74	ProteomeXchange datasets
211	experiments
14,925	MS runs
444,752,369	spectra searched
120,422,937	PSMs
372,811	distinct peptides
16,178	canonical core proteins

About

The Maize PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Publicly-available Zea mays datasets were downloaded from ProteomeXchange and reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

Explore

SEARCH

form...

BROWSE

Chromosome Summary

Chromosome	Entries	Canonical		Uncertain		Redundant		Not Observed
Mitochondrial	163	16	9.8%	9	5.5%	18	11.0%	120	73.6%
Plastidial	111	41	36.9%	14	12.6%	21	18.9%	35	31.5%
Scaffolds	721	10	1.4%	22	3.1%	294	40.8%	395	54.8%
1	5,892	2,541	43.1%	598	10.1%	813	13.8%	1,940	32.9%
2	4,751	1,936	40.7%	491	10.3%	741	15.6%	1,583	33.3%
3	4,103	1,779	43.4%	448	10.9%	556	13.6%	1,320	32.2%
4	4,093	1,645	40.2%	390	9.5%	651	15.9%	1,407	34.4%
5	4,485	1,910	42.6%	470	10.5%	681	15.2%	1,424	31.8%
6	3,412	1,329	39.0%	381	11.2%	507	14.9%	1,195	35.0%
7	3,070	1,316	42.9%	296	9.6%	456	14.9%	1,002	32.6%
8	3,536	1,458	41.2%	359	10.2%	600	17.0%	1,119	31.6%
9	2,988	1,139	38.1%	328	11.0%	477	16.0%	1,044	34.9%
10	2,705	1,058	39.1%	263	9.7%	429	15.9%	955	35.3%
2023-09 Total	40,030	16,178	40.4%	4,069	10.2%	6,244	15.6%	13,539	33.8%

Column descriptions ▲

Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold

Publications

The Zea mays PeptideAtlas: A New Maize Community Resource
Klaas J. van Wijk, Tami Leppert, Zhi Sun, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Luis Mendoza, Qi Sun, and Eric W. Deutsch
Journal of Proteome Research Article ASAP
DOI: 10.1021/acs.jproteome.4c00320
[ bioRxiv preprint ]

Download

Below are individual Zea mays PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A build subtitled "PSM FDR=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

Maize 2023-09 PSM FDR = 0.00008Latest Build

Database tables exported as TSV dump file [348MB]
Database tables exported as mysql dump file [325MB]
Peptide CDS and chromosomal coordinates [752MB]
Peptide CDS coordinates [471MB]
Peptide sequences in FASTA format [10MB]
Spectral library (HR-HCD) [501MB]
Spectral library (HR-QTOF) [158MB]
Spectral library (LR-HCD) [93MB]
Spectral library (TMT_HR-HCD) [653MB]
Spectral library (TMT_LR-IT-CID) [5MB]
Spectral library (iTRAQ_HR-HCD) [496MB]
Spectral library (iTRAQ_HR-QTOF) [113MB]

Help

Complete description of each of the available download formats

Maize Protein Sequences Download

Filename	Size	# Sequences	Description
V5_Zea_Mays_B73_core_proteome.fa	15M	40,030	Core proteome consists of one isoform per gene from the MaizeGDB proteome annotation from the Zea mays B73 version 5 genome assembly plus the mitochondrial and plastid proteomes from Refseq
Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.protein.2.fa	30M	72,539	MaizeGDB proteome annotation from the Zea mays B73 version 5 genome assembly (multiple isoforms per gene) [ link ]
Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.protein.2.fa	93M	143,679	MaizeGDB proteome annotation from the Zea mays B73 version 4 genome assembly [ link ]
Zea_mays.AGPv3.22.pep.all.rename.2.fa	29M	63,241	MaizeGDB proteome annotation from the Zea mays B73 version 3 genome assembly [ link ]
Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.protein.2.fa	25M	51,716	MaizeGDB proteome annotation from the Zea mays W22 cultivar genome assembly [ link ]
uniprot_2023.06.12_uID.remove.2.fa	31M	63,236	UniProtKB Zea mays reference proteome downloaded 2023-06-12 [ link ]
GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_protein.2.faa	29M	57,578	NCBI RefSeq proteome annotation from the Zea mays B73 version 5 genome assembly and Annotation Release 103 [ link ]
GCA_000005005.6_B73_RefGen_v4_protein.2.faa	69M	131,270	NCBI RefSeq proteome annotation from the Zea mays B73 version 4 genome assembly [ link ]
mitochondrion.2.fasta	48K	163	Zea mays mitochondrial proteome from NCBI RefSeq Zea mays B73 version 5
plastid.2.fasta	32K	111	Zea mays plastidial proteome from NCBI RefSeq Zea mays B73 version 5
contaminants.fasta	256K	499	PeptideAtlas custom set of 499 common contaminant proteins
crap_GFP.fasta	4.0K	3	Additional 3 fluorescent proteins eGFP, eYFP, RFP
Maize_PeptideAtlas_search.fasta	218M	456,684	Full database used in the searches

Other Resources

MaizeGDB: Maize Genetics and Genomics Database
PPDB: The Plant Proteome Database

Acknowledgements

We gratefully acknowledge the support for the Maize PeptideAtlas from NSF grant 1922871 “TRTech-PGR: A PeptideAtlas for Arabidopsis thaliana and other plant species; harnessing world-wide proteomics data and mining for biological features”.