeLa cervical cancer cells; histone and whole-cell lactylation samples	HBO1-knockout versus WT HeLa cells. SILAC heavy=WT and light=HBO1-KO, mixed 1:1; orient KO/WT as L/H. Histone and whole-cell preparations must be analyzed separately.	Anti-L-lactyllysine antibody-conjugated Protein A agarose immunoaffinity enrichment of peptides	PTM Biolabs	Not specified in accessible enrichment protocol	"https://doi.org/10.1038/s41467-024-47900-6
https://www.ebi.ac.uk/pride/archive/projects/PXD051415
Methods: SILAC quantification and lactylated peptide enrichment"	One histone SILAC acquisition and eight whole-cell Kla acquisitions configured as fractions 1-8 of one HeLa experiment in mqpar. Original offline fraction preparation and independent biological n remain unspecified. Both workflows use FAIMS -45/-65 V; eight files are not eight biological replicates.
PXD053029	PRIDE	40680722	YTHDC1 lactylation regulates its phase separation to enhance target mRNA stability and promote RCC progression	2025/07	Homo sapiens	9606	Cell line	TIMS-DDA	Bruker TIMS	Label-free	6	C_1_Slot2-20_1_5362.d;C_2_Slot2-20_1_5363.d;C_3_Slot2-20_1_5364.d;H24_1_Slot2-21_1_5366.d;H24_2_Slot2-21_1_5367.d;H24_3_Slot2-21_1_5368.d	2148	1030	PXD053029_mqpar.xml	Human ACHN renal cell carcinoma cells	ACHN hypoxia for 24 h (H24_1-3) versus normoxia (C_1-3). Original processed parameters/summary confirm PXD053029 is the lactylome; the article resource-table proteome/lactylome accessions are swapped.	Pre-washed antibody-bead enrichment of modified peptides for lactylome analysis	PTM Bio	Not specified; the source reports lot number 001	"https://doi.org/10.1016/j.molcel.2025.06.017
https://www.ebi.ac.uk/pride/archive/projects/PXD053029
Abstract; PRIDE project description and sample protocol"	C_1-3 and H24_1-3: six acquisitions. Independent biological replication versus technical repeats is not explicitly established for these selected files. The ACHN-HMC3 hypoxia overlap is descriptive only; do not treat acquisition counts as confirmed biological n.
PXD053276	PRIDE	39935788	Multi-omics study on the effect of moderate-intensity exercise on protein lactylation in mouse muscle tissue	2025/01	Mus musculus	10090	Animal model	TIMS-DDA	Bruker TIMS	Label-free	6	XA04524B2LPLa_Con_1_Slot2-7_1_21842.d;XA04524B2LPLa_Con_2_Slot2-8_1_21844.d;XA04524B2LPLa_Con_3_Slot2-9_1_21846.d;XA04524B2LPLa_EX_1_Slot2-10_1_21848.d;XA04524B2LPLa_EX_2_Slot2-11_1_21850.d;XA04524B2LPLa_EX_3_Slot2-12_1_21852.d	1317	261	PXD053276_mqpar.xml	Mouse hind-leg skeletal muscle; 8-week-old male C57BL/6J mice, approximately 21 +/- 1 g at enrollment.	Con: sedentary control; EX: moderate treadmill exercise 60 min/day, 5 days/week, for 6 weeks, after a 5-day adaptation; tissue collected 24 h after final training.	PTM-1404 resin immunoaffinity enrichment of lactylated peptides	PTM Bio	PTM-1404	"DOI: 10.3389/fcell.2024.1472338
PRIDE PXD053276
Evidence E01-E04"	3 quantitative muscle samples/group (Con_1-3, EX_1-3), 1 selected TIMS-DDA acquisition/sample, fraction=1; Con=sedentary and EX=6-week treadmill training, collection 24 h after final training. Table 3 confirms 3 columns/group; individual-mouse provenance and pooling remain unreported, so independent biological n is unresolved.
PXD053474	PRIDE	39569522	Subcellular Proteomic Mapping of Lysine Lactylation	2024/12	Homo sapiens	9606	Cell line	Standard	Orbitrap	Label-free	19	20240110-Whole-cell-Lactylation-F1.raw;20240110-Whole-cell-Lactylation-F1-2.raw;20240110-Whole-cell-Lactylation-F2.raw;20240110-Whole-cell-Lactylation-F3.raw;20240110-Whole-cell-Lactylation-NoFrac.raw;20240111-Cytoplasm-Lactylation-F1.raw;20240111-Cytoplasm-Lactylation-F2.raw;20240111-Cytoplasm-Lactylation-F3.raw;20240111-Cytoplasm-Lactylation-F4.raw;20240112-Nucleus-Lactylation-F1.raw;20240112-Nucleus-Lactylation-F2.raw;20240112-Nucleus-Lactylation-F3.raw;20240112-Nucleus-Lactylation-F4.raw;20240114-Mitochondria-Lactylation-F1.raw;20240114-Mitochondria-Lactylation-F2.raw;20240114-Mitochondria-Lactylation-F3.raw;20240114-Mitochondria-Lactylation-F4.raw;20240116-Membrane-Lactylation-F1.raw;20240116-Membrane-Lactylation-F2.raw	364	226	PXD053474_DDA_mqpar.xml	Human HCT116 colon carcinoma cells; whole-cell, cytoplasmic, nuclear, mitochondrial and membrane fractions	Sodium-lactate-treated HCT116 cells (25 mM, 48 h); subcellular and whole-cell lactylome coverage. No untreated control among selected files.	Anti-Kla antibody conjugated to Protein A/G Plus agarose for lactylated-peptide affinity enrichment	PTM Bio Inc. (anti-Kla antibody); Santa Cruz Biotechnology (Protein A/G Plus agarose)	PTM-1401RM (anti-Kla antibody); sc-2003 (Protein A/G Plus agarose)	"https://doi.org/10.1021/jasms.4c00366
https://www.ebi.ac.uk/pride/archive/projects/PXD053474
Abstract; PRIDE project description and sample protocol"	19 acquisitions: four configured WholeCell fractions (filenames F1/F1-2/F2/F3; mqpar fractions 1-4), separate WholeCellNoFrac, four fractions each for cytoplasm/nucleus/mitochondria, and two membrane fractions. Original F1-2 preparation/reinjection meaning and biological n remain unresolved.
PXD055230	PRIDE	39772686	Infection-induced lysine lactylation enables herpesvirus immune evasion	2025/01	Homo sapiens;Human cytomegalovirus	9606;10359	Virus-infected cell	Standard	Orbitrap	Label-free	15	LaIP_TB40_24hpi_DDA_R1.raw;LaIP_TB40_24hpi_DDA_R2.raw;LaIP_TB40_24hpi_DDA_R3.raw;LaIP_TB40_48hpi_DDA_R1.raw;LaIP_TB40_48hpi_DDA_R2.raw;LaIP_TB40_48hpi_DDA_R3.raw;LaIP_TB40_72hpi_DDA_R1.raw;LaIP_TB40_72hpi_DDA_R2.raw;LaIP_TB40_72hpi_DDA_R3.raw;LaIP_TB40_96hpi_DDA_R1.raw;LaIP_TB40_96hpi_DDA_R2.raw;LaIP_TB40_96hpi_DDA_R3.raw;LaIP_TB40_mock_DDA_R1.raw;LaIP_TB40_mock_DDA_R2.raw;LaIP_TB40_mock_DDA_R3.raw	14716;745	3667;155	PXD055230_DDA_mqpar.xml;PXD055230_virus_mqpar.xml	Human MRC-5 lung fibroblasts	HCMV TB40/E versus mock; infected samples at 24, 48, 72 and 96 h. Selected files cover the HCMV series.	Anti-lactyllysine antibody-conjugated agarose-bead immunoaffinity purification of peptides	PTM BIO	Not specified in accessible enrichment protocol	"https://doi.org/10.1126/sciadv.ads6215
https://www.ebi.ac.uk/pride/archive/projects/PXD055230
Methods: cell infection, lactyl-peptide enrichment and sample preparation"	Three biological replicates per condition: mock and four infection time points, 15 unique raw acquisitions. Each prepared sample used six to eight culture dishes. R1-3 denote biological replicates; human/virus XML searches reuse these raws. In the current k_site_positive-derived time analysis, intensities were not normalized to total-proteome abundance; time effects are exploratory lactylation-evidence changes, not occupancy changes.
PXD056791	PRIDE	39642882	Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis	2025/02	Homo sapiens	9606	Cell line	Standard	Orbitrap	Label-free;SILAC	8	240620_Kla_IP_Mut_2_5of9ul_1.raw;240620_Kla_IP_Mut_2_5of9ul_2.raw;240620_Kla_IP_Mut_2_5of9ul_3.raw;240620_Kla_IP_WT_2_5of9ul_1.raw;240620_Kla_IP_WT_2_5of9ul_2.raw;240620_Kla_IP_WT_2_5of9ul_3.raw;IPKla_Histone_SILAC_heavy192R.raw;IPKla_Histone_SILAC_light192R.raw	689	286	PXD056791_label-free_mqpar.xml;PXD056791_silac_mqpar.xml	Human U87 glioma cells; Kla-IP and histone samples	SUCLG1-depleted U87 cells rescued with WT SUCLG1 versus K192R. Histone SILAC: heavy192R uses H/L and light192R uses L/H for K192R/WT, confirmed in Fig. S5E. Six LFQ WT/Mut RAW-to-rescue assignments remain tentative.	Anti-Kla antibody-conjugated bead immunoprecipitation of histone peptides	PTM Bio Inc., Chicago, IL	PTM-1404	"https://doi.org/10.1016/j.cmet.2024.11.005
https://www.ebi.ac.uk/pride/archive/projects/PXD056791
PRIDE sample protocol: histone Kla quantification"	Two histone SILAC label-swap acquisitions: heavy192R uses H/L and light192R uses L/H for K192R/WT. Label swapping does not establish independent biological n. Six label-free WT/Mut Kla-IP files (_1-3 per arm) lack a verified sample-to-intervention key and repeat provenance.
PXD056805	PRIDE	39822760	H3K14la drives endothelial dysfunction in sepsis‐induced ARDS by promoting SLC40A1/transferrin‐mediated ferroptosis	2025/01	Mus musculus	10090	Animal model	TIMS-DDA	Bruker TIMS	Label-free	12	ZD055LPLa_G1M3_Slot1-28_1_3552.d;ZD055LPLa_G1M4_Slot1-29_1_3554.d;ZD055LPLa_G1M5_Slot1-30_1_3556.d;ZD055LPLa_G1M6_Slot1-31_1_3558.d;ZD055LPLa_G1M8_Slot1-32_1_3560.d;ZD055LPLa_G1M9_Slot1-33_1_3562.d;ZD055LPLa_G3M1_Slot1-34_1_3564.d;ZD055LPLa_G3M2_Slot1-35_1_3566.d;ZD055LPLa_G3M3_Slot1-36_1_3568.d;ZD055LPLa_G3M7_Slot1-37_1_3570.d;ZD055LPLa_G3M8_Slot1-38_1_3572.d;ZD055LPLa_G3M9_Slot1-39_1_3574.d	1567	565	PXD056805_mqpar.xml	Whole mouse lung tissue lactylome; male C57BL/6J mice, 6-10 weeks, 20-30 g. Do not label the selected MS data as isolated pulmonary endothelial cells.	Article compares septic versus control mouse lungs. The study uses both CLP/sham and LPS (5 mg/kg)/saline models, but the selected G1M/G3M labels are not explicitly keyed to condition, specific model or collection time.	Not verified from accessible original article or repository protocol	Not verified from accessible original article or repository protocol	Not verified from accessible original article or repository protocol	"DOI: 10.1002/mco2.70049
PRIDE PXD056805
Evidence E01-E04"	12 selected lung TIMS-DDA acquisitions (6 G1M, 6 G3M), each experiment/fraction=1. Article reports septic/control whole-lung lactylome, but G1/G3 direction, CLP versus LPS model, collection time and independent-mouse/pooling structure are unresolved. Keep condition=unknown and exclude directional contrasts until a code key is obtained.
PXD057080	PRIDE	39730655	Effects of moderate intensity exercise on liver metabolism in mice based on multi-omics analysis	2024/12	Mus musculus	10090	Animal model	TIMS-DDA	Bruker TIMS	Label-free	6	XA04524LPLaR1_C_48_Slot2-34_1_10817.d;XA04524LPLaR1_C_74_2_Slot2-35_1_10815.d;XA04524LPLaR1_C_80_Slot2-36_1_10819.d;XA04524LPLaR1_E_51_1_Slot2-37_1_10823.d;XA04524LPLaR1_E_68_Slot2-38_1_10821.d;XA04524LPLaR1_E_71_Slot2-39_1_10825.d	1360	586	PXD057080_mqpar.xml	Mouse liver tissue	Six weeks of moderate treadmill exercise versus sedentary control; liver collected within 24 h after final exercise.	Pre-washed antibody-bead enrichment of modified peptides for lactylome analysis	PTM Bio	Not specified; the source reports lot number xxx	"https://doi.org/10.1038/s41598-024-82150-y
https://www.ebi.ac.uk/pride/archive/projects/PXD057080
Methods; PRIDE project description and sample protocol"	Six individual mice, three biological replicates per group; one selected raw per mouse. Filename IDs: C=48/74/80, E=51/68/71 (numeric IDs are not independently annotated). Filename _1/_2 suffixes do not add biological samples.
PXD058023	PRIDE	40748753	Protein lactylation of citrate synthase promotes the AKI-CKD transition by activating the NLRP3 inflammasome	2025/08	Mus musculus	10090	Animal model	TIMS-DDA	Bruker TIMS	Label-free	9	SA285LPLa_AKI3d1_Slot1-13_1_8771.d;SA285LPLa_AKI3d2_Slot1-14_1_8773.d;SA285LPLa_AKI3d3_Slot2-15_1_8849.d;SA285LPLa_AKI7d1_Slot1-16_1_8777.d;SA285LPLa_AKI7d2_Slot1-17_1_8779.d;SA285LPLa_AKI7d3_Slot1-18_1_8781.d;SA285LPLa_control1_Slot1-19_1_8783.d;SA285LPLa_control2_Slot1-20_1_8785.d;SA285LPLa_control3_Slot1-21_1_8787.d	1267	498	PXD058023_mqpar.xml	Mouse kidney tissue	Severe bilateral renal ischemia/reperfusion injury (35 min ischemia): baseline/day 0 versus days 3 and 7.	Not verified from accessible original article or repository protocol	Not verified from accessible original article or repository protocol	Not verified from accessible original article or repository protocol	"https://doi.org/10.1016/j.celrep.2025.116084
https://www.ebi.ac.uk/pride/archive/projects/PXD058023
Abstract; PRIDE project description and sample protocol"	Three biological tissue samples per time point, nine acquisitions. control1-3 correspond to the baseline group; AKI3d1-3 and AKI7d1-3 to days 3 and 7. No selected drug-treatment arms.
PXD062720	PRIDE	40634292	Irinotecan alleviates chemoresistance to anthracyclines through the inhibition of AARS1-mediated BLM lactylation and homologous recombination repair	2025/07	Homo sapiens	9606	Cell line	TIMS-DDA	Bruker TIMS	Label-free	2	FE458LPLa_A_1_Slot1-34_1_14665.d;FE458LPLa_A_3_Slot1-36_1_14669.d	6978	2476	PXD062720_mqpar.xml	UM-UC-3 bladder cancer cells isolated from cell-derived xenograft tumors	Epirubicin-treated parental versus epirubicin-resistant UM-UC-3 CDX-derived cells. Conditional working map used only for exploratory analysis, based on user-shared information and not independently confirmed in the article/PRIDE: A_1=parental+EPI; A_3=resistant+EPI. This is resistant-versus-parental under a shared EPI background, not EPI versus untreated.	Anti-L-lactyllysine antibody-conjugated agarose-bead immunoaffinity enrichment of lactylated peptides	PTM Bio, China	PTM-1404	"https://doi.org/10.1038/s41392-025-02302-y
https://www.ebi.ac.uk/pride/archive/projects/PXD062720
Methods: Identification of proteins with lysine lactylation by LC-MS/MS; PRIDE sample protocol
User-shared working sample map (conditional; not independently confirmed in primary archive): https://chatgpt.com/share/6adee875-f0e4-83e9-9d7e-5d6a2c369442"	Two selected acquisitions, one working-mapped A_1 and one A_3. The mapping source is user-shared information rather than an independent PRIDE confirmation; animal identity, pooling and biological/technical repetition remain unresolved. Only descriptive log2(A_3/A_1) direction is reported; no P value or FDR is valid from these files alone.